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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 518 Documents

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Allozyme variation of the endemic and vulnerable Dyera lowii Hook.f. in Central Kalimantan: Implications for genetic resources conservation Wahyudiningsih, Tri Suwarni; Naiem, Mohammad; Indrioko, Sapto; Sumardi, Issirep
Indonesian Journal of Biotechnology Vol 19, No 1 (2014)
Publisher : Universitas Gadjah Mada

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Dyera lowii is an endemic and vulnerable tree species of commercial value as chewing gum found inpeat swamp forests, scatteredly distributed in Sumatra, Kalimantan, and Peninsular Malaysia. Their existenceis now under severe threat due to habitat conversion. This study is aimed to assess genetic diversity withinfour natural populations (Hampangen, Parahangan, Sebangau, Selat Nusa ) and one plantation in CentralKalimantan based on allozyme variation. Electrophoresis procedures were conducted with an isoelectricfocusing polyacrylamide slab gel system. The result showed high genetic diversity (HE=0.52) and gene fl ow(3.402) seemed to be effective. A total of 14 alleles were found among all the analysed population. Meannumber of alleles per locus (Aa) was 3.206, and the effective number of alleles per locus (Ae) was 2.21. Geneticdifferentiation between populations (FST) was signifi cant at the moderately level (0.0685). Most allozymevariation was found within population (93.2%). Special attention is essential to conserve a private allele ofGot-1-e (9%) at Selat Nusa population. Sebangau population missed the alleles of Est-2-b and Got-1-a, as foundin other populations. Selat Nusa population is expected to enhance the effective management for geneticresources conservation of this vulnerable species in the future.

Superoxide Dismutase of Micrococcus sp. S2 and Its Involve in Paraquat Detoxification Margino, Sebastian; Martani, Erni; Magdalena, Medhina
Indonesian Journal of Biotechnology Vol 12, No 1 (2007)
Publisher : Universitas Gadjah Mada

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As an active ingredient of herbicide, paraquat will induce formation of superoxide radicals. The previousresearch succeeded in isolating paraquat degrading bacteria from peat soil, Micrococcus sp. S2, that tolerant to highconcentration of paraquat. An anti-oxidative enzyme, namely superoxide dismutase (SOD, EC.1.15.1.1), wasbelieved to be responsible for the paraquat tolerance. This research was conducted to study the characteristic of theSOD synthesize by Micrococcus sp. S2 and its ability on neutralize superoxide which arise from paraquat reoxidation.To observe the effect of paraquat on Micrococcus sp. S2, the bacteria was grown in 10% Luria Bertani brothmedium amended with several concentrations of paraquat, from 0 (control) up to 100 mg/ml. Within incubationtime of 72 hours, bacterial growth, activity of superoxide dismutase and paraquat residue were analyzed. Theisozymes of superoxide dismutase were distinguished using two kinds of specific inhibitor, namely HO and KCN. 2 2The results showed that paraquat significantly inhibit the growth of Micrococcus sp. S2. The higher paraquatcocentration in the medium caused the higher growth inhibition. However, the bacteria is still survive in the mediumcontaining toxic herbicide, and this ability was suggested related to superoxide dismutase activity in removing thesuperoxide radicals. Analysis using gel electrophoresis indicated that at least three types of SOD isozyme weresynthesized by Micrococcus sp. S2; they were Ferri-SOD (Fe-SOD), Mangani-SOD (Mn-SOD), and the last one wassuspected to be the Cupro Zinc-SOD (CuZn-SOD). The Mangani-SOD was suspected to play an important roles ondetoxifying superoxide which arise from paraquat oxidation.Keywords : Micrococcus sp.S2, paraquat, superoxide dismutase, isozymes

Effects of Dissolved Oxygen Tension and Ammonium Concentration on Polyhydroxybutyrate Synthesis from Cassava Starch by Bacillus cereus IFO 13690 ., Margono; ., Rochmadi; Syamsiah, Siti; Cahyanto, Muhammad Nur
Indonesian Journal of Biotechnology Vol 14, No 1 (2009)
Publisher : Universitas Gadjah Mada

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Attempting to get low price of raw material for producing polyhydroxybutyrate is always studied. Tapioca starch is one of the raw material with low price. The objective of this research was to study the effects of initial ammonium concentration and dissolved oxygen tension (doT) on producing PHB by Bacillus cereus IFO 13690 with tapioca starch as the carbon source. This fermentation was carried out in 5 L fementors with a 2 L working volume, temperature of 30 oC, and agitation of 500 rpm. The pH medium was controlled at 5.6 after it came down from the initial pH of 6.8. Meanwhile, the initial doT was 100 % air saturation and also came down to and maintained at doT of experiment, i.e. 1 , 5 , or 10 % air saturation. The best result was obtained when the initial ammonium concentration was 5 g/L and the doT value maintained at 5 % air saturation. By this conditions, the cell growth reached 5,457 g cell dry weight/L containing PHB of 2.42 % cell dry weigh after 29 hours fermentation.

