Indonesian Journal of Biotechnology
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.
Articles
457 Documents
<![CDATA[The genetic variations and relationship of Madura tobacco (Nicotiana tabacum L.) based on molecular characteristics ]]>
<![CDATA[Fitri Nadifah]]>;
<![CDATA[Budi Setiadi Daryono]]>
<![CDATA[ Indonesian Journal of Biotechnology Vol 21, No 2 (2016) ]]>
Publisher : <![CDATA[Universitas Gadjah Mada ]]>
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DOI: 10.22146/ijbiotech.10582
<![CDATA[Madura has at least 22 genotypes of local tobaccos (Nicotiana tabacum L.). This diversity could potentially produce new genotype of tobaccos with superior characters. However, information of the genetic diversity of Madura tobaccos is still limited. The aim of this study was to determine the genetic variation and relationship of 24 genotypes of Madura tobaccos with Random Amplified Polymorphic DNA (RAPD) analysis. In this research we were used 6 single primers for amplification: (OPA-18, OPB-12, OPB-14, OPC-1, OPC-8 and OPC-19) and 2 mixture primers ((OPB-12+OPC-8) and (OPC-1+OPC-19)). Genetic similarity and clustering was analyzed with Unweighted Pair Group Method Arithmetic (UPGMA) method with Numerical Taxonomy and Multivariate Analysis System (NTSYS) version 2.10 software. From this research we found that OPA18425, OPB12450, OPC8500, (OPC19+OPC1)550 and OPC8800 can be used as specific markers. Polymorphic bands percentage with mixture primers was relatively equal with single primers (<60%). The dendogram showed that Madura tobacco genotypes consist of 2 main clusters: cluster A (22 genotypes) and cluster B (2 genotypes: Bukabu Sa’ang and Prancak-95). Madura tobaccos had high genetic similarity between genotypes ranging from 0.80-1.00.]]>
<![CDATA[Marker Assisted Selection for Bacterial Leaf Blight Rice Mutant Lines Resistant ]]>
<![CDATA[A. Aryanti]]>;
<![CDATA[A. Almaida]]>;
<![CDATA[Rika Heryani]]>;
<![CDATA[Nana Supriatna]]>
<![CDATA[ Indonesian Journal of Biotechnology Vol 20, No 1 (2015) ]]>
Publisher : <![CDATA[Universitas Gadjah Mada ]]>
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DOI: 10.22146/ijbiotech.15264
<![CDATA[Induction of mutation using gamma rays for improving of Mira-1 rice variety has been conducted.Rice mutant lines M2 generation have been obtained from mutation by the doses of 25, 50, 75, 100, 150 and200 Gy of gamma rays. Selection of mutant lines tolerant to the disease was only observed in the field neithergenetically. Marker assisted selection is a tool to obtain a new rice variety tolerant to the disease of bacterialleaf blight (BLB) genetically. Xanthomonas oryzae pv.oryzae (Xa) was the pathogen of BLB, and the identificationof rice mutant lines which were containing of Xa5, Xa13 and Xa21 genes have been done using PolymeraseChain Reaction ( PCR ) method. The result showed that one mutant line, and four mutant lines from mutationby the doses of 25 Gy and 150 Gy were containing Xa5, Xa13 and Xa21 genes the same as that of Code ricevariety as positive control, and none in Kencana Bali rice variety as negative control. Mira-1 rice variety as theparent plant was only contains Xa5 and Xa21 genes. The doses of 50 Gy and 100 Gy were very affective onremoving of all bands for identification of those genes. The purpose of this research was to obtain the mutantlines which were contain of those Xa genes as indicator for resistant to BLB disease genetically.]]>
<![CDATA[Application of Molecular Biology for Identification of Virus Resistance Gene in Melon ]]>
<![CDATA[Budi Setiadi Daryono]]>
<![CDATA[ Indonesian Journal of Biotechnology Vol 20, No 1 (2015) ]]>
Publisher : <![CDATA[Universitas Gadjah Mada ]]>
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DOI: 10.22146/ijbiotech.15265
