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Indonesian Journal of Biotechnology

ijbiotech
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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.

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Articles 8 Documents

Search results for , issue "Vol 22, No 1 (2017)" : 8 Documents clear

Simultaneous clustering analysis with molecular docking in network pharmacology for type 2 antidiabetic compounds Nur Azizah Komara Rifai; Farit Mochamad Afendi; I Made Sumertajaya
Indonesian Journal of Biotechnology Vol 22, No 1 (2017)
Publisher : Universitas Gadjah Mada

The database of drug compounds and human proteins plays a very important role in identifying the protein target and the compound in drug discovery. Recently, a network pharmacology approach was established by updating the research paradigm from the current “one disease-one target-one drug” to a new “drug-target-disease network”. Ligand-protein interactions can be analyzed quantitatively using simultaneous clustering and molecular docking. The docking method offers the ability to quickly and cheaply predict the ligand-protein binding free energy (DG) in structure-based virtual screening. Meanwhile, simultaneous clustering was used to find subgroups of compounds that exhibit a high correlation with subgroups of target proteins. This study is focused on the interaction between the 306 compounds from medicinal plants (brotowali Tinospora crispa, ginger Zingiber officinale, pare Momordica charantia, sembung Blumea balsamifera, synthetic drugs (FDA-approved) and the 21 significant human proteins associated with type 2 diabetes. We found that brotowali (B018), sembung (S031), pare (P231), and ginger (J036, J033) were close to the synthetic drugs and can possibly be developed as antidiabetic drug candidates. Likewise, the proteins AKT1, WFS1, APOE, EP300, PTH, GCG, and UBC which assemble each other and which have a high association with INS can be seen as target proteins that play a role in type 2 diabetes.

Biofilm formation analysis and molecular identification of copper-resistant bacteria isolated from PT Freeport Indonesia’s tailings Maria Massora; Erni Martani; Eko Sugiharto; Roberth Sarwom; Tumpal Sinaga
Indonesian Journal of Biotechnology Vol 22, No 1 (2017)
Publisher : Universitas Gadjah Mada

Copper is an essential macronutrient for living organisms. Nevertheless, at high concentrations, it is toxic to most forms of life, including microorganisms. In this research, we examined the biofilm formation ability and identified the molecular characteristics of copper-resistant bacteria isolated from PT Freeport Indonesia’s tailings. Four bacteria isolates from PT Freeport Indonesia’s tailings were used in this study. Qualitative analysis of biofilm formation by copper-resistant bacteria was performed using the Scanning Electron Microscopy (SEM) method and Microtiter Plate Biofilm Assay. The results showed that the C53 isolate could be categorized as a strong biofilm former, and three other isolates (C38, C40, and C43) as medium biofilm formers. The identity of the selected isolates was based on 16S rRNA gene sequence analysis: C38 isolate had a 99% similarity to Bacillus cereus strain HM85, C43 isolate had a 99% similarity to Bacillus subtilis strain EN16, C40 isolate had a 99% similarity to Lycinibacillus fusiformis strain MB52, and C53 isolate had a 98% similarity to Pseudomonas aeuruginosa strain GGRJ21. The capability of the C53 isolate to form strong biofilm can be exploited in bioremediation processes aiming to remove copper from tailings.

Assessment of genetic diversity among surian Toona sinensis Roem in progenies test using random amplified polymorphic DNA markers Jayusman Jayusman; Muhammad Na’iem; Sapto Indrioko; Eko Bhakti Hardiyanto; ILG Nurcahyaningsih
Indonesian Journal of Biotechnology Vol 22, No 1 (2017)
Publisher : Universitas Gadjah Mada

Surian Toona sinensis Roem is one of the most widely planted species in Indonesia. This study aimed to estimate the genetic diversity between a number of surian populations in a progeny test using RAPD markers, with the goal of proposing management strategies for a surian breeding program. Ninety-six individual trees from 8 populations of surian were chosen as samples for analysis. Eleven polymorphic primers (OP-B3, OP-B4, OP-B10, OP-H3, OP-Y6, OP-Y7, OP-Y8, OP-Y10, OP-Y11, OP-Y14, and OP-06) producing reproducible bands were analyzed for the 96 trees, with six trees per family sampled. Data were analyzed using GenAlEx 6.3, NTSYS 2.02. The observed percentage of polymorphic loci ranged from 18.2% to 50%. The mean level of genetic diversity among the surian populations was considered to be moderate (He 0.304). Cluster analysis grouped the genotypes into two main clusters, at similarity levels of 0.68 and 0.46. The first two axes of the PCoA explained 46.16% and 25.54% of the total variation, respectively. The grouping of samples into clusters and subclusters did not correspond with family and their distances, but the grouping was in line with the genetic distances of the samples.

