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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 20 Documents

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Search results for , issue "Vol 18, No 2 (2013)" : 20 Documents clear

Agrobacterium-Mediated Stable Transformation of Medicinal Plant Andrographis paniculata Callus Expressing β-glucuronidase (GUS) Gene Erly Marwani; Agustina Tangapo; Fenny Martha Dwivany
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

This study was carried out to establish a stable genetic transformation in callus culture of Andrographispaniculata mediated by Agrobacterium tumefaciens. The leaf disks of A. paniculata were infected with A. tumefaciensLBA4404 carrying a binary vector pCAMBIA1304 that contain β-glucuronidase (GUS) and hygromycinphosphotransferase (hpt) genes. The infection was conducted by dipping method for one hour, followed byco-cultivation in the dark for three days. To examine transient GUS expression, the co-cultivated leaf disks wereassayed for β-glucuronidase activity and to obtain stable transformed callus, the co-cultivated leaf disks wereselected on the callus induction medium which contain 20 mg/l hygromycin for selection. The transformedcallus was periodically subcultured every three weeks into the fresh selection medium over the 15 weeksperiod. To test a stable transformation, the callus was subjected to PCR analysis for GUS gene detection. Theresults indicated that the co-cultivated leaf disks expressed GUS activity and proliferated to produce callus onthe selective medium. Analysis of PCR on the transformed callus indicated the presence 976 bp fragment thatconfi rmed the presence of β-glucuronidase gene. These fi ndings imply that the β-glucuronidase was stably integrated into A. paniculata callus culture.Keywords: Andrographis paniculata, Agrobacterium tumefaciens, andrographollide, transformed callus,β-glucuronidase gene.

Purification and Characterization of Protease From Bacillus sp. TBRSN- 1 Sebastian Margino; J. Jumi'ati; N. Ngadiman
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

Potato Cyst Nematode (PCN), Globodera rostochiensis, is one of the important potato’s pests and causedeconomic looses up to 70% in the several centrals of potato plantations in Indonesia. PCN’s shell componentof egg shell containing chitin (inner layer) and viteline/ protein (outer layer). The purpose of this researchwas to purify of protease Bacillus sp. TBRSN-1, isolate from tomato’s rhizosfer in Yogyakarta province. Thepurifi ed protease could be used for cutting the life cycle of PCN. Results showed that Bacillus sp. TBRSN-1could produce extracellular protease and purifi cation using DEAE-cellulose ion-exchange chromatographyand Sephacryl S-300 gel fi ltration chromatography resulted in specifi c activity 4.31 fold and 1.68% recovery.Analysing using SDS-PAGE 12.5% and molecular weight 48.1 kDa. Km and Vmax values of the protease forcasein substrate were 7.83 mg/ml and 4.03 μg/h, respectively. The optimum activity at the temperature30oC and pH 7.0. Keywords : protease, purifi cation, indigenous Bacillus sp. TBRSN-1

Comparative Analysis of Genes Induced by Respiratory Syncytial Virus and DsRNA in Human Epithelial Cells Gino Valentino Limmon
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

Epithelial cells are the primary target of respiratory viral infections and play a pivotal role in virusinducedlung infl ammation and in anti viral immune response. A common signal for the presence of viralinfections and induction of infl ammation is recognition of double stranded RNA (dsRNA). Thus far, therehas not been a high-throughput transcrptome analysis of RSV- or dsRNA-induced genes in primary humanbronchial epithelial cells (PHBE), nor there has been a comparison between dsRNA- and RSV-inducedgenes. To establish the transcriptome profi les and to determine the contribution of dsRNA in the inductionof infl ammation during respiratory virus infection, we compared the gene expression profi les of PHBE cellsthat were infected with Respiratory Syncytial Virus (RSV) or were treated with dsRNA. Our transcriptomeanalysis showed that RSV infection and and dsRNA treatment induced up-regulation of 2024 and 159 genesin PHBE respectively. Comparison of genes revealed that RSV and dsRNA commonly induced 75 genes inPHBE cells. The common up-regulated genes were functionally grouped in multiple response pathwaysinvolved in infl ammation and immune responses. Interestingly, there were several previously unreportedgenes that were up-regulated in primary human epithelial cells that are relevant to a TH2 allergic phenotype.This comparison of a high-throughput gene expression study offers a comprehensive view of transcriptionalchanges induced by dsRNA and RSV, and importantly compares dsRNA-induced genes with RSV-inducedgenes in PHBE cells. Keywords: RSV, dsRNA, transcriptome, immune response, infl ammation