CYP3A4*1G gene Polymorphism on Javanese People Sutrisna, Em; Dwiprahasto, Iwan; Astuti, Indwiani; Kristin, Erna
Indonesian Journal of Biotechnology Vol 16, No 2 (2011)
Publisher : Universitas Gadjah Mada

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AbtractMost of drugs are metabolized by cytochrome P 450 (CYP) enzyme. Cytochrome P450 3A4 is the cytochrome that is involved in metabolizing more than 60% of all medicine used in human. The variation of this CYP3A4 gene will affect the catalytic activity of this enzyme. Recently, CYP3A4*1G in intron 10 was found in Chinese and Japanese population. There is a substitution of G to A at position 82266 in intron 10. The purpose of this research was to investigate the frequency of allele and genotype CYP3A4*1G. Samples were taken from bloods of the subjects of the research. The examination of CYP3A4*1G was conducted by RTLP-PCR method.As the results of this research, the frequency of CYP3A4*1G in Javanese people is CYP3A4*1/*1 0.25, CYP3A4*1/*1G 0.55 and CYP3A4*1G/*1G 0.20. Frequency of allele G: 0.53, allele A: 0.47. The Fisher’s exact- test shows that the allele and genotype frequencyis p. 1.000. The allele and genotype frequency of Javanese people isstill in Hardy-Weinberg equilibrium.Keywords : CYP3A4*1G gene, polymorphism, Javanese people

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

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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)

The Efficacy of Fucoidan on Gastric Ulcer Juffrie, Mohammad; Rosalina, Ina; Damayanti, Wahyu; Djumhana, Ali; A, Ariani; Ahmad, Harjono
Indonesian Journal of Biotechnology Vol 11, No 2 (2006)
Publisher : Universitas Gadjah Mada

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Hyperacidity causes gastric injury, and in severe situations, ulcer could develop. The growth factors known asthe basic fibroblast growth factor (bFGF) and the epidermal growth factor (EGF) have been recognized to promoteulcer healing. Fucoidan is extracted from a brown seaweed of Okinawa called Mozuku or Cladosiphon okamuranus.Fucoidan is effective for the healing of gastric ulcers by inducing epithelial cells to produce growth factors. The aimof this study is to explore the efficacy of fucoidan in patient who suffered by gastric ulcer. A randomized control trialdouble blind was conducted to 33 eligible samples. By using four-blocks random samples were divided into fucoidanand placebo groups. 100 mg of fucoidan was given to the fucoidan group and 100 mg of glucose was given to theplacebo group. Due to ethical reasons, for both groups were given a proton pump inhibitor. There was no differencein the age category between the fucoidan group (mean: 46.23 ± 14.8 years) and the placebo group (mean: 46.18 ± 18.4years) (p: 0.28). There was also no difference in sex between the fucoidan group (female: 10/33; male 7/33) and theplacebo group (female: 7/33; male: 9/33); p: 0.38. According to the SAKITA and MIWA criterias 32 patients fulfilledA1 which indicate active severe ulcer, and 1 patient fulfilled A2 which indicate active moderate ulcer. Most of theulcers were gastric ulcer. There was a significant improvement of the grade of ulcer in fucoidan group (94%) (16/17)compared to placebo group (37.5%) (6/16,p: 0.005). There was a significant reduction of abdominal pain after 5 daysin the fucoidan group, compared to the placebo group (p: 0.04). Vomiting tends to decrease in day 6 of the fucoidangroup however its proportion is similar with that of the placebo group (p: 0.9). Fucoidan is effective for ulcer healingand reducing ulcer symptoms.Key words : fucoidan, gastric ulcer, anti-peptic activity

The assessment of genetic variability and taxonomic affinity of local pummelo accessions from Yogyakarta, Indonesia based on RAPD Ratna Susandarini; Rina Arifati; Abdul Razaq Chasani; Siiti Subandiyah
Indonesian Journal of Biotechnology Vol 19, No 2 (2014)
Publisher : Universitas Gadjah Mada

Pummelo (Citrus maxima) is one of three biotypes considered as true species within the genus Citrus.A major issue of pummelo taxonomy in Indonesia is the high number of cultivars showing variability inphenotypic characters but of unknown genetic diversity. In this study, the assessment of genetic variabilityand taxonomic affi nity of local accessions of C. maxima from Yogyakarta was examined based on RAPDfi ngerprinting. The availability of universal primers and technical simplicity makes RAPD as a molecular toolof choice for the assessment of genetic variability at various taxonomic levels. In this study, 13 accessions of C.maxima collected from Yogyakarta were observed for their genetic variability. An additional three registeredcultivars were included for comparative purpose. Two decamer primers used for the amplifi cation of DNAproduced 222 bands with 174 of them were polymorphic. The data was subjected to cluster analysis to observethe grouping of accessions and taxonomic affi nity. Results indicated high genetic variability among accessions.The dendrogram constructed using UPGMA method based on simple matching coeffi cient showed twomain clusters were which was in line to morphological characters. The grouping of accessions showed cleardifferentiation between accessions bearing white and those with reddish fruit fl esh, and thus demonstratestaxonomic value of this study in recognizing important agronomic character for this tropical fruit crop.

