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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 523 Documents

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Production and Extraction Of Antibacterial Bacteriocin from Pediococcus sp. NWD 015 N. Nofisulastri; Zaenal Bachruddin; Eni Harmayani
Indonesian Journal of Biotechnology Vol 11, No 2 (2006)
Publisher : Universitas Gadjah Mada

objectives were to study the growth pattern of Pediococcus sp. NWD 015 and bacteriocin activity, extractionand characterization of bacteriocin, and to determine the effect of storage time and temperature on bacteriocinactivity. Results showed that the bacteriocin activity increased during growth and reached the highest activity duringstationary phase. The maximum bacteriocin production reached after incubation of the cell for 12 h at 37oC in TGEbroth and decreased after 96 h incubation. Extraction with adsorbtion-desorbtion method could increased a specificactivity of bacteriocin. Bacteriocin from Pediococcus sp. NWD 015 is inactivated by Proteinase-K; however it is stillactive by heat treatment at 121oC for 15 min and over pH 2 – 11. Bacteriocin of Pediococcus sp. NWD 015 was effectiveagaints Enterococcus faecalis, Staphylococcus aureus, Eschericia coli, Listeria monocytogenes but not against Salmonellathypimurium. The molecular weight of bacteriocin is 4.95 kDa.Keywords : Bacteriocins, Pediococcus sp NWD 015.

Characterization of Aspergillus Niger 65i6 lipase from solid-state fermentation using Jatropha seed cake medium Chusnul Hidayat; Sari Darmasiwi; Maulina Nurikasari; Muhammad Nur Cahyanto
Indonesian Journal of Biotechnology Vol 20, No 2 (2015)
Publisher : Universitas Gadjah Mada

Jatropha curcas seed cake contains a high amount of protein, and consequently has very high potentialas a medium for lipase production. The objective of this research was to characterize lipase from Aspergillusniger 6516, which was produced by solid-state fermentation on Jatropha curcas seed cake as the medium. The effects of pH and temperature on enzyme activity were evaluated, along with substrate specifcity and enzyme stability. Fermentation was performed at a water concentration of 63% and temperature of 30 °C for 7 days. The results showed that the optimum pH and temperature for Aspergillus niger 6516 lipase activities were 8.0 and 40 °C, respectively. The lipase had the substrate specifcity to hydrolyze long-chain fatty acids and was stable in polar organic solvents. The lipase had a molecular weight, Km and vmax about 19 kDa, 0.27 µmol/ml, and 52.63 µmol/ml/min, respectively. The results also suggested that the produced lipase from Aspergillus niger 6516 was an alkaline lipase. Based on these results, we conclude that Jatropha seed cake is a suitable medium for lipase production.

Antigen Presentation Ability of Salmonella Carrying DNA Vaccine Model and MCP-3 gene Endang Winiati Bachtiar; Peter Smooker; Peter J Coloe
Indonesian Journal of Biotechnology Vol 16, No 1 (2011)
Publisher : Universitas Gadjah Mada

The objective of this study is to determine the antigen presentation ability of a DNA vaccine model that is co-delivered with that of recombinant Salmonella enterica serovar Typhimurium (STM1) expressing chemokine macrophage chemotactic protein-3 (MCP-3). The DNA vaccine, pVROVA, was constructed by amplification of the ovalbumin coding region from sOVA-C1. Dendritic cells (DCs) were obtained from IL-4 and GMCSF stimulated mouse bone marrow stem cell. Cultured DCs were incubated with STM1 carrying a model ovalbumin gene (pVROVA). Furthermore, MHC class I antigen presentation of a dominant OVA peptide was assayed in vitro. The experiments were designed to determine the effect of co-delivering MCP-3 with that of ovalbumin in STM1. Our results show that a plasmid pROVA-carrying ovalbumin gene was succesfully constructed and sequence analysis of the ovalbumin-coding revealed an identity match of 100% with that of the chicken ovalbumin DNA sequences from the GenBank database. We also found that the presence of the MCP-3 encoding plasmid in STM1 or E. coli DH1 could increase the recovery of both STM1 and E. coli DH1 over those that carry the empty plasmids. Antigen presentation assay also indicates that MCP-3 can positively influence the presentation of ovalbumin. Conclusion: the infection of DCs by STM1-carrying DNA vaccine and MCP-3 results in an increase of processing and presentation of ovalbumin in vitro.Keywords : DNA vaccine, MCP-3, APC, Salmonella, Dendritic cells