Bioactivity and genetic screening of marine actinobacteria associated with red algae Gelidiella acerosa Maria Ulfah; Noer Kasanah; Niken Satiti Nur Handayani
Indonesian Journal of Biotechnology Vol 22, No 1 (2017)
Publisher : Universitas Gadjah Mada

Bacterial resistance to existing antibiotics has driven a search for new antibiotics from marine actinobacteria. Bioactivity and genetic screening of actinobacteria associated with red algae Gelidiella acerosa were conducted to discover new antibacterial compounds against Vibrio alginolyticus. A total of 14 actinobacteria isolates were obtained from G. acerosa. The isolates were subjected to genetic screening for nrps (non-ribosomal peptide synthetase) and FADH2-dependent halogenase genes. The isolates’ ability to produce secondary metabolites was examined by fermentation in various media in a six-well mini plate. The bioactivity of the secondary metabolites was screened using a microtiter assay and the agar overlay method. The results showed that all 14 isolates had the nrps gene, whereas none had the halogenase gene. Meanwhile, eight of the actinobacteria isolates showed antibacterial activity against V. alginolyticus.

Cloning of acetyl-CoA acetyltransferase gene from Halomonas elongata BK-AG18 and in silico analysis of its gene product Ni Putu Yuliastri; Enny Ratnaningsih; Rukman Hertadi
Indonesian Journal of Biotechnology Vol 22, No 1 (2017)
Publisher : Universitas Gadjah Mada

Polyhydroxybutyrate (PHB) is a biodegradable polymer that can be used as a substitute for petrochemical plastics. Bacteria accumulate PHB in their cells as carbon and energy reserves because of unbalanced growth conditions. This study aimed to amplify phbA from the chromosomal DNA of Halomonas elongata BK-AG18, a PHB-producing bacterium that was previously isolated from the Bledug Kuwu mud crater of Central Java, Indonesia. The obtained phbA amplicon was 1176 bp. This fragment was cloned into a pGEM-T Easy cloning vector and used to transform Eschericia coli TOP10. The recombinant colonies were selected using blue-white screening, confirmed by size screening, reconfirmed by re-PCR, and sequenced. When putative phbA sequences were aligned with H. elongata DSM2581 chromosome using BLASTN, this sequence showed 99% identity. The deduced amino acid sequences of this clone showed 100% identity to PhbA of H. elongata DSM2581, suggesting that the obtained cloned fragment is a phbA gene. The 3D structure predicted by I-TASSER showed that PhbA of H. elongata BK-AG18 had a high similarity to the acetyl CoA acetyltransferase structure of Ralstonia eutropha H16. PhbA of H. elongata BK-AG18 possesses three catalytic residues, namely Cys88, His348, and Cys378.

Expression of haloacid dehalogenase gene and its molecular protein characterization from Klebsiella pneumoniae ITB1 Ridani Rino Anggoro; Enny Ratnaningsih
Indonesian Journal of Biotechnology Vol 22, No 1 (2017)
Publisher : Universitas Gadjah Mada