In vitro Antiplasmodial Activity and Cytotoxicity of Vincadifformine and Its Semisynthetic Derivatives M. Mustofa; Michèle Mallié; Alexis Valentin; Guy Lewin
Indonesian Journal of Biotechnology Vol 11, No 1 (2006)
Publisher : Universitas Gadjah Mada

An indole alkaloid with aspidospemane structure possessing a potential antiplasmodial activity, vincadifformine, has been isolated from Aspidosperma pyrifolium Mart. Moreover, 10 derivatives were prepared from the vincadifformine. The study was conducted to evaluate the in vitro antiplasmodial and cytotoxic activity of the vincadifformine and their semisynthetic derivatives. The in vitro antiplasmodial activity was evaluated on Plasmodium falciparum chloroquine-resistant (FcM29) and –sensitive (Nigerian) strains after 24-h and 72-h incubation, while cytotoxic activity was estimated on Hela cells and Cytotoxicity Index (CI = IC50 on HeLa cells/IC50 on FcM29 strain) was calculated to evaluate the safety of tested compounds. Experiment results showed that two compounds (4 and 8) exhibited good antiplasmodial activities in comparison with parent compound, vincadifformine and other tested compounds with IC50 ranging from 5.3 to 12.8 µM on FcM29 strain and 11.4 to 24.0 µM on Nigerian strain. In addition, the CI of two compounds were also lower after 24-h incubation (CI, 2.0 and 4.8) than that of after 72-h incubation (CI, 9.5 and 11.5). Further study will be conducted to evaluate quantitative structure-activity relationship (QSAR) in order to design new antimalarial drugs.

Genetic Determination and Clonal Relationships of Staphylococcus aureus Isolated from Dairy Cows in Baturraden, Central Java, Indonesia Fatkhanuddin Aziz; Siti Isrina Oktavia Salasia; Mitra Slipranata
Indonesian Journal of Biotechnology Vol 19, No 2 (2014)
Publisher : Universitas Gadjah Mada

Cases of mastitis in cows at Baturraden are leading to signifi cant and ongoing problems due to reducedproduction and lower milk quality. This study was designed to identify which of selected virulence determinantgenes of S. aureus are involved in the Baturraden infection, and to determine the clonal relationship amongthese isolates. Seventeen isolates were identifi ed as S. aureus based on their biochemical properties and speciesspecifi city for 23S rRNA and nuc genes. S. aureus isolates were genotypically characterized for the selectedvirulence determinants: coa, clfA, fnbA, fnbB, cap5, spa IgG and spa X- region genes. Clonal relationship analysisamong isolates was carried out using AFLP and results compared with previously confi rmed relationshipsbetween selected S. aureus isolated from other regions. The results show that eight isolates contain all thegenes, but six isolates lack fnbB and two isolates lack cap5 genes. AFLP analysis showed that all isolates of S.aureus originating from cows in Baturraden belong to one cluster. This study provides additional knowledgeabout S. aureus infection in Baturraden cows, including the number of virulence determinant genes that mayplay a role in pathogenicity.

Induced-Coagulated Plasma-Fibrin Gels as a Biological Scaffold for Cell Attachment and Proliferation of Umbilical Cord-Derived Mesenchymal Stem Cells (UC-MSC) Rio Hermantara; Fiano A. Kerans; Rizal R; E. Henny Herningtyas; Lutfan Lazuardi
Indonesian Journal of Biotechnology Vol 19, No 2 (2014)
Publisher : Universitas Gadjah Mada

Fibrin gels are an ideal natural biological scaffold for tissue engineering because they are biocompatible,biodegradable, and have many biological surface markers. However, most research on fi brin gels used commercialfi brin kits that could be costly and limited in some areas. In this study, fi brin gels were made by inducing bloodcoagulation by adding a common diagnostic kit to assess the time for blood to clot, called activated partialthromboplastin time (aPTT). This induced coagulated plasma (iCoplas)-fi brin gels was evaluated for its ability toenhance biological activity of umbilical cord-derived mesenchymal stem cell (UC-MSC), which were cell attachmentand proliferation. Fibrinogen concentration had infl uence on cell attachment, where only 50% of the cells couldattach to 77 mg/dl fi brinogen gels whereas 93% cells adhered to 154 mg/dl fi brin gels. There were no signifi cantdifferences in cell proliferation on polysterene culture dish and fi brin gels (p>0.05). These results showed thatiCoplas-fi brin gels could be used as a fi brin-based scaffold, yielding no signifi cant difference than polysterene-tissueculture dish cultures in cell attachment and cell proliferation on 154 mg/dl fi brinogen concentration.

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