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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 10 Documents

Search results for , issue "Vol 19, No 2 (2014)" : 10 Documents clear

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.

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.

Evaluation of different promoters driving the GFP reporter gene in seaweed Kappaphycus alvarezii Muh. Alias L. Rajamuddin; A. Alimuddin; Utut Widyastuti; Irvan Faizal
Indonesian Journal of Biotechnology Vol 19, No 2 (2014)
Publisher : Universitas Gadjah Mada

Promoter regulates expression level of foreign gene in transgenic organism. This study was performed to select asuitable promoter as the fi rst step towards production of valuable trait-enhanced seaweed by transgenic technology. Greenfl uorescent protein (GFP) gene was used as a reporter to determine the activity of promoter in seaweed Kappaphycusalvarezii. GFP gene constructs driven by cytomegalovirus (pCMV-GFP), caulifl ower mosaic virus (pCaMV-GFP),medaka β-actin (pmBA-GFP) and Japanese fl ounder keratin (pJfKer-GFP) promoters were introduced by electroporationmethod. Electroporation was performed using a gene pulser (BIORAD) with voltage of 300 V, pulse length of 0.5 ms,pulse numbers of 4, and pulse interval of 0.1 s. Promoter activity was determined by analyzing GFP gene expressionlevel using a fl uorescent microscope. The results showed that CMV regulated highest number of fi lament callus(34.10%±1.49) expressing GFP at medium to strong fl uorescence levels. CaMV promoter had relatively similar activitywith CMV, but lower number of fi lament callus expressing GFP (10.48%±0.25). mBA promoter drove GFP expressionat medium level and similar number of fi lament callus (8.85%±2.31) expressing GFP with CaMV, while JfKer promoterhad lowest activity by means in number of fi lament callus expressing GFP (4.79%±0.26) and GFP expression level. PCRanalysis for transgenic confi rmation showed a DNA band of PCR product from pCMV-GFP and pCaMV-GFP expressingfi lament callus in the same size (about 0.6 kb) with positive control of plasmid. Thus, CMV and CaMV promoters wasan appropriate promoter and foreign gene could be transferred to fi lament callus by electroporation method. Combiningthis achievement with developing a culture method of fi lament callus to be thallus, stable transgenic breeding in K.alvarezii can be feasible.

Somatic embryogenesis of Sandalwood (Santalum album L.) Toni Herawan; Mohammad Na'iem; Sapto Indrioko; Ari Indrianto
Indonesian Journal of Biotechnology Vol 19, No 2 (2014)
Publisher : Universitas Gadjah Mada

Sandalwood (Santalum album L.) is native species of Indonesia, especially in East Nusa Tenggara, is oneof the twenty two species of the genus Santalum in the world. Sandalwood is an important tree because it hashigh economic value can produce sandal oil these can be used for perfumes, cosmetics, pharmaceuticals, andare often used in religious ceremonies. In vitro particularly somatic embryogenesis has been widely appliedin the propagation of sandalwood. The Objective of this research is to obtain regeneration of sandalwoodthrough somatic embryogenesis using leaves explant from various clones. Medium for embryo induction is MS(Murashige and Skoog, 1962) solid medium containing treatment of 2,4-D (2,4-Dichlorophenoxyacetic acid)at various concentrations. To the media 0,15 mg /l kinetin, 40 g/l sucrose, and 2,5 g/l gelrite were added.Culture were incubated in the dark. Medium for Embryo development (maturation) is MS solid mediumcontaining treatment of BAP (Benzyl-amino-purine) at various concentrations. To the media 0,01 mg /l NAA(Napthalene-acetic-acid), 40 g/l sucrose, and 2,5 g/l gelrite were added. Culture were incubated in the light. Tostudy the specifi c structure of sandalwood somatic embryo early detection was conducted using histologicalanalysis. Results of anova showed that the clones, media, and interaction between clones with media did notsignifi cantly affect the development of sandalwood callus percentage. Results of anova showed that the clonesand BAP concentration signifi cantly effect to the embryo development of sandalwood.