Legume Nodulating Bacterium, Achromobacter xylosoxidans Found in Tropical Shrub Agroecosystem, Sumatera, Indonesia Sri Wedhastri; Dinar Mindrati Fardhani; Siti Kabirun; Jaka Widada; Donny Widianto; Rusdi Evizal; Irfan Dwidya Prijambada
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

Legume nodulating bacteria (LNB), known also as rhizobia, are soil bacteria, which are able to form rootnodules and fi x nitrogen in the leguminous plants. The LNB availability in the soil depends on the type ofagroecosystem, where plant grows. In this study, we isolated LNB from the shrub agroecosystem in Sumatera,Indonesia, and obtained four selected bacterial strains. Among them, the isolate UGM48a formed root nodulein Macroptilium atropurpureum and showed highest number of nitrogenase activity. UGM48a also contains nifHand nodA genes. An analysis of the PCR-amplifi ed 16S rDNA and BLASTn analysis showed that UGM48adisplayed 96% similarity with Achromobacter xylosoxidans. In addition, UGM48a were successfully nodulatedGlycine max (L.) merr var. wilis. This is the fi rst report detecting A. xylosoxidans as nodule-forming species forGlycine max possesing the positive copy of nodA gene. Keywords : Legume Nodulating Bacteria, shrub agroecosystem, Achromobacter xylosoxidans, nodA, Glycine max

The Phylogenetic Relationship Among Varieties of Lansium domesticum Correa Based on ITS rDNA Sequences Laila Hanum; Rina Sri Kasiamdari; S. Santosa; R. Rugayah
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

Lansium domesticum Corr. with vernacular name in Indonesian duku has been reported containingtherapeutic bioactive compounds, and some of these compounds shown to be potent antitumor, anticancer,antimalaria, antimelanogenesis, antibacteria, and antimutagenic activities. This plant is commonly known asduku, kokosan and langsat by the local community in Indonesia. The morphological appearance of all varieties isnearly the same, and identifi cation of the varieties is very diffi cult for growers. Variation of DNA sequences ofthe ITS (Internal transcribed spacer) region can be used as a molecular character to determine the phylogeneticrelationship of different varieties of L. domesticum. The aims of this study were to determine taxonomy status ofduku, kokosan, and langsat, also phylogenetic relationship among varieties of L. domesticum based on ITS rDNAsequencing. DNA was isolated from leaves of plant and then amplifi ed using F1 and R1 primers. Nucleotidesequences were identifi ed using Sequence Scanner Software Programm version 1.0, nucleotide sequences from18S, ITS1, 5.8S, ITS2 and 26S region, that has been mergered using EditSeq and SegMan in software Suite forSequence Analysis DNASTAR Lasergene DM version 3.0.25. The results of study showed that DNA fragmentsranging in size from 782-810 bp. Different pattern of DNA fragments indicated polymorphism among duku,kokosan, and langsat. Based on the results of the ITS rDNA sequencing and phylogenetic tree analysis. Itwas determined that Lansium and Aglaia are a separated genus with the similarity index value of 0.98. Duku,kokosan and langsat were divided into two cluster, namely cluster kokosan-langsat and cluster duku with thesimilarity index value of 0.996. Keywords : Phylogenetic relationship, ITS region, L. domesticum, duku, kokosan, langsat

Ethanol Fermentation on Mixed Sugars Using Mixed Culture of Two Yeast Strains J. Jasman; Irfan Dwidya Prijambada; Chusnul Hidayat; Donny Widianto
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

