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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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Detection and Cloning of a Gene Involved in Zwitermicin A Synthesis from Plant Growth Promoting Rhizobacteria of Bacillus sp CR64 Aris Tri Wahyudi; Rika Indri Astuti; Nisa Rachmania Mubarik; Sarah Asih Faulina
Indonesian Journal of Biotechnology Vol 15, No 1 (2010)
Publisher : Universitas Gadjah Mada

Utilization of soil bacteria as biocontrol agent is becoming popular due to its valuable and effective mechanisms to suppress plant pathogenic microbes. We have previously isolated Bacillus sp, designated as Bacillus sp CR64, which exhibited effective plant growth promoting and antifungal activities. In this study, CR64 was examined in inhibiting the growth of Rhizoctonia solani, the causing agent of root rot disease. Partial sequence analysis of 16S rRNA gene revealed that this isolate similar with Bacillus cereus (94%). Furthermore, a gene designated zmaR was detected by means of specific amplification of DNA fragment approximately 950 bp. This fragment was then cloned onto pCRII-TOPO (3.9 kb) and sequenced using DNA sequencer ABI PRISM 310. Sequence analysis revealed that it had highest homology with the ZmaR protein (89% identity; 90% similarity) of B. thuringiensis serovar kurstaki (AAF82729.2). Alignment analysis with other ZmaR sequences from other antibiotic-producing Bacilli exhibited an almost fully conserved region within ZmaR sequences.Key words : PGPR, Bacillus sp CR64, Zwitermicin A, Cloning, Antifungal.

Cloning of acetyl-CoA acetyltransferase gene from Halomonas elongata BK-AG18 and in silico analysis of its gene product Ni Putu Yuliastri; Enny Ratnaningsih; Rukman Hertadi
Indonesian Journal of Biotechnology Vol 22, No 1 (2017)
Publisher : Universitas Gadjah Mada

Polyhydroxybutyrate (PHB) is a biodegradable polymer that can be used as a substitute for petrochemical plastics. Bacteria accumulate PHB in their cells as carbon and energy reserves because of unbalanced growth conditions. This study aimed to amplify phbA from the chromosomal DNA of Halomonas elongata BK-AG18, a PHB-producing bacterium that was previously isolated from the Bledug Kuwu mud crater of Central Java, Indonesia. The obtained phbA amplicon was 1176 bp. This fragment was cloned into a pGEM-T Easy cloning vector and used to transform Eschericia coli TOP10. The recombinant colonies were selected using blue-white screening, confirmed by size screening, reconfirmed by re-PCR, and sequenced. When putative phbA sequences were aligned with H. elongata DSM2581 chromosome using BLASTN, this sequence showed 99% identity. The deduced amino acid sequences of this clone showed 100% identity to PhbA of H. elongata DSM2581, suggesting that the obtained cloned fragment is a phbA gene. The 3D structure predicted by I-TASSER showed that PhbA of H. elongata BK-AG18 had a high similarity to the acetyl CoA acetyltransferase structure of Ralstonia eutropha H16. PhbA of H. elongata BK-AG18 possesses three catalytic residues, namely Cys88, His348, and Cys378.

High Frequency Spontaneous Deletions within the IcaADBC Operon of Clinical Staphylococcus epidermidis Isolates. Titik Nuryastuti; Henny C. van der Mei; Henk J. Busscher; Roel Kuijer; Abu Tholib Aman; Bastian P. Krom
Indonesian Journal of Biotechnology Vol 17, No 2 (2012)
Publisher : Universitas Gadjah Mada

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

Impact of Curcuma mangga Val. Rhizome Essential Oil to p53, Bcl-2, H-Ras and Caspase-9 expression of Myeloma Cell Line Endang Astuti; Retno Sunarminingsih; Umar Anggara Jenie; Sofia Mubarika; S. Sismindari
Indonesian Journal of Biotechnology Vol 19, No 1 (2014)
Publisher : Universitas Gadjah Mada

Cancer is a disease, a public health problem, which is found in the world as well as in Indonesia. Ingeneral, some of cancer theraphies are ineffective, characterized by the resistance performance of cancer cell line,the exposed normal cell and by the side effects. Nowadays, studies to fi nd the specifi c and safely anti-cancerdrugs were increased by the time. Several studies revealed that Curcuma mangga Val. Rhizome contains somesecondary metabolites, essential or non-essential oil, which has cytotoxic activities to the cancer cells. Basedon these anti-cancer potentials, this study has several aims to recognize anti-cancer selectivity and molecularmechanism by inducting apoptosis and inhibiting myeloma cell proliferation. To C. mangga Val. essential oil,immunocyto chemical test was performed to determine the expression of p53, caspase-9, Bcl-2, H-Ras proteinwhile TUNEL test was performed to determine the number of apoptosis cells.The results of this study shown that anti-cancer molecular mechanism of C. mangga Val. essential oil tomyeloma cell line was performed by increasing apoptosis; by increasing the expression of pro-apoptosis p53,caspase-9 protein and reducing protein which is increasing proliferation Bcl-2 and H-Ras.

