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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 1 (2013)" : 20 Documents clear

Cloning and Expression of hGAD65 Gene in E. Coli BL21 Rista Nikmatu Rohmah; Soraya Widyasari; A. Aulanni’am; F. Fatchiyah
Indonesian Journal of Biotechnology Vol 18, No 1 (2013)
Publisher : Universitas Gadjah Mada

The aim of this study is to construct the hGAD65 gene and to identify the hGAD65 clone by using PCR & RFLP. The samples were derived from normal person & DM patient’s blood. Blood DNA was isolated by salting out method and then amplified by PCR with a pair of specific primer, GAD65-F-BamH1-807 & GAD65-R-Xho1-945. The PCR-product was cloned into vector pET-28a and the pET28a-hGAD65-clone was transformed into E.coli BL21 competent cells. The pET28a-hGAD65-clone was confirmed by PCR and RFLP by BamH1 & XhoI. The PCR product of pET28a-hGAD65-clone was one band of 159bp and has two bands 5.3 kb and 159 bp by RFLPwith both restriction enzymes. The GAD65 protein is expressed in 65kD of pET28a-hGAD65-clone. PET28a-hGAD65-clone was able to recognize by gold standard monoclonal antibody specifically. These results indicated that the hGAD65 gene inserted into pET28a properly and provided the GAD65 protein expression. Key words: hGAD65, PCR, pET-28a, RFLP

A Novel Variant of HOXA10 gene, Ser19Cys, among Patients with Endometriosis and its Relationship with the Severity of the Disease Pinda Hutajulu; Djaswadi Dasuki; Ahmad Hamim Sadewa; Totok Utoro
Indonesian Journal of Biotechnology Vol 18, No 1 (2013)
Publisher : Universitas Gadjah Mada

Endometriosis is a gynecological disease associated with inherited genetic traits. HOXA10 gene whichis expressed in uterine plays an important role in the pathogenesis of endometriosis. The protein affects thedevelopment of pinopodes as a biomarker of endometrial receptivity in endometriosis.The aim of this study isto examine if there is a mutation or polymorphism within HOXA10 gene among patients with endometriosis.Thirty twopatients and 32 healthy women were recruited as subjects of this study. The exon 2 of HOXA10which covers most of coding region was amplifi ed using PCR. The presence of a mutation or polymorphismwas detected by direct seguencing. The distribution of genotype and allele was analyzed using Chi square test with p<0.05 is considered as signifi cantly different. A novel heterozygous variant within exon 2 of HOXA10 which substitute an adenine into thymine was detected at base position 55. This missense alteration changed amino acid serine to cystein (Ser19Cys). Interestingly, this variant was detected in 12 endometriosis cases (38%) but none in control. Patients carry HOXA10 Ser19Cys variant were associated with dismenorea and more frequent in stage I endometriosis. The role of this variant in the function of HOXA10 protein and frequency among Indonesians need to be clarifi ed. We found a novel heterozygous HOXA10 gene variant, Ser19Cys.The genotype frequency is 38% among endometriosis patients but none in control. This variant found in patient with dismenore and endometriosis stage 1. Key words: HOXA10 gene, endometriosis, Ser19Cys polymophism

The Application of Polymerase Chain Reaction – Restriction Fragment Polymorphisms (PCR-RFLP) to Determine Genetic Diversity of Madura Cattle in Sapudi Island Tety Hartatik; Slamet Diah Volkandari; S. Sumadi; W. Widodo
Indonesian Journal of Biotechnology Vol 18, No 1 (2013)
Publisher : Universitas Gadjah Mada

The aim of this study was to determine genetic diversity of Madura cattle using Polymerase Chain Reaction – Restriction Fragment Length Polymorphisms (PCR-RFLP) analysis of the cytochrome b (cytb) gene. Samples used for the experiments were blood of 43 cattle that consist of 15 cattle obtained from Madura Island, 23 cattle from Sapudi Island, and 5 Limousin-Madura (Limura) cattle. A fragment of 464 base pair of cytb gene was amplifi ed by forward primer L14735 and reverse primer H15149. The PCR product was digested with TaqIand HinfI restriction enzymes to identify genetic patterns. Data of PCR-RFLP showed two haplotypes, that were A and B, in cattle obtained from both Madura Island and Sapudi Island. The frequencies of haplotype A and B of cattle from Sapudi Island were 69.57% and 30.47%, respectively. More diverse frequencies were observed in cattle obtained from Madura Island, where haplotype A and B were 86.67% and 13.33%, respectively. In this experiment, Limura cattle had only haplotype A. As a conclusion, PCR-RFLP of the cytb gene had been able to determine a genetic diversity of Madura cattle. Key words: Genetic diversity, Madura cattle, haplotype.

