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Daerah istimewa yogyakarta
INDONESIA
Indonesian Journal of Biotechnology
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.
Arjuna Subject : -
Articles 518 Documents
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Molecular Genotyping of HBV by using Nested PCR-RFLP among Hepatitis B Patients in Daerah Istimewa Yogyakarta Province and Surrounding Area Haryanto, Aris; Mulyani, Nenny Sri; Widowati, Titis; Wijayanti, Nastiti; Hadi, Purnomo
Indonesian Journal of Biotechnology Vol 13, No 2 (2008)
Publisher : Universitas Gadjah Mada

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Abstract

Hepatitis B virus (HBV) can be classified into 8 genotypes, genotype A to H. Genotype of HBV is important for clinical and etiological investigations. Research for HBV genotyping, HBV transmission study using nested PCR and HBV genotyping based on RFLP using restriction enzymes have been reported. However, both of those methods have been not applied for HBV genotyping study among hepatitis B patients in endemic area, like Indonesia yet. Molecular genotyping of HBV will describe epidemiology, pathogenesis and clinical implication of HBV. Combination of nested PCR and RFLP (nested PCR-RFLP) method to determine HBV genotype in Indonesia is still less information. The objectives of study were to develop a system for HBV genotyping by nested PCR combined with RFLP (nested PCR-RFLP) method based on nucleotide sequence of surface protein encoding</div><div>gene (S gene) in HBV genome and to confirm HBV genotypes which predominantly found among hepatitis B patients in Daerah Istimewa Yogyakarta Province and surrounding area. Total of 149 sera from chronic hepatitis B patients from Daerah Istimewa Yogyakarta and surrounding areas were collected for in this work. Viral DNA were extracted from sera of hepatitis B patients and used as template for first round nested PCR amplification using outer primers set. Amplicons of first round PCR were used as template for second round amplification using inner primers set. Then, amplicons of second round nested PCR were restriction digested by Sty I and Bsr I enzymes. For HBV genotyping then the restriction products were analyzed by RFLP based on restriction pattern. Results showed that the first round nested PCR amplification generated DNA fragments of whole S gene in length 1.233 bp, and in second round nested PCR amplification using inner primer set generated DNA fragments 585 bp in length. Genotype analysis for all samples using nested PCR-RFLP methods by restriction digested of Sty I and Bsr I enzymes found only 2 HBV genotypes among hepatitis B patients, namely genotype B and C. Quantification</div><div>data showed that most of hepatitis B patients found infected by HBV genotype B (92,8%), genotype C (3,6%) and unidentified genotype (3,6%). Nested PCR-RFLP methods for HBV genotyping is simple and inexpensive for clinical diagnostic in large scale.
Application of Multiplex RT-PCR for Detection of Cucurbit-infecting Tobamovirus Daryono, Budi Setiadi; Natsuaki, Keiko T.
Indonesian Journal of Biotechnology Vol 16, No 1 (2011)
Publisher : Universitas Gadjah Mada

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Abstract

Cucumber green mottle mosaic virus (CGMMV) and Kyuri green mottle mosaic virus (KGMMV) are seed borne viruses and they are also transmitted mechanically during agricultural practice and through water. Hence, these viruses have potential diseases widely distributed throughout the world. To detect different strains of CGMMV and KGMMV, several specific primers for each virus were designed for single and multiplex RT-PCR. The results of single and multiplex RT-PCR showed that CGMMV was detected in zucchini isolated in Bali-Indonesia, while KGMMV was detected both in zucchini isolated in Bali-Indonesia and Cucumis metuliferus isolated in Thailand. Furthermore, artificial co-infection of these two viruses was prepared and carried out using two different ways of viral RNAs extraction. Based on the results, it could be reported that viral RNAs for cDNA amplification by multiplex RT-PCR could be extracted from a mixture of infected leaves or separate extraction of each viruses infected leaves. In addition, results presented in this study demonstrated the application of multiplex RT-PCR to simultaneously detect CGMMV and KGMMV from cucurbit leaves using a mixture of four primers and its feasibility as a sensitive and rapid laboratory assay. Since, no multiplex RT-PCR technique has been described for the detection of CGMMV and KGMMV, this technique can be a good option for sensitive and reliable tool for detection of two major cucurbit infecting Tobamoviruses.Keywords : Cucurbit infecting Tobamovirus, multiplex RT-PCR, seed borne viruses
Improvement of Seed Orchard Management Based on Mating System of Cajuputi Trees Kartikawati, Noor Khomsah; Naiem, Mohammad; Hardiyanto, Eko Bhakti; Rimbawanto, Anto
Indonesian Journal of Biotechnology Vol 18, No 1 (2013)
Publisher : Universitas Gadjah Mada