The Use of DNA Microsatellite Markers for Genetic Diversity Identification of Soybean (Glycine max (L) Meriil.) as a Supplementary Method in Reference Collections Management Nina Agusti Widaningsih; Edi Purwanto; N. Nandariyah; R. Reflinur
Indonesian Journal of Biotechnology Vol 19, No 2 (2014)
Publisher : Universitas Gadjah Mada

Large number of new soybean varieties are mostly derived from crosses of elite genotypes resulted ina narrowing of both the genetic diversity and the phylogenetic relationship between soybean varieties. Thus,discrimination among soybean varieties is becoming more diffi cult, especially when morphological traits wereapplied. In Plant Variety Protection (PVP) system, new varieties of soybeans including granted PVP right, localand breeding varieties registered in PVP offi ce were frequently increased, implicate on increasingly the numberof soybean varieties collections. To assist the management of varieties collections, a standard fi ngerprinting datais further needed. In comparison to the management of plant collection in the fi eld, molecular marker systemswhich are rapid, reliable, informative and relatively simple are continually sought for practical applications ingermplasm conservation, management and enhancement. This study aimed to identify the genetic diversity andphylogenetic relationship of soybean varieties that have earned PVP Right as well as local varieties and breedingvarieties registered in the PVP offi ce using microsatellite or simple sequence repeats (SSR) markers.This study was conducted in Molecular Biology laboratory, Indonesian Center for Agricultural Biotechnologyand Genetic Resources Research and Development (ICABIOGRAD) Bogor, from February to May 2013. The datawere analyzed using the genetic analysis package NTSYSpc 2.02i and PowerMarker V3.25. The result showed arelatively narrow genetic diversity among 45 varieties of soybean analyzed in present study which were indicatedby the small number of genotypes and total number of alleles (NA), and the low value of gene diversity and PICvalues (<0.75). Cluster analysis showed that the grouping varieties are not related to morphological characters butrelated to phylogeny relationship between varieties. Despite the group of varieties were not clustered in accordancewith morphological characteristics, SSR marker can be a powerful tool for discriminating varieties, so that it couldbe useful for initial varieties identity in conjunction with genetic diversity analysis.

Polymorphism of Transcription Factor 7-Like 2 Gene and HOMA-β Level of Individuals With and Without Type 2 Diabetes Mellitus Family History Waode Astria Sahrani; Indwiani Astuti; Ahmad Hamim Sadewa
Indonesian Journal of Biotechnology Vol 19, No 2 (2014)
Publisher : Universitas Gadjah Mada

Family history has considered as a risk factor of type 2 diabetes. Transcription factor-7 like 2 (TCF7L2) hasrole to regulates insulin secretion and blood glucose homeostasis. The aim of current study was to determine thers7903146 polymorphism of TCF7L2 gene and homeostatic model assessment-β (HOMA-β) level on individual withand without type 2 Diabetes Mellitus (DM) family history. This work is a case-control study. Thirty six subjectswith type 2 DM family history and 36 subjects without type 2 DM family history were recruited. HOMA-βmeasure to analyze the insulin secretion. Polymorphisms of TCF7L2 gene was analyzed by using PCR-RFLPmethod. Statistical analysis was performed by using T-test, Mann-Whitney and Chi-square with signifi cancelevel 0.05. The frequency of the T allele of the cases were 4.2% and the controls were 2.8% (p=0.500). The oddratio was 0.649 (CI;95%:0.106-4.055). The HOMA-β levels of the cases were signifi cant low (132.56±62.48)compared with the controls (266.09±1.68) with p=0.000. The subjects with type 2 DM family history have asimilar frequency of having T alleles and CT/TT genotypes. The subjects with type 2 DM family history hassignifi cantly lower HOMA-β levels than subject without DM family history.