The objective of this study was to evaluate the use of mixed cultures of the recommended yeast strainsfrom a previous study on ethanol fermentation using a substrate mixture consisting of sucrose, glucose, andfructose. There were three mixed (combination) cultures namely OUT7096/OUT7913, OUT7096/OUT7921,and OUT7913/OUT7921. The fermentation medium contained sugar mixture consisting of glucose, fructose,and sucrose with a composition generally close to the composition of sugars in sweet sorghum juice. Overall,fermentation is carried out in two stages. First fermentation was performed using the three mixed culturesto determine the best combination based on the concentration of ethanol produced and the concentration ofresidual sugar. Second fermentation was conducted using the best mixed culture obtained from the fi rst stage.This second stage was intended to describe the pattern of the changes in the concentration of ethanol, sugarsand biomass during the fermentation progresses and to determine some kinetic parameters namely ethanolyield (Yp/s), growth yield (Yx/s) and specifi c growth rate (μ). The results of the fi rst fermentation showed thatthe best mixed culture was OUT7913/OUT7921 and the subsequent fermentation using this culture providethe highest ethanol yield (Yp/s) = 0.47 g.g-1 that was reached at 53rd hour, growth yield (Yx/s) = 0.425 g.g-1, andμ = 0.12 hour-1.Keywords : fermentation, ethanol, mixed culture, mixed sugar

Stachybotrys chartarum: A Novel Biological Agent for The Extracellular Synthesis of Silver Nanoparticles and Their Antimicrobial Activity Abdel Ghany Tarek Mohamed
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

Microbial assisted biosynthesis of nanoparticles is a rapidly progressing area of nanobiotechnology. Inthis paper Stachybotrys chartarum assisted extracellular synthesis of silver nanoparticles (AgNPs) is reportedwhen challenged with 1mM silver nitrate (AgNO3). The characterization of AgNPs was carried out visualobservation and UV-Vis spectrophotometry. Further analysis carried out by Fourier Transform InfraredSpectroscopy (FTIR), provides evidence for the presence of proteins as capping agent, which helps in increasingthe stability of the synthesized AgNPs. Transmission Electron Microscopy (TEM) investigations confi rmedthat AgNPs were formed. The synthesized silver nanoparticles were found in the range of 65-108 nm. Finally,the antimicrobial susceptibility of AgNPs synthesized was investigated which exhibited more potent activityagainst bacteria than fungi compared with using silver nitrate at concentration 1mM. Keywords: Antimicrobial activity, Stachybotrys chartarum, Silver nanoparticles

The Development of Pathogenicity of Avian Influenza Virus Isolated from Indonesia Michael Haryadi Wibowo; Agus Eko Srihanto; Khrisdiana Putri; Widya Asmara; Charles Rangga Tabbu
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

Highly pathogenic avian infl uenza outbreak in Indonesia has been reported in various poultry due toH5N1 subtype. The presence of multiple basic amino acids within the cleavage site of HA glycoprotein hasbeen identifi ed to be associated with the pathogenicity of avian infl uenza virus. The study was retrospectivestudy which was designed to characterize the cleavage site and fusion site region of haemagglutinin gene ofAIV isolated from various poultry in 2003 to 2013. Isolation, Identifi cation and propagation were carried outto collect viral stock. For virus detection, reverse transcriptase PCR (RT-PCR) method on H5 and N1 genefragment was performed. All of RT-PCR HA gene positive products were sequenced for further nucleotideanalysis and to determine the nucleotide composition at the targeted fragment. The results are all AIV isolateswere identifi ed as H5N1 subtype. The sequence analyses revealed some motives of basic amino acid motivethat were classifi ed as highly pathogenic avian infl uenza virus. Further analyses on fusion domain of all AIVisolated during the period 2003 to 2013 showed conserved amino acid. Keywords: avian infl uenza, haemagglutinin, cleavage site, basic amino acid, fusion site

