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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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Isolation and Purifi cation of Chitinase Bacillus sp. D2 Isolated from Potato Rhizosfer Sebastian Margino; Chatarina Behar; Widya Asmara
Indonesian Journal of Biotechnology Vol 17, No 1 (2012)
Publisher : Universitas Gadjah Mada

Potato Cyst Nematodes (Globodera rostochiensis) is one of the important potato’s pests and caused economic looses up to 70% in the several centrals of potato plantations in Indonesia. Potato Cyst Nematodes (PCN) shell component of egg shell containing chitin (inner layer) and vitelline/protein (outer layer), so the purpose of research was to fi nd out of chitin degrading bacteria for controlling of egg’s PCN by cutting of their life cycle. The results showed that Bacillus sp. D2 isolated from potato rhizosphere could produce extra cellular chitinase in the medium containing of 0.20% colloidal chitin and fermented for 72 hours. Result of chitinase purifi cation using ammonium sulphate precipitation and DEAE-Cellulose ion-exchange chromatography showed a specifi c activity 2691,052 U/mg and analyzing using SDS-PAGE 12.5% resulted in molecular weight 30 kDa. The apparent Km and Vmax of chitinase towards colloidal chitin were 2 mg/ml and 2.2 μg/h, respectively.

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

High Resolution Microsatellite Marker Analysis of Some Rice Landraces Using Metaphor Agarose Gel Electrophoresis K. Kristamtini; T. Taryono; Panjisakti Basunanda; Rudi Hari Murti
Indonesian Journal of Biotechnology Vol 20, No 1 (2015)
Publisher : Universitas Gadjah Mada

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 .

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

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

Limited evidence for white spot syndrome virus susceptibility associated with expression of PmVRP15 in local population of giant tiger shrimp (Penaeus monodon) Aushia Tanzih Al Haq; M. Murwantoko; T. Trijoko; Nastiti Wijayanti; Ch. Retna Handayani; Rarastoeti Pratiwi
Indonesian Journal of Biotechnology Vol 20, No 2 (2015)
Publisher : Universitas Gadjah Mada

White spot syndrome virus (WSSV) is a devastating viral disease in shrimp aquaculture. Infection ofWSSV in penaeid shrimps affects immune defense and changes gene expression. PmVRP15 has been reported as a part of the WSSV propagation pathway that is highly up-regulated in hemocytes at the acute phase of WSSV infection. This study analyzed the expression of PmVRP15 in local populations of giant tiger shrimp (Penaeus monodon) to be associated with susceptibility to WSSV. Tested populations consisted of an inbreeding population (G8) and outbreeding population (G8iA) from Jepara, Indonesia. Susceptibility was determined by cumulative mortality, median lethal time (LT50), and severity of infection at time of death. Though all populations were susceptible to WSSV, the frst mortality in G8 occurred at 18 hours post-infection (hpi) with mild infection, while frst mortality of G8iA occurred at 30 hpi with severe infection. The LT50 of G8 was signifcantly lower than that of G8iA, indicating that G8iA was less susceptible to WSSV than G8. Relative PmVRP15 transcripts of G8iA were insignifcantly down-regulated, whereas relative PmVRP15 transcripts of G8were insignifcantly upregulated. Although it’s still not conclusive, the results of this study suggest that PmVRP15 has weak potentialas a WSSV susceptibility marker in G8 and G8iA broodstock selection.

Characterization of Haemolysin of Staphylococcus aureus Isolated from Food of Animal Origin Dwi Ariyanti; Siti Isrina Oktavia Salasia; Syarifudin Tato
Indonesian Journal of Biotechnology Vol 16, No 1 (2011)
Publisher : Universitas Gadjah Mada

Staphylococcus aureus is an important pathogen bacteria causing food poisoning and various infection in animals and humans. Haemolysin is one of the virulence factors of Staphylococcus aureus. The aims of the research were to characterize haemolysins of Staphylococcus aureus isolated from various food of animal origin, phenotypic- and genotypically. In the present study, eleven Staphylococcus aureus isolated from various food of animal origins from traditional markets and supermarkets in Yogyakarta, Sidoarjo, Jakarta, and Bandung were characterized for haemolysin, pheno- and genotypically. Characterization of haemolysin phenotypically based on haemolysis pattern of Staphylococcus aureus on sheep blood agar plate. Genes encoding hemolysin were amplified with specific primers by using polymerase chain reaction (PCR) technique. The results of the studies showed that Staphylococcus aureus on sheep blood agar plates revealed an alpha haemolysis pattern (18,18%), beta haemolysis (27,27%) and gamma haemolysis (54,55%). Based on amplification of the gene encoding haemolysin of Staphylococcus aureus with specific primers showed hla genes (81,81%), and hla combined with hlb genes (18,18%). The amplification of gene hla and hlb had a single amplicon with a size of approximately 534 bp and 833 bp, respectively. The haemolysin characteristics of Staphylococcus aureus from various food of animal origin could be used as important information to control staphylococcal food poisoning.Keywords : Staphylococcus aureus, haemolysin, PCR, food of animal origins