Molecular Identification of Phenol-Degrading and Biofi lm-Forming Bacteria from Wastewater and Peat Soil Arifah Khusnuryani; Erni Martani; Tri Wibawa; Jaka Widada
Indonesian Journal of Biotechnology Vol 19, No 2 (2014)
Publisher : Universitas Gadjah Mada

Phenol is hazardous aromatic pollutant which needs to be treated to reduce its hazardous effects.Bioremediation using bacteria which can form biofi lm offer an alternative wastewater treatment that is cheaperand environmentally safe. Eighteen strains of phenol-degrading and biofi lm-forming bacteria were isolatedfrom peat soil, also hospital and textile wastewater. Screening for phenol degradation ability of isolates wereperformed using Folin-ciocalteau reagent, while for biofi lm formation ability were performed using microtiterplate and crystal violet dye. Based on the ability to degrade phenol and to form biofi lm, four isolates (HP3,DOK135, DL120, andATA6) were choosen as phenol-degrading bacteria as well as biofi lm-forming bacteria.Based on phenotypic and genotypic characterization, isolate HP3 was highly similar to Rhodococcus equi strainDSM20307T, while DOK135 was highly similar to Enterobacter mori strain R18-2.The results also suggested thatDL120 and ATA6 could be classifi ed to the genus of Micrococcus and Bacillus respectively

The Susceptibility of katG Ser315Thr Mycobacterium tuberculosis mutant Against Anti Tuberculosis Drugs Ning Rintiswati; P. Praseno
Indonesian Journal of Biotechnology Vol 19, No 2 (2014)
Publisher : Universitas Gadjah Mada

Mycobacterium tuberculosis resistant strains is a matter of great concern for TB control Program since nocure for some multi drug resistance TB (MDR-TB) cases. These strains could spread around the world, makea great challenges for control measures. Mycobacterium tuberculosis strains resistance to anti tuberculosis drugsis mainly caused by the alteration in several genes encoding the molecular targets. Mutation of katG at codon315 especially Ser315Thr are responsible for INH resistance in a large proportion of TB cases. The aim of thisstudy is to know the frequency of of katG Ser315Thr of M. tuberculosis mutant and the pattern of resistance toAnti TB drugs. The study design was observational laboratoric. Eighty fi ve M. tuberculosis INH resistant clinicalisolates were screened for mutation of katGSer315Thr by using PCR-RFLP and DNA sequence analysis.Theresults showed that katG Ser 315Thr were identifi ed in 23 (27,05%) of INH resistance isolates. Frequency ofMDR among the katG Ser315Thr mutants almost double than the non mutant. The result suggested that thethe katG Ser315Thr mutation may play important role in the development of MDR-TB.

In Vitro Screening of Falcataria moluccana (Miq.) with Gall Rust (Uromycladium tepperianum (Sacc.) Filtrate as Media Selection Asri Insiana Putri; Mohammad Na'iem; Sapto Indrioko; Sri Rahayu; Ari Indrianto
Indonesian Journal of Biotechnology Vol 19, No 2 (2014)
Publisher : Universitas Gadjah Mada

In vitro screening of Falcataria moluccana (Miq.) was conducted by tissue culture method. Seeds fromtwo different site of community forest, 400 m (S1) and 800 m (S2) above sea level, were used as material.Double concentration of MS (Murashige & Skoog, 1962) with 40 mg/l gall rust (Uromycladium tepperianum(Sacc.) fi ltrate were used for media selection. The results of this research showed that 66 % axenic plantlets invitro from S1 and 27 % from S2 were still survived after 3 months incubation without subculture. The meanof fresh weight (2. 21 ± 0. 26 g) and dry weight (1. 97 ± 0. 12 g) from S1 plantlets lower than the mean of freshweight (2. 87 ± 0,18 g) and dry weight (2. 16 ± 0. 14 g) from S2 plantlets. Qualitative of terpenes, saponins andquantitative of total phenolics were analyzed from those gall rust extract, as source of fi ltrate media, attackedand un-attacked of F. moluccana. They all qualitatively have capability to produce terpenoid and saponin. Itis notice that U. tepperianum, un-cultured pathogen, contain of those compound that may play a role as codeterminantsof pathogenecity. While the highest total phenolic compound were contained in gall rust extract(2. 35 %), followed by attacked F. moluccana branches (1. 18 %) and un-attacked F. moluccana branches (0. 44%). This indicated that phenolic compound in gall rust has higher activity as a response of F. moluccana to U.tepperianum pathogen pressures and result of this study suggest the great value of gall rust fi ltrate for use asmedia selection in vitro.

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