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Abstract

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
Mineral Phosphate Solubilizing Bacteria Isolated from Various Plant Rhizosphere under Different Aluminum Content Damarjaya, Dolly Iriani; Widada, Jaka; Senoo, Keishi; Nishiyama, Masaya; Otsuka, Shigeto
Indonesian Journal of Biotechnology Vol 10, No 2 (2005)
Publisher : Universitas Gadjah Mada

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Abstract

The objectives of this study was to isolate and characterize the mineral phosphate solubilizing bacteriafrom rhizosphere and evaluate their potential as plant growth promoting bacteria in Al-toxic soils. The halozone formation method was used to isolate PSB using the media containing insoluble phosphates (Ca-P or Al-P)as a source of phosphate. Eight of acid and Al-tolerant PSB isolates that were able to solubilize Ca-P wereobtained from rhizosphere of clover, wheat, corn, and sunflower grown in Al-toxic soil. Identification of theisolates based on the 16S rRNA gene sequence analysis demonstrated that the isolates were strains of Burkholderia(5 strains), Pseudomonas (1 strain), Ralstonia (1 strain), and unidentified bacterium (1 strains). All PSB isolatesshowed the capability to dissolve Ca-P, and only 1 strain (Ralstonia strain) was able to dissolve Al-P in agar platemedium. The P-solubilization by these isolates was correlated with pH of medium. Inoculation of the bacterialstrains on clover on Al-toxic medium showed that all isolates increased the plant dry weight compared withuninoculated treatment. Our results showed that those PSB isolates have potential to be developed as a biofertilizerto increase the efficiency of P-inorganic fertilizer used in Al-toxic soils.
Ethanol Production by Fermentation of Various Sweet-Stalk Sorghum Juices Using Various Yeast Strains Widianto, Donny; Arofatullah, Akbar; Yuwono, Triwibowo; Prijambada, Irfan Dwidya
Indonesian Journal of Biotechnology Vol 15, No 2 (2010)
Publisher : Universitas Gadjah Mada

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Abstract

The ethanol production by fermentation of sweet-stalk sorghum juice is affected by the juice composition and the capability of the yeast strain to ferment it. Eight yeast strains were tested on their growth and ethanol fermentation abilities in sweet-stalk sorghum juices extracted from three cultivars of sweet sorghum. The best specific growth rate of the yeast strains grown aerobically in the yeast extract peptone dextrose (YEPD) broth and the sweet-stalk sorghum juices of KCS105, FS501, and FS902 cultivars, were achieved by OUT7903, OUT7913, OUT7903, and OUT7027 yeast strains, respectively. However, the best specific CO2 evolution rate of the yeast strain during fermentation of the juices was achieved by OUT7027 yeast strains. The highest ethanol concentration, ethanol yield, and sugar conversion efficiency (SCE) were obtained by strain OUT7921 when it was employed to ferment sweet-stem sorghum juice of FS902 cultivar. It was also observed that the juice extracted from sweet-stalk sorghum of FS902 cultivar is the most suitable medium for all yeast strains to achieve their best fermentation abilities. Thus, it is likely that the growth and ethanol production ability of a yeast strain in sweet-stalk sorghum juice depend on the physiological responses of the yeasts to nutrientcomposition of the sorghum juice and the sorghum cultivar from which the juice was extracted.Key words : Sweet-stalk sorghum juice, ethanol, fermentation, yeast
High Frequency Spontaneous Deletions within the IcaADBC Operon of Clinical Staphylococcus epidermidis Isolates. Nuryastuti, Titik; van der Mei, Henny C.; Busscher, Henk J.; Kuijer, Roel; Aman, Abu Tholib; P. Krom, Bastiaan
Indonesian Journal of Biotechnology Vol 17, No 2 (2012)
Publisher : Universitas Gadjah Mada