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

Genetic Analysis of Glycoprotein Gene of Indonesian Rabies Virus Heru Susetya; Ito Naoto; Makoto Sugiyama; Nobuyuki Minamoto
Indonesian Journal of Biotechnology Vol 10, No 1 (2005)
Publisher : Universitas Gadjah Mada

The amino acid sequences of the Glycoprotein gene (G gene) of field rabies virus SN01-23 from Indonesia was determined. This isolate showed homology of 93% in the ectodomain of the Glycoprotein gene to that of the RC-HL strain, which is used for production of animal vaccine in Japan. The high identity in the ectodomain between this field isolate and strain RC-HL suggest that the rabies animal vaccine used in Japan will be effective for rabies street viruses in Indonesia. Result of phylogenetic analysis using the nucleotide sequences of the G genes of rabies street viruses showed that SN01-23 from Indonesia is more closely related to a rabies virus from China than to viruses from Thailand and Malaysia. This genetic data and historical background suggest that rabies viruses in China had been transferred to Indonesia through dogs brought by humans migrating from China to Indonesia.

Synergistic effects of para-hydroxy meta-methoxy chalcone (pHmMC)- doxorubicin treatments on T47D breast cancer cells Retno Arianingrum; Retno Sunarminingsih; Edy Meiyanto; Sofia Mubarika
Indonesian Journal of Biotechnology Vol 20, No 2 (2015)
Publisher : Universitas Gadjah Mada

Resistance to some cancer chemotherapeutic drugs has been identifed. One strategy to overcome that problem is by combining two or more of the drugs to get co-chemotherapeutic effects. A derivate chalcone, 3 - (4’-hydroxy-3’-methoxyphenyl)-1-phenyl-2-propene-1-on or para hydroxy meta methoxy chalcone (pHmMC), has been reported to have cytotoxic activity on some cancer cells through some pathways. The aim of this study was to investigate the effects of combinations of pHmMC and Doxorubicin (Dox) on the cytotoxicity, anti-proliferation, apoptosis, and the cell cycle of T47D (breast cancer cell-lines) in vitro. The cytotoxic and antiproliferative activity were determined by MTT (3-[4,5-dimethylthiazol-2-yl)-2,5 diphenyl tetrazolium bromide] assay. The combination index (CI) was used to determine the synergistic, additive or antagonistic effects of the combinations. Flowcytometry method was performed to determine the combination effects on the apoptosis and cell cycle. The results indicated that the combinations had a higher inhibitory effect on the cell growth compared to those of single treatments of pHmMC and Dox. All the doses used in the combinations were lower of the single doses at their IC50s. The results showed all the combinations gave synergistic (CI: 0.3 – 0.7) up to strong synergistic (CI: 0.1 – 0.3) effects. The synergistic effects of the combinations were due to increased apoptosis and induced cell cycle arrest in S and G2/M phases on the cancer cell lines.