Ability of Curcuminoid from Curcuma domestica Val. in Reducing the Secretion of Reactive Oxygen Intermediates by Synovial Fluid Monocytes in Patients with Osteoarthritis Nyoman Kertia; Ahmad Husain Asdie; Wasilah Rochmah; M. Marsetyawan
Indonesian Journal of Biotechnology Vol 16, No 2 (2011)
Publisher : Universitas Gadjah Mada

Increasing the secretion of reactive oxygen intermediates (ROI) by monocytes in the synovial fluid is anindicator to determine the severity of joint inflammation. Previous studies have shown that curcumin inhibitthe osteoarthritis progression with its ability to inhibite the activity of the nitric oxide synthase (NOS) enzymefrom macrophages. In this prospective randomized open end blinded evaluations = PROBE study, 80 patientswith knee osteoarthritis were eligable. The subject were devided in to two group: group who received 3 x 30mg of curcuminoid from Curcuma domestica Val. extract (curcuminoid group) and group who received 3 x 25mg of diclofenac sodium (diclofenac group) as comparison. The treatment was for 4 weeks time. The secretionof ROI by sinovial fluid monocytes was calculated by scoring the amount of formazan formation after neutralred staining in nitrobleu tetrazolium reduction assay. The result of this study showed that the secretion of ROIby synovial fluid monocytes was significantly decreased in both groups (p <0.001) respectively. There wasno significant difference in decreasing of ROI secretion of synovial fluid monocytes between both treatmentgroups (p = 0.92).

Cloning and Sequence Analysis of Capsid Protein Gene of Iridovirus Indonesian Isolates M. Murwantoko; Christina Retna Handayani; Rarastoeti Pratiwi
Indonesian Journal of Biotechnology Vol 14, No 1 (2009)
Publisher : Universitas Gadjah Mada

Iridovirus was known as agents that caused serious systemic disease in freshwater and marine fishes. The mortality up to 100% of orange-spotted grouper (Epinephelus coioides) due to iridovirus infection has been reported in Indonesia. The gene encoding capsid protein of iridovirus is supposed to be conserved and has the potency for the development of control methods. The objectives of this study are to clone the gene encoding capsid protein iridovirus and to analyze their sequences. The spleen tissues of orange-spotted grouper were collected and extracted their DNA. The DNA fragment of capsid protein of iridovirus genes were amplified by PCR using designed primers with the extraction DNA as templates. The amplified DNA fragments were cloned in pBSKSII and sequenced. The genes encoding capsid protein of iridovirus from Jepara and Bali were successfully amplified and cloned. The Jepara clone (IJP03) contained complete open reading frame (ORF) of the gene composed by 1362 bp nucleotides which encoded 453 amino acids. Those Jepara and Bali (IGD01) clones shared 99.8% similarity in nucleotide level and 99.4% at amino acid level. Based on those sequences, Indonesian iridovirus was belonged to genus Megalocystivirus and shared 99,6-99,9% similarity on nucleotide level with DGIV, ISKNV, MCIV, and ALIV

Transient transformation of artemisinic aldehyde ∆ 11 (13) double bond reductase (dbr2) gene into Artemisia annua L. Elfahmi Elfahmi; Fany Mutia Cahyani; Andre Ditya Maulana Lubis; Tati Kristanti; Sony Suhandono
Indonesian Journal of Biotechnology Vol 21, No 2 (2016)
Publisher : Universitas Gadjah Mada

Global demand of antimalarial drug artemisinin has a gap with production capacity from existing sources since the low content of this compound from Artemia annua L. Genetic engineering-based strategy for A. annua plant on key enzymes in artemisinin biosynthetic pathway is needed. Artemisinic aldehyde ∆ 11 (13) double bond reductase (dbr2) is one of the key enzyme on artemisinin biosynthesis which was studied in this research. Agrobacterium tumefaciens-mediated transformation of A. annua using dbr2 was carried out. Synthetic dbr2 was ligated into pCAMBIA1303 and transformed into Escherichia coli DH5α. pCAMBIA1303-dbr2 plasmid was transformed to A. tumefaciens AGL1. Leaves of A. annua were infected by positive transformant of recombinant A. tumefaciens (OD600 ≈ 1) supplemented with acetosyringone 50 ppm, and Silwet S-408 0.02%. Samples were incubated in desiccators connected with vacuum pump, this method is called infiltration vacuum. Leaves were covered in dark for 45 min, and co-cultivated on MS co-cultivation media for 3 days. All leaves were washed in 300 ppm cefotaxime and divided into 2 parts; 3 leaves for GUS histochemical assay and 300 mg of leaves for HPLC analysis. Transient transformation was done in triplicate. In GUS histochemical assay, pCAMBIA1303 and pCAMBIA-dbr2 showed positive blue spot where coefficient of variance was less than 5%. PCR analysis for genomic DNA of transformed A. annua showed a positive result of inserted dbr2 recombinant indicated by migration profile and direct sequencing analysis. It could be concluded that pCAMBIA-dbr2 construct and transformation into A. annua have been successfully performed.