<![CDATA[Source of resistance to an Indonesia isolate of Cucumber mosaic virus (CMV-B2) in melon cultivarYamatouri has been reported. Moreover, Creb-2, a locus that confers resistance to CMV-B2 in Yamatouri hasbeen determined as a single dominant gene. To elucidate the resistance mechanism conferred by Creb-2 inmore detail, it is necessary to clone the Creb-2 gene and determine its molecular structure. One approach isby amplification and cloning of melon resistance gene analogs (MRGAs) based on degenerated PCR primersdesigned from conserved amino acids in the NBS-LRR motifs (P-loop, Kinase-2, and the GLPL) and Toll/Interleukin-1 receptor-like region (TIR). This study was aimed to identify and characterize the resistance geneanalogs from Cucumis melo L. cv. Yamatouri by employing polymerase chain reactions (PCR) as a molecularbiology tools with degenerate primers based on conserved motifs of cloned R genes. The application of molecularbiology such as DNA isolation, degenerate primers and PCR condition, cloning, sequencing, linkage analysisand mapping of resistance gene analogs to Creb-2 gene in melon will be widely discussed in this paper]]>
<![CDATA[Diversity of Nonribosomal Peptide Synthetase Genes in the AnticancerProducing Actinomycetes Isolated from Marine Sediment in Indonesia ]]>
<![CDATA[Camelia Herdini]]>;
<![CDATA[Shinta Hartanto]]>;
<![CDATA[Sofia Mubarika]]>;
<![CDATA[Bambang Hariwiyanto]]>;
<![CDATA[Nastiti Wijayanti]]>;
<![CDATA[Akira Hosoyama]]>;
<![CDATA[Atsushi Yamazoe]]>;
<![CDATA[Hideaki Nojiri]]>;
<![CDATA[Jaka Widada]]>
<![CDATA[ Indonesian Journal of Biotechnology Vol 20, No 1 (2015) ]]>
Publisher : <![CDATA[Universitas Gadjah Mada ]]>
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DOI: 10.22146/ijbiotech.15266
<![CDATA[Marine actinomycetes is a group of bacteria that is highly potential in producing novel bioactivecompound. It has unique characteristics and is different from other terrestrial ones. Extreme environmentalcondition is suspected to lead marine actinomycetes produce different types of bioactive compoundfound previously. The aim of this study was to explore the presence and diversity of NRPS genes in 14anticancer-producing actinomycetes isolated from marine sediment in Indonesia. PCR amplificationand restriction fragment analysis of NRPS genes with HaeIII from 14 marine actinomycetes were doneto assess the diversity of NRPS genes. Genome mining of one species of marine actinomycetes (strainGMY01) also was employed towards this goal. The result showed that NRPS gene sequence diversity in 14marine actinomycetes could be divided into 4 groups based on NRPS gene restriction patterns. Analysisof 16S rRNA gene sequences of representatives from each group showed that all isolates belong to genusof Streptomyces. Genome mining result showed that strain GMY01 harboring 10 different NRPS geneclusters that encode secondary metabolites, as pure NRPS or hybrid between NRPS and other compounds.These results indicated that marine actinomycetes having a high potential to be developed as source ofanticancer drugs development.]]>
<![CDATA[High Resolution Microsatellite Marker Analysis of Some Rice Landraces Using Metaphor Agarose Gel Electrophoresis ]]>
<![CDATA[K. Kristamtini]]>;
<![CDATA[T. Taryono]]>;
<![CDATA[Panjisakti Basunanda]]>;
<![CDATA[Rudi Hari Murti]]>
<![CDATA[ Indonesian Journal of Biotechnology Vol 20, No 1 (2015) ]]>
Publisher : <![CDATA[Universitas Gadjah Mada ]]>
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DOI: 10.22146/ijbiotech.15269
<![CDATA[Microsatellite markers or simple sequences repeats are DNA - based molecular techniques that areused to see the different among accessions and inbred lines. There are three methods to analysis the results ofthe polymerase chain reaction of microsatellite markers namely polyacrylamide gel electrophoresis (PAGE),capillary electroforesis, and Metaphor Agarose Gel Electroforesis (MAGE), and the Use of MAGE assessedmore easily and economically the polymorphic pattern of DNA markers. This study aimed to obtain fast,effective and efficient in term of easy and cheap technique to identify microsatellite markers of some blackrice cultivars and F2 populations from crosses between black with white rice. The results showed that MAGEsuccessfully separated clearly SSRs alleles with different sizes of less than 25 bp .]]>
<![CDATA[Black Rice Bran Extracts and Fractions Containing Cyanidin 3-glucoside and Peonidin 3-glucoside Induce Apoptosis in Human Cervical Cancer Cells ]]>
<![CDATA[Rarastoeti Pratiwi]]>;
<![CDATA[Woro Anindito Sri Tunjung]]>;
<![CDATA[R. Rumiyati]]>;
<![CDATA[Alfi Rizqi Amalia]]>
<![CDATA[ Indonesian Journal of Biotechnology Vol 20, No 1 (2015) ]]>
Publisher : <![CDATA[Universitas Gadjah Mada ]]>
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DOI: 10.22146/ijbiotech.15271