Characterization of Streptomyces spp. Producing Indole-3-acetic acid as Biostimulant Agent Charlie Ester de Fretes; Langkah Sembiring; Yekti Asih Purwestri
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

Twenty six isolates of Streptomyces spp. obtained from Cyperus rotundus L. rhizosphere were tested forability to produce indole-3-acetic acid (IAA) in yeast malt extract (YM) medium containing 2 mg/mL tryptophan.Screening of the isolates for ability to produce IAA was carried out by adding Salkowski reagent in bacteriaculture and was measured quantitatively by spectrophotometer at λ 530 nm. Thin Layer Chromatography (TLC)method was used to determine IAA. To ensure the IAA production in Streptomyces isolates, gene involved inIAA biosynthesis was detected by amplifying Tryptophan Monooxigenase (iaaM) gene. The study of the effectof tryptophan on the production of IAA was measured at different concentrations of tryptophan (0, 1, 2, 3,4, 5 mg/mL) in the bacterial culture. The result showed that there were two Streptomyces spp. isolates whichcould produce IAA, namely the isolates of Streptomyces sp. MS1 (125.48 μg/mL) and Streptomyces sp. BR27(104.13 μg/mL). The TLC result showed that the compound in both isolates was identifi ed to be IAA. Theamplifi cation results showed that iaaM gene was detected in both isolates. This results indicated that the IAMpathway is predicted involved in the biosynthesis of IAA in the selected isolates. Both of the isolates were ableto produce IAA after 24 h incubation and the highest production was at 120 h incubation with the concentrationof tryptophan was 2 mg/mL dan 1 mg/mL, respectively. Therefore, it is concluded that Streptomyces spp.isolates are able to produce IAA and potentially to be utilized as biostimulat agent. Keywords: Streptomyces spp., indole-3-acetic acid (IAA), indole-3-acetamide (IAM), Tryptophan Monooxigenasegene (iaaM)

A Study on Production of Poly-β-Hydroxybutyrate Bioplastic from Sago Starch by Indigenous Amylolytic Bacteria Nur Arfa Yanti; Langkah Sembiring; Sebastian Margino; Nurhayani H. Muhiddin
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

Bacillus sp. PSA10 and Bacillus sp. PPK5 were two indigenous strain amylolytic bacteria from SoutheastSulawesi that have ability to produce bioplastic poly-β-hydroxybutyrate (PHB) from sago starch. The study wasattempted to determine the mechanism of PHB production by bacteria amylolytic was grown on sago starchcontainingmedia. Two amylolytic bacteria i.e. Bacillus sp. PSA10 and Bacillus sp. PPK5 was grown for 168 hin a mineral salts medium with sago starch as carbon source. Growth of amylolytic bacteria was monitoredby cell dry weight. Extraction of PHB was done by N-hexane acetone-diethyl ether method and PHB contentwas quantifi ed with UV spectrophotometer at 235 nm. Glucose level was determined by using kit of glucoseGOD 10” and was quantifi ed with spectrophotometer at 500 nm. Sago starch concentration was determinedby phenol method using specthrophotometer at 490 nm. The result of the study showed that Bacillus sp.PSA10 was produced PHB up to 66,81 % (g PHB/g cell dry weight) at 48 h and Bacillus sp. PPK5 up to 24,83% (g PHB/g cell dry weight) at 84 h. Bacillus sp. PSA10 has ability to converse sago starch to be PHB directlywithout glucose accumulation in the media, whereas Bacillus sp. PPK5 have to accumulate glucose as productof sago starch hydrolysis to produce of PHB. PHB synthesis by Bacillus sp. PHB production on sago starchof the Bacillus sp. PSA10 was found to be growth-associated whereas Bacillus sp. PPK5 was found to be nongrowth-associated. Therefore, two indigenous amylolytic bacteria were having of difference in biosynthesismechanism of PHB in sago starch medium and their characteristics of PHB synthesis should be consideredin developing cultivation methods for the effi cient production of PHB. Keywords : Production, PHB, Amylolytic bacteria, Sago starch.

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