Improvement of Seed Orchard Management Based on Mating System of Cajuputi Trees Noor Khomsah Kartikawati; Mohammad Naiem; Eko Bhakti Hardiyanto; Anto Rimbawanto
Indonesian Journal of Biotechnology Vol 18, No 1 (2013)
Publisher : Universitas Gadjah Mada

Breeding plan of cajuputi in Indonesia is aimed to increase plantation productivity of oil yield and 1.8 cineole content. Seed orchard of cajuputi at Paliyan, Gunungkidul, established using selected and genetically improved materials, has been producing seeds for operational plantation. This seed orchard would perform optimally if the mating systems of all individuals contribute to the inheritance of all genetic potential of the offsprings. Therefore, investigation of the mating systems of cajuputi was indispensible. The study has been carried out on 10 selected mother trees and the 24 offsprings of each mother trees using 8 microsatellite markers of nuclear DNA, namely Hin-2 (100-132 bp), Hin-4 (79-114 bp), Hin-5 (128-148 bp), Hin-7 (136-224 bp), Sal-1 (93-99 bp), Sal-3 (118-219 bp), Xho-1 (96-111 bp) and Xho-4 (150-216 bp), respectively. The result showed relatively high genetic variation of the offspring (HE=0.602, HO=0.594) originated from parent trees in the seed orchard. Parent trees tend to outcross(tm=0.951, ts=0.806), although seeds originated from biparental inbred (tm – ts = 0.145) and correlated paternity(rp=0.098) have also been observed. This genetically viable population could maintain its reproduction fi tness forshort term and adapt to the dynamic environmental changes for long term. Key words: mating system, cajuputi, seed orchard, microsatellite

The Diversity of Legume-Nodulating Bacteria from Several Agroecosystems in Sumberjaya, Lampung Sri Wedhastri; Yuliana Prahastiwi; Jaka Widada; Donny Widianto; Siti Kabirun
Indonesian Journal of Biotechnology Vol 18, No 1 (2013)
Publisher : Universitas Gadjah Mada

Bacteria that capable of forming root nodules on legumes are known as Rhizobia. They have also known as Legume- Nodulating Bacteria (LNB). They can fi x nitrogen from the atmosphere. Diversity of Legume-Nodulating Bacteria is affected by biotic factors (such as their genetic factors, plants, and competition with the other soil microbes) and abiotic factors (such as land use, soil’s temperature, pH, chemistry and soil’s properties). The aim of this experiment is to know the diversity of eleven Legume- Nodulating Bacteria based on their phenotypic and genotypic characters. The eleven LNB used in this experiments were isolated from several agroecosystems in Sumberjaya, Lampung. The analysis of these LNB diversity were carried out by characterizing both phenotypic and genotypic properties. The diversity analysis showed that the eleven LNB isolates had high diversity, based on nodule formation, and classifi ed into two groups of cross inoculation group. Key words: Rhizobia, phenotypic diversity, genotypic diversity

Partial Purifi cation, Stability Analysis, and Preservation of Xylanase from Xylanolytic Alkalophylic Bacteria Chusnul Hanim; Muhamad Nur Cahyanto; Lies Mira Yusiati; Ali Wibowo
Indonesian Journal of Biotechnology Vol 18, No 1 (2013)
Publisher : Universitas Gadjah Mada

A xylanase, which produces xylose from oat spelt xylans, was isolated from the culture medium of xylanolytic alkalophylic bacteria mutant. The enzyme was purifi ed by ammonium sulphate with level 30, 40, 50, 60, 70, 80, and 90%. The purify of the fi nal preparation was demonstrated by sodium dodecyl sulphatepolyacrylamide gel electrophoresis. The molecular masses of the purifi ed xylanase were 137.61 and 165.34 kDa. Result of ammonium sulphate saturation with the highest activity was used as standart for saturation for enzyme production and preservation, using corn, tapioca, soy bean meal and gaplek fl our as carriers. Addition of 60% ammonium sulphate showed the highest xylanase activity (62.03 U/g), and produced 89.40% enzyme recovery. Tapioca, as a carrier, produced the highest xylanase activity. Key words: preservation, purifi cation, stability analysis, xylanase.

Phylogeny and Origin of Glucose-6-Phosphate Dehydrogenase (G6PD) Deficiency Mutations in Indonesia Maria Omega; Ross T. Barnard
Indonesian Journal of Biotechnology Vol 18, No 1 (2013)
Publisher : Universitas Gadjah Mada

The aim of this study is to analyze the relationship between the types of G6PD mutations found in Indonesia and the relationships of mutations found in Indonesia to those found in other countries. We summarize the distribution of G6PDs in West Indonesia and East Indonesia. Moreover, we use bioinformatics methods to construct phylogenetic trees and compare the sequences containing the regions amplifi ed by the commonly used PCR primer pairs. Previous work has shown that Mediterranean G6PD and Chinese CoimbraG6PDare distributed in West Indonesia, whilst G6PD mutations in East Indonesia are Jammu/ViangchanG6PD and Chinese Gaohe G6PD. G6PD Jammu/Viangchan was mostly distributed in Flores Island, East Indonesia along with G6PDGaohe. We constructed phylogenetic trees using the G6PD sequences from various regions in Indonesia and other countries. It appears from phylogenetic trees and percentages of identity that FloresIndonesian G6PD defi ciency (Jammu/Viangchan G6PD, originating in India) is 92.5% identical to the G6PD defi ciency of Chinese origin (GaoheG6PD). It was interesting to note that the genetic region containing the Javanese Indonesian G6PD defi ciency (MediterraneanG6PD, fi rst found in Italy) located in the western parts of Indonesia is closely related (99% identity) to the Chinese G6PD defi ciency(Coimbra G6PD). We concludethat G6PD mutations in West Indonesia are closely related to G6PD mutations from China. G6PD mutations in East Indonesia are also closely related to G6PD mutations from India and China, but more distantly, and to different types to those in West Indonesia. A prediction of protein structure was carried out which allowed visualization of the locations of mutation on the three dimensional structure of G6PD. Key words: G6PD, phylogeny, origin, genetic mutations