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Abstract

Staphylococcus epidermidis has been shown to undergo a phase variation correlating with expression of the icaADBC operon which contributes to biofilm formation. Biofilm formation of Enterococcus faecalis is related to heterogeneity in electrophoretic mobility. Here the relationship between phase variants of clinical isolates of S. epidermidis, icaADBC presence and electrophoretic mobility distributions is investigated. Of 105 S. epidermidis clinical isolates, 5 showed phase variation on Congo Red agar plate. Biofilm forming capability of the blackcolonies and inability of the red colonies were confirmed using a microtiter plate assay and confocal laser scanning microscopy. Upon analysis of electrophoretic mobility distributions, the black colonies displayed heterogeneity at pH 2 which was absent in the red colonies of the same strain. Surprisingly, it was shown that in all red colonies had lost the icaADBC genes. Determination of gene copy number using Real Time PCR targeting icaA showed reduction of gene copy within a culture with phase variation. In conclusion, using three fundamentally different approaches phase variation of the five clinical isolates was observed. Variants appeared through loss of icaA and icaC gens. To our knowledge this is the first report indicating S. epidermidis strains irreversible switching from biofilm + to biofilm – phenotype by deletion of ica genes. Key words: deletion, ica genes, Staphylococcus epidermidis, IcaADBC operon
Cloning Gene Encoding Micronema 3 (Mic3) Protein of Tachyzoite Toxoplasma Gondii Local Isolate Artama1, Wayan T.; Dewi, Ni Nyoman Ayu; Subekti, Didik Tulus
Indonesian Journal of Biotechnology Vol 10, No 1 (2005)
Publisher : Universitas Gadjah Mada

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Abstract

Microneme 3 (MIC3) protein tachyzoites Toxoplasma gondii is one of protein which plays an important roleduring cell host invasion. Gene encoding MIC3 protein has been studied and it was suggested a potent vaccinecandidate against Toxoplasma gondii infection. The aim of this research is to clone and sequence the gene encodingMIC3 protein of tachyzoites Toxoplasma gondii local isolate by amplification using polymerase chain reaction withspecific primers. The amplified DNA fragment was cloned into pGEM-T and transformed into E. coli XL-1 Blue byheat shock method. Recombinant plasmids were isolated using alkali lysis method and analyzed by digestionusing restriction endonuclease enzymes PstI, HindIII, NcoI and EcoRV. The recombinant plasmids then sequencedto find out the nucleotide sequence of insert gene by ABIPRISM 377 DNA Sequencer. The DNA sequence thenwere analyzed by computer software for alignment. The result showed that transformation in E. coli XL-1 Blue bypGEM-T produced one clone that was encoding MIC3 protein. Analysis of 489 bp from 5’ and 447 from 3’ of genesequence showed 97-98% homology with gene encoding for MIC3 protein of RH isolate.Keywords: MIC3 protein, Toxoplasma gondii, tachyzoite, recombinant DNA
The synthesis of polymeric dual-functional antimicrobial surface based on poly(2-methyl-2-oxazoline) Pidhatika, Bidhari; Rakhmatullina, Ekaterina
Indonesian Journal of Biotechnology Vol 19, No 1 (2014)
Publisher : Universitas Gadjah Mada