<![CDATA[Anthocyanin of pigmented rice inhibits the growth of cancer cells. The cytotoxicity and apoptosisinducing properties of local black rice (cv Cempo Ireng) extracts and fractions, which contain anthocyaninincluding cyanidin 3-glucoside and peonidin 3-glucoside, on human cervical cancer cell line (HeLa cells) hasbeen evaluated. The pigmented rice bran was extracted and fractionated using methanol-HCl. The MTT testwas performed on HeLa cell cultures to observe the IC50 value. Preparative TLC was performed to obtain thefractions of black rice bran. Cyanidin 3-glucoside and peonidin 3-glucoside were identified in the pigmentedrice bran extract and fractions using UHPLC. Flowcytometry analysis was performed to measure the percentageof apoptotic cells. Our results suggest that the fractions are more toxic than the methanolic crude extract withIC50 values of 85.95 ± 5.56 μg/mL (the lowest one) and 408.13 ± 51.9 μg/mL, respectively. The concentration ofcyanidin 3-glucoside and peonidin 3-glucoside in the methanolic extract were 1.89 and 0.84 μg/mg, respectively.The apoptosis induction by fractions F2 and F4 (52 and 55%) were significantly higher compared to fractionF3 and F5 (30 and 33%) and doxorubicin (21%). Cyanidin 3-glucoside was detected in F4 (0.14 μg/ml) whilepeonidin 3-glucoside in F2 (0.012 μg/ml), however both were not detected in F3 and F5.]]>
<![CDATA[An Active of Extracellular Cellulose Degrading Enzyme from Termite Bacterial Endosimbiont ]]>
<![CDATA[M. Saifur Rohman]]>;
<![CDATA[Endang Pamulatsih]]>;
<![CDATA[Yudi Kusnadi]]>;
<![CDATA[Triwibowo Yuwono]]>;
<![CDATA[Erni Martani]]>
<![CDATA[ Indonesian Journal of Biotechnology Vol 20, No 1 (2015) ]]>
Publisher : <![CDATA[Universitas Gadjah Mada ]]>
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DOI: 10.22146/ijbiotech.15273
<![CDATA[Cellulase is an ezyme that specifically cleaves the 1,4-β-glycosidic bond of cellulose to produce thesmall fragments of simple carbohydrate. This work was aimed to characterize the extracellular cellulase fromPaenibacillus spp., which was previously isolated from macro termites, Odontotermes bhagwatii in our laboratory.Two Paenibacillus isolates were used in this experiment, namely Paenibacillus cellulositrophicus SBT1 andPaenibacillus, sp. SBT8. Analysis of the total proteins in the supernatants showed that P. cellulositrophicus SBT1and Paenibacillus sp. SBT8 roughly produced as much as 18.6 mg/l and 24.8 mg/l of extracellular cellulases,respectively. Enzymatic assay showed that SBT1 and SBT8 cellulase exhibited enzymatic acitivity of 0.17 U/mg and 0.12 U/mg, respectively. Temperature dependencies analysis indicated that both cellulases exhibitedmaximum activity at 35oC. At the temperature higher than 55oC, the enzymatic activities of both cellulases wereroughly 20% reduced compared to the maximum activity. SBT1 and SBT8 cellulases were both active at acidicpH. At basic pH (pH 8) the enzymatic activities of both cellulases were reduced roughly 30% compared to thatof acidic pH. Supplementing of Mg2+, Zn2+, and Ca2+ in range of 1-10 mM increased the enzymatic activity ofboth cellulases roughly 33 to 50%.]]>
<![CDATA[Sequences Analysis of a Gene Encoding Extracellular Xylanase in Streptomyces costaricanus 45I-3 ]]>
<![CDATA[S. Sipriyadi]]>;
<![CDATA[Aris Tri Wahyudi]]>;
<![CDATA[Maggy Thenawidjaja Suhartono]]>;
<![CDATA[Anja Meryandini]]>
<![CDATA[ Indonesian Journal of Biotechnology Vol 20, No 1 (2015) ]]>
Publisher : <![CDATA[Universitas Gadjah Mada ]]>
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DOI: 10.22146/ijbiotech.15274
<![CDATA[Streptomyces costaricanus 45I-3 is a bacterial strain belongs to actinomycetes group isolated from peat soil. Thebacterium is known to produce extracellular xylanase. The aims of this study were to analyze DNA sequence andsub-clone gene involved in the synthesis of extracellular xylanase. Complete DNA sequence predicted to encodexylanase genes was isolated from bacterial genome using Inverse Polymerase Chain Reaction (I-PCR). Total DNAsequence of 1664 bp in size obtained from I-PCR consisted of two open reading frames (ORF) in opposite direction.ORF1 was 1029 bp and ORF2 (partial sequence) was 309 bp. Analysis sequence using BlastX indicated that ORF1was homologous with xylanase bacterium enrichment culture clone Xyl8B8 (GenBank accession No. AFH35005.1),i.e. 95% in identity and 99% in similarity. In addition, ORF2 was homologous with glyoxalase bacterium enrichmentculture clone Xyl8B8 (GenBank accession No. AFH35007.1), i.e. 95% in identity and 98% in similarity. Analysis ofamino acid sequence revealed that ORF1 consisted of 2 domains, i.e. glyco-hydrolase 11 (GH11) and CarbohydrateBinding Type 2 (CBM2). Active site was found at 130th amino acid on GH11 domain. Visualization of 3-dimensionstructure showed that 1029 bp fragment is of 19 areas.]]>