Isolation of actinomycetes from maize rhizosphere from Kupang, East Nusa Tenggara Province, and evaluation of their antibacterial, antifungal, and extracellular enzyme activity Umi Fatmawati; Yulin Lestari; Anja Meryandini; Abdjad Asih Nawangsih; Aris Tri Wahyudi
Indonesian Journal of Biotechnology Vol 23, No 1 (2018)
Publisher : Universitas Gadjah Mada

Actinomycetes are the one of the components of the rhizospheric microbial population and useful for producing secondary metabolites such as lytic enzymes, antibiotics, and antifungal. The aim of the study was to isolate the actinomycetes from maize rhizosphere collected from Kupang, East Nusa Tenggara. The screening was focused on the actinomycetes that showed the ability to produce antibacterial, antifungal, and extracellular enzymes such as amylase, cellulase, and protease. The actinomycetes were isolated using Humic-Acid Vitamin B (HV) agar media. The antagonistic assay was tested against Escherichia coli, Staphylococcus aureus, Sclerotium rolfsii and Fusarium oxysporum. Isolate JKP-8 was an isolate that showed the highest activity in inhibiting the growth of E. coli and S. aureus bacteria. Isolate JKP-5 showed the highest activity in inhibiting the growth of F.oxysporum. There were no actinomycetes isolates that showed an ability to inhibit the growth of S. rolfsii fungus based on dual culture assay. JKP-3 and JKP-4 isolates exhibited the highest ability to hydrolyze amylum, while JKP-5 and JKP-8 isolates exhibited the highest ability to hydrolyze CMC. The results of the amplification of 16S rRNA gene in selected potential isolates JKP 5 and JKP 8 indicated that both isolates belong to the genus Streptomyces.

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

Expression Analysis and Nuclear Import Study of Full-length Isoforms Importin α as 6x Histidin-tagged Fusion Protein on the Intracellular Localization of Recombinant HBV Core Protein Aris Haryanto
Indonesian Journal of Biotechnology Vol 10, No 1 (2005)
Publisher : Universitas Gadjah Mada

Isoform importin α molecules play a central role in the classical nuclear import pathway, that occurs through the nuclear pore complex (NPC) and typically requires a specific nuclear localization signal (NLS). In this study, it was investigated the role of isoforms importin α in the nuclear import of wild type recombinant hepatitis B virus core protein (WT rHBc), phosphorylated recombinant HBV core (rHBc) and recombinant HBV core without NLS by co-immunoprecipitation. Four recombinant full-length isoforms importin α as 6x histidin-tagged fusion protein were expressed and analysed from expression plasmid vectors Rch1, pHM 1969, pHM 1967 and pHM 1965. The results indicated that importin α-1, importin α-3, importin α-4 and importin α-5 can be expressed and isolated from E. coli transformed recombinant DNA plasmid as protein in size around 58-60 kDa. By the nuclear transport study shown that isoforms importin α are involved in the nuclear import of WT rHBc, phosphorylated rHBc and rHBc without NLS. It also indicated that they have an important role for nuclear transport of from cytoplasm into the nucleus.

Elimination of shallot bulb viruses through heat treatment Margo Sulistio; Endang Sulistyaningsih; Siti Subandiyah
Indonesian Journal of Biotechnology Vol 20, No 2 (2015)
Publisher : Universitas Gadjah Mada

Shallot (Allium cepa L. Aggregatum group) is usually cultivated vegetatively. As a result, viruses tend to accumulate within the host plants and spread to healthy plants every crop cycle, reducing yield and bulb quality. There are a very limited number of studies about the elimination of shallot viruses through heat treatment. The objective of this research was to eliminate shallot viruses through heat treatment to produce virus-free plantlets. The leaves of Biru Lancor with specifc visual virus symptoms were detected by Reverse Transcription–Polymerase Chain Reaction (RT-PCR). Then bulbs of Biru Lancor that were positively infected by viruses were used as materials for heat treatment. The treatments were a control (without treatment), electric treatment at 15 mA for 10 minutes, heat treatment in an incubator at 37°C for 4 weeks, heat treatment in a waterbath at 45°C for 60 minutes, and combination of heat treatment in an incubator at 37°C for 4 weeks and heat treatment in a waterbath at 45°C for 60 minutes. After being subjected to heat treatment, the pseudo stem were cultivated in the MS Medium + 1 mg/L BAP + 1 mg/L IBA.Virus detection by RT-PCR was conducted 28 days after planting using samples of leaves from each plantlet. The results of this research showed that the treatments of electric treatment at 15 mA for 10 minutes and combination of heat treatment in the incubator at 37°C for 4 weeks and heat treatment in the waterbath at 45°C for 60 minutes could suppress the incidence of Shallot latent virus (SLV) until 100%. Heat treatment might have an important role in the degradation of virus particles by boosting Virus-Induced Gene Silencing (VIGS) as plant responses to virus infection.

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