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Abstract

There is a high interest in the development of antimicrobial coatings to fi ght bacterial infections.We present the development of dual-functional antimicrobial surface, in which a biopassive platform wasfunctionalized with bioactive compounds on the surface, using a graft copolymer system poly(L-lysine)-graftpoly(2-methyl-2-oxazoline)-quarternery ammonium compound (PLL-g-PMOXA-QAC). Alkyne functionalitywas introduced to the PMOXA chain at α-terminus by initiating the living cationic polymerization of 2-methyl-2-oxazoline with a propargylic-initiator. The reaction was terminated with carboxy derivative-terminator thatallows grafting of the polymeric chain from the β-terminus to poly(L-lysine) (PLL) backbone, resulting in graftcopolymer alkynyl PLL-g-PMOXA. The conjugation between alkynyl PLL-g-PMOXA and QAC was thenperformed using click reaction. The chemical structures of the polymers were characterized by MALDI-TOFspectrometry and NMR spectroscopy. The results demonstrate that we have successfully synthesized PLL-g-PMOXA-QAC copolymer with grafting density (number of lysine/number of PMOXA) of 0.33. The resultingPLL-g-PMOXA-QAC copolymer was then immobilized onto carboxylated tissue cultured polystyrene (TCPS)surface and exposed to bacteria solution to test its dual-functional properties. Preliminary live-and-deadbacteria study indicates dual-functionality of the PLL-g-PMOXA-QAC-coated surface.
T47D cells arrested at G2M and Hyperploidy Formation Induced by a Curcumin’s Analogue PGV-1 Da’i, Muhammad; Jenie, Umar Anggara; AM, Supardjan; Kawaichi, Masashi; Meiyanto, Edy
Indonesian Journal of Biotechnology Vol 12, No 2 (2007)
Publisher : Universitas Gadjah Mada

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Abstract

its chemical structure than curcumin. As a curcumin analogue, PGV-1 was considered to have anticanceractivities. This research was conducted to study the effect of PGV-1 on the cycle progression of T47D cells. Cytotoxiceffects of PGV-1 on T47D cells were determined using MTT assay, and the the effect on cell cycle progressionwas carried out using flowcytometry. Western blot analysis was used to analyze protein expression correspondingto cell cycle progression. The result showed that at the concentration of 2.5 μM PGV-1 inhibited cell cycleprogression through G2/M arrest and induced of cells hyperploidy formation. The hyperploidy formation inducedby PGV-1 was related to the increase of cdc-2 expression. PGV-1 2.5 μM elevated the level of p21 CIP/KIPthrough p53- independent manner. Apoptosis was also induced by PGV-1 at early phase of treatment indicated byPARP cleavage due to activation of caspase-3/7 after 12 h treatment. The results above suggest that PGV-1 inhibitsthe growth of T47D cells targeted on microtubules.Keywords: PGV-1, G2/M arrest, apoptosis, p21
Construction and Immunogenicity Testing of Salmonella, STM1 Vaccine Vector Expressing HIV-1 Antigen Bachtiar, Endang Winiati; Smooker, Peter; Coloe, Peter J
Indonesian Journal of Biotechnology Vol 14, No 2 (2009)
Publisher : Universitas Gadjah Mada

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Abstract

Objective of this study: to determine the ability of Salmonella enterica serovar Typhimurium STM1 as a delivery vehicle for the HIV p24 gene and HIV env gene. The STM1 delivery HIV-p24 vaccination was carried out in the form of a recombinant or a DNA vaccine whereas only a DNA vaccine was used for HIV env. Naked DNA vaccination was also tested and immune responses were evaluated following immunisation in mouse model. Results: vaccination cellular immune responses induced by recombinant p24 STM1 (STM1/pHly-p24) were greater than those elicited by the p24 DNA vaccine in STM1 (STM1/VR-p24), (but statistically not significance) than those induced by oral vaccination. However, IgA responses induced by oral vaccination with either a recombinant or DNA vaccine of p24 in STM1 are higher than those induced by IP vaccination. Conclusions: This result confirms</div><div>other studies that Salmonella was able to deliver HIV antigens to the immune system and induced specific immune responses to the HIV antigen.

Page 7 of 52 | Total Record : 518

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