Organohalogen compounds are widely used industrially and agriculturally, as well as in households as flame retardants and refrigerants. However, these compounds can become significant pollutants through their accidental or deliberate release into the environment in large quantities. Dehalogenase is an enzyme with the potential to be used in the removal of organohalogen contaminants. A previous study successfully subcloned a 690 bp of haloacid dehalogenase gene (hakp1) from Klebsiella pneumoniae ITB1 into a pET-30a(+) expression system to achieve high enzyme productivity. IPTG was used as an inducer to express a pET-hakp1 recombinant clone in Escherichia coli BL21 (DE3). The molecular mass of the haloacid dehalogenase Hakp1 protein was 30 kDa as determined by SDS-PAGE. Zymogram analysis showed that this recombinant protein has dehalogenase activity as shown by the formation of AgCl white precipitate. A quantitative assay of haloacid dehalogenase Hakp1 gave a specific activity of 84.29 U/mg with the optimum temperature of 40°C at pH 9. Predicted three-dimensional structure of Hakp1 showed α/β motif folding which comprised of cap and core domain. The predicted active sites of Hakp1 were Asp8, Glu10, Leu22, Phe23, Trp90, Ser125, Ser126, Lys159, and Asp184 with Asp8, Glu10, Ser126, and Lys159 act as binding residue. This recombinant haloacid dehalogenase clone provides an alternative agent for effective bioremediation of organohalogen pollutants.

Mid-gestational exposure to histone deacetylase inhibitor suberoylanilide hydroxamic acid influence cortical interneuron and astrocyte in mouse brain Nunung Yuniarti; Berry Juliandi; Tsukasa Sanosaka; Kinichi Nakashima
Indonesian Journal of Biotechnology Vol 22, No 1 (2017)
Publisher : Universitas Gadjah Mada

Suberoylanilide hydroxamic acid (SAHA) has been reported preclinically to diffuse across the placenta and to be found in fetal plasma, suggesting that it can influence the fetus if taken by a pregnant cancer patient. In utero exposure of SAHA to mouse embryos during mid-gestation was found to perturb corticogenesis. However, the influence of in utero administration of SAHA to mouse embryos during mid-gestation on astrocyte, glial cell, and inhibitory neurons (interneurons) is yet to be reported. Pregnant dams were divided into control and SAHA groups and given methyl cellulose (as control) and SAHA orally once a day for 3 days during mid-gestation, starting from embryonic day (E)12 until E14. Astrocyte, interneuron, and behavior analyses were performed on the pups from postnatal day 7 until adulthood (3 months old). Brains were harvested and immunohistochemistry, Western Blot, and RT-PCR were performed on their cortex area. Transient exposure of SAHA to mouse embryos resulted in a decrease and increase in cortical astrocyte and interneuron, respectively. Meanwhile, adult SAHA mice displayed significantly increased anxiety, decreased memory, altered long-term cognitive functions, and reduced social interactions. Our study suggests that exposure to SAHA during prominent neurogenic periods might imbalance the normal excitatory:inhibitory neuron ratio required for the precise regulation of physiological functions in the brain.

Anthocyanin, nutrient contents, and antioxidant activity of black rice bran of Oryza sativa L. ‘Cempo Ireng’ from Sleman, Yogyakarta, Indonesia Pratiwi Apridamayanti; Rarastoeti Pratiwi; Yekti Asih Purwestri; Woro Anindito Sri Tunjung; Rumiyati Rumiyati
Indonesian Journal of Biotechnology Vol 22, No 1 (2017)
Publisher : Universitas Gadjah Mada

The chemical contents and health benefits of black rice bran of some rice cultivars have been investigated. However, there has been little research on the ‘Cempo Ireng’ cultivar from Sleman, Yogyakarta. The aim of this present study was to determine the anthocyanin, antioxidant activity, and macro- and micronutrients contents of black rice bran from this local cultivar. The anthocyanin in the black rice bran was extracted using the maceration method with methanol as a solvent. The extract obtained was separated through a preparative thin layer chromatography (TLC) of silica GF254 and a mobile phase composed of n-butanol, acetic acid, and water. Two fractions were collected and analyzed for the anthocyanin content. The preparative TLC spots were separated for further detection and measurement of cyanidin 3-O-glucoside using HPLC followed by LC-MS. The antioxidant activity of the fractions were measured using the DPPH free radical scavenging method. The results showed that the anthocyanin in fraction 1 was identified as cyanidin 3-O-glucoside (66.1 ± 10.6 µg/g). The IC50 of fractions 1 and 2 were 200.96 and 218.36 µg/mL, respectively. Analysis of the macro- and micronutrients revealed that the black rice bran of ‘Cempo Ireng’ had nutrient contents comparable with other rice cultivars. Therefore, this local black rice bran can be used as a source of antioxidants and macro-- and micronutrients.

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