<![CDATA[Induction of Somatic Embryogenesis through Overexpression of ATRKD4 Genes in Phalaenopsis “Sogo Vivien” ]]>
<![CDATA[Exsyupransia Mursyanti]]>;
<![CDATA[Aziz Purwantoro]]>;
<![CDATA[Sukarti Moeljopawiro]]>;
<![CDATA[Endang Semiarti]]>
<![CDATA[ Indonesian Journal of Biotechnology Vol 20, No 1 (2015) ]]>
Publisher : <![CDATA[Universitas Gadjah Mada ]]>
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DOI: 10.22146/ijbiotech.15276
<![CDATA[Phalaenopsis “Sogo Vivien “is a mini orchid hybrid with beautiful flowers and numerous inflorescences.Mass propagation of this orchid is needed to meet the market demand. Objective of this research was toinduce somatic embryogenesis of P.”Sogo Vivien” through insertion of AtRKD4 gene into orchid. T-DNAcontaining 35S::GAL4::AtRKD4::GR was inserted into 16-22 days after sowing orchid protocorms mediated byAgrobacterium tumefaciens EHA 105. Activation of the AtRKD4 gene was induced by glucocorticoid inductionsystem, using 15μM Dexamethasone (Dex). The results showed that 34 out of 2,648 orchid embryos developedinto protocorms on hygromycin selection medium, whereas only 4 out of 2,897 non-transformant protocormsdeveloped from embryos. A 500 bp of HPT genes was amplified from transformant candidates using specificprimers for HPT (HygF1 and HygR1) and 380 bp was amplified using specific primers for AtRKD4 (AtRKD4F1 and AtRKD4 R1), indicated that transgenes have been integrated into orchid genomes. Finally, 17 plantletswere positively carrying AtRKD4 and HPT genes, the efficiency of transformation was 0.63 %. Somatic embryoswere also emerged from leaf explants of transformant on hormone-free NP medium and became normalplantlets. It is probably due to the high activity of AtRKD4 genes in orchids]]>
<![CDATA[Identification of BSA B1 Bacteria and Its Potency of Purified Cellulase to Hydrolyze Chlorella zofingiensis ]]>
<![CDATA[Rifqi Zahroh Janatunaim]]>;
<![CDATA[Radhiyah Mardhiyah Hamid]]>;
<![CDATA[Ghea Putri Christy]]>;
<![CDATA[Yekti Asih Purwestri]]>;
<![CDATA[Woro Anindito Sri Tunjung]]>
<![CDATA[ Indonesian Journal of Biotechnology Vol 20, No 1 (2015) ]]>
Publisher : <![CDATA[Universitas Gadjah Mada ]]>
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DOI: 10.22146/ijbiotech.15277
<![CDATA[Cellulase has been widely used as biocatalyst in industries. Production of cellulase from microorganismshas many advantages such as short production time and less expense. Our previous study indicated that oneof cellulolytic bacteria from digestive tract of milkfish (Chanos chanos), namely BSA B1, showed the highestcellulase activity. The objective of this study was to determine the phylogenetic of BSA B1 strain using 16SrRNA gene sequence. Furthermore, this study also determine the specific activity of purified cellulase from BSAB1 strain and its potency to hydrolyze Chlorella zofingiensis cellulose. Cellulase was purified using ammoniumsulphate precipitation, dialysis, and ion exchange chromatography. The purified cellulase was used to hydrolyzecellulose of C. zofingiensis. The result demonstrated that BSA B1 strain was closely related with Bacillus aeriusand Bacillus licheniformis. The specific activity of the crude enzyme was 1.543 U mL-1; after dialysis was 4.384 UmL-1; and after chromatography was 7.543 U mL-1. Purified cellulase exhibited activity in hydrolyzed both CMCand C. zofingiensis. Compared to commercial cellulase, purified cellulase had lower activity in hydrolyzed CMCbut higher activity in hydrolyzed C. zofingiensis. Ethanol dehydration could potentially increase the reducingsugar yield in cellulose hydrolysis when used appropriately. Morphology of C. zofingiensis cell has changedafter incubation with cellulases and ethanol dehydration indicated degradation of cell wall.]]>