Low cost and comprehensive pork detection in processed food products with a different food matrix Fenny Aulia Sugiana; Henni Widyowati; Muhammad Ali Warisman; Suryani Suryani; Desriani Desriani
Indonesian Journal of Biotechnology Vol 23, No 1 (2018)
Publisher : Universitas Gadjah Mada

The adulteration of processed beef-based meat products with pork is a sensitive issue in Indonesia. In this study, we developed a detection method for the low cost identification of pork in processed meat products. We used the cost-efficient Taq DNA polymerase, DreamTaq Green PCR master mix (2x), and duplex PCR method to recognize pork simultaneously with 18S rRNA detection. A positive control containing a pork gene inserted into pGEM®-T easy was prepared, along with a negative control. The results of the duplex PCR were used to assess its specificity, detection limit, and its ability to recognize pork in processed meat products with a different food matrix. 18S rRNA detection was for confirming DNA integrity of DNA extracted from the processed food, while the positive control confirmed that the reagents were working well and the negative control confirmed a non-contamination problem. Following this, the duplex PCR was optimized and the optimum concentration primer for duplex PCR detection was found to be 3 µm for pork and 0.2 µm for 18S rRNA. As little as 3.125 ng of the DNA template could be used to detect whether a sample contained pork. Duplex PCR is a simple, fast, sensitive, specific, and low cost method of detecting pork in processed meat products.

Legume Nodulating Bacterium, Achromobacter xylosoxidans Found in Tropical Shrub Agroecosystem, Sumatera, Indonesia Sri Wedhastri; Dinar Mindrati Fardhani; Siti Kabirun; Jaka Widada; Donny Widianto; Rusdi Evizal; Irfan Dwidya Prijambada
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

Legume nodulating bacteria (LNB), known also as rhizobia, are soil bacteria, which are able to form rootnodules and fi x nitrogen in the leguminous plants. The LNB availability in the soil depends on the type ofagroecosystem, where plant grows. In this study, we isolated LNB from the shrub agroecosystem in Sumatera,Indonesia, and obtained four selected bacterial strains. Among them, the isolate UGM48a formed root nodulein Macroptilium atropurpureum and showed highest number of nitrogenase activity. UGM48a also contains nifHand nodA genes. An analysis of the PCR-amplifi ed 16S rDNA and BLASTn analysis showed that UGM48adisplayed 96% similarity with Achromobacter xylosoxidans. In addition, UGM48a were successfully nodulatedGlycine max (L.) merr var. wilis. This is the fi rst report detecting A. xylosoxidans as nodule-forming species forGlycine max possesing the positive copy of nodA gene. Keywords : Legume Nodulating Bacteria, shrub agroecosystem, Achromobacter xylosoxidans, nodA, Glycine max

Sequences Analysis of a Gene Encoding Extracellular Xylanase in Streptomyces costaricanus 45I-3 S. Sipriyadi; Aris Tri Wahyudi; Maggy Thenawidjaja Suhartono; Anja Meryandini
Indonesian Journal of Biotechnology Vol 20, No 1 (2015)
Publisher : Universitas Gadjah Mada

Streptomyces costaricanus 45I-3 is a bacterial strain belongs to actinomycetes group isolated from peat soil. Thebacterium is known to produce extracellular xylanase. The aims of this study were to analyze DNA sequence andsub-clone gene involved in the synthesis of extracellular xylanase. Complete DNA sequence predicted to encodexylanase genes was isolated from bacterial genome using Inverse Polymerase Chain Reaction (I-PCR). Total DNAsequence of 1664 bp in size obtained from I-PCR consisted of two open reading frames (ORF) in opposite direction.ORF1 was 1029 bp and ORF2 (partial sequence) was 309 bp. Analysis sequence using BlastX indicated that ORF1was homologous with xylanase bacterium enrichment culture clone Xyl8B8 (GenBank accession No. AFH35005.1),i.e. 95% in identity and 99% in similarity. In addition, ORF2 was homologous with glyoxalase bacterium enrichmentculture clone Xyl8B8 (GenBank accession No. AFH35007.1), i.e. 95% in identity and 98% in similarity. Analysis ofamino acid sequence revealed that ORF1 consisted of 2 domains, i.e. glyco-hydrolase 11 (GH11) and CarbohydrateBinding Type 2 (CBM2). Active site was found at 130th amino acid on GH11 domain. Visualization of 3-dimensionstructure showed that 1029 bp fragment is of 19 areas.

Page 22 of 52 | Total Record : 518

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