Chemosystematic of Enterobacteriaceae Familia Obtained from Blood Cultures Based on Total Protein Profiles Sri Darmawati; Langkah Sembiring; Widya Asmara; Wayan T. Artama; Syaiful Anwar
Indonesian Journal of Biotechnology Vol 18, No 1 (2013)
Publisher : Universitas Gadjah Mada

The purpose of this study was to determine the chemosystematic of 14 strains of bacteria in blood cultures from Semarang using 1 reference strain S. typhi NCTC 786, based on the total protein profi les with the similarity relationship analysis based on Simple Matching Coeffi cient (SSM) analysis and algorithm methodof unweighted pair group with averages (UPGMA) presented in a dendrogram. The results showed that thechemosystematic based on the total protein profi les using SDS-PAGE method can classify the member ofbacterial strains of each species. The Clusters respectively consist of 4 strains of S. typhi (similarity: 89.7%),2 strains of Ser. marcescens (similarity: 89.7%), two strains of E. coli, and one strain of Salmonella ssp, S. typhi NCTC 786 (similarity: 100%). Those three incorporated clusters had the similarity value of 75.3%. Those four strains of Ent. cloacae composed in one cluster (similarity: 100%) are incorporated in a cluster consisting of one strain of Kleb. pneumoniae (similarity: 92.9%). Both clusters were incorporated in a cluster consisting of S. typhi NCTC 786 (similarity: 67.9%). Key words: Enterobacteriaceae, chemosystematic, blood cultures, protein profile

Apolipoprotein E as Risk Factor for Coronary Heart Disease Pramudji Hastuti; Abdul Salam M. Sofro; Ahmad Husain Asdie; Ahmad Hamim Sadewa
Indonesian Journal of Biotechnology Vol 18, No 1 (2013)
Publisher : Universitas Gadjah Mada

Allelic variation of apolipoprotein E (apo E) has been shown to infl uence the concentrations of total cholesterol and low density lipoprotein cholesterol (LDL-C) and considered to play a role as one of risk factors for coronary heart disease (CHD). The aim of this study was to examine the relationship between Apo E polymorphism and the risk of CHD. Blood samples were collected from 33 CHD patients in Dr. Sardjito Hospital Yogyakarta, and 38 apparently healthy control individuals in a cross sectional study. The common allelic variants of ApoE were screened employing polymerase chain reaction and restriction fragment length polymorphism. The results obtained were analyzed by t-test and signifi cantly different if p <0.05 and risk factor was calculated by odd ratio. Frequency of ApoE ε2, ε2 and ε4 alleles in CHD patients were 12.1%, 69.7% and 18.2% while in controls were 18.4%, 72.4% and 9.2% respectively. Dyslipidemia condition was a strongrisk factor for CHD. By controlling lipid profi le and applying multifactorial statistic analysis, it was shown that ε4 gene carrier was the risk factor for CHD, but not in triglyceride level, whereas ε2 carrier gene was not the risk factor for CHD. Dislipidemia was the risk factor for CHD and ApoE ε4 gene carrier was the risk factor for CHD. Key words: apolipoprotein E, ApoE ε4 gene carrier, coronary heart disease, dyslipidemia.

Genotyping of Rotavirus by Using RT-PCR Methods Hera Nirwati; Tri Wibawa; Abu Tholib Aman; Yati Soenarto
Indonesian Journal of Biotechnology Vol 18, No 1 (2013)
Publisher : Universitas Gadjah Mada

There is a great diversity of rotavirus genotypes circulating worldwide, with dominant genotypes changing from year to year. Rotavirus genotyping was performed by using reverse transcription PCR with type-specifi c-primers. Since rotavirus is a RNA virus that has high mutation rate, there was a possibility of technical diffi culty in genotyping due to mutation in the primer binding sites. During Indonesian rotavirus surveillance study 2006-2009, it was reported that 17% of samples subjected for G type and 21% of samplessubjected for P type were untypeable. The objective of this study was to identify genotypes of the samples that were untypeable previously using RT-PCR based on the method described by Das et al. (1994) and Gentsch et al. (1992). There were 30 samples subjected to G type and 61 samples subjected to P type to be re-typed using method described by Gouvea et al. (1990) and Simmond et al. (2008) for G and P typing, respectively. By using another set of primer, the genotype of all samples was identifi ed. This study highlights the importance of a constant reconsideration of primer sequences employed for the molecular typing of rotaviruses. Key words: rotavirus, G typing, P typing

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