Comparative Analysis of Rice Transformation Using Agrobacterium tumefaciens and Rhyzobium leguminosarum Syamsidah Rahmawati; Osmat Azzam Jefferson; Didy Sopandie; S. Suharsono; Inez Hortense Slamet-Loedin
Indonesian Journal of Biotechnology Vol 15, No 1 (2010)
Publisher : Universitas Gadjah Mada

This study was aimed to study the effectiveness of Rhizobium transformation system compared to the most widely used Agrobacterium mediated transformation system on three rice cultivars, Ciherang (Indica), Nipponbare (Japonica), and Rojolele (Javanica). Six day old calli induced from immature embryos were inoculated with Rhizobium leguminosarum bv trifolii ANU845 and Agrobacterium tumefaciens LBA288 that harbored with vector pCAMBIA 5106. This plasmid contained a minimum set of transfer machinery genes and had a gusplus and an hptII gene driven by 35S CaMV promoter in the T-DNA. The results showed that the transformation frequencies (number of PCR positive plants per number of calli inoculated) ranging from 0 to 12.05 % depend on the genotype and transfer agent used. The highest transformation frequency (12.05%) was obtained in Ciherang transformed with R. leguminosarum. Most of the transgenic rice obtainedby Rhizobium transformation were normal in morphology and fertile similar to those obtained by Agrobacterium transformation. Integration, expression and inheritance of transgenes were demonstrated by molecular and genetic analysis in T0 and T1 generations.Key words : Rhizobium leguminosarum, immature embryos, Agrobacterium tumefaciens

Evaluation of N-benzoylthiourea derivatives as possible analgesic agents by predicting their physicochemical and pharmacokinetic properties, toxicity, and analgesic activity Suko Hardjono; Siswandono Siswandono; Rina Andayani
Indonesian Journal of Biotechnology Vol 22, No 2 (2017)
Publisher : Universitas Gadjah Mada

This study aimed to predict the physicochemical properties, pharmacokinetic properties (ADME), toxicity, and analgesic activity of 30 compounds of N-benzoylthiourea derivatives that are potential analgesic drugs. One of the mechanisms of action of N-benzoylthiourea derivatives is the inhibition of the cyclooxygenase-2 (COX-2) isoenzyme. An in silico test was performed by docking a compound that would predict its activity with the target COX-2 isoenzyme, PDB ID: 1PXX, using the MVD (Molegro Virtual Docker) program. The result of the docking was a form of energy bond indicated by the value of the rerank score (RS), where compounds that had lower RS values were predicted to have a higher activity. The pkCSM and Protox online tools were used to predict various physicochemical properties. Based on the RS values, the N-benzoylthiourea derivatives can be predicted to have lower analgesic activity than diclofenac, the reference ligand. Three of the N-benzoylthiourea derivatives—N-(2,4-bis-trifluoromethyl)-benzoylthiourea, N-(3,5-bis-trifluoromethyl)benzoylthiourea, and N-(3-trifluoromethoxy)-benzoylthiourea—had RS values of -90.82, -94.73, and -92.76, respectively, suggesting that these compounds were predicted to have analgesic activity relatively similar to diclofenac (RS value = -95.16). Furthermore, the majority of the N-benzoylthiourea derivatives were predicted to have good pharmacokinetic properties (ADME), and cause relatively low toxicity.

Paternity Analysis of Tea (Camellia sinensis L. Kuntz) Hybrids Using Isozyme Marker Titin Setyorini; T. Taryono; S. Suyadi; Sapto Indrioko
Indonesian Journal of Biotechnology Vol 17, No 2 (2012)
Publisher : Universitas Gadjah Mada

Tea plant has been categorized as self-incompatible crop. This is the reason behind the high genetic diversity. Natural pollination is possible to occur and the male parent is usually unknown, therefore, there is a need of method to identify male parent of hybrids through paternity analysis. Isozyme markers have been successfully used for paternity analysis due to their co-dominant polymorphism. This research aimed to predict male parents of hybrids by figuring out the mating system through isozyme banding patterns. In this experiment, seven enzyme systems were evaluated, of which only two of the enzyme systems i.e. esterase and shikimate dehydrogenase showing clear band pattern of Est-1, Est-2, and Shd-1 loci. The mating system of tea could be categorized as a mixed mating model, with high estimated out-crossing rate of 98.6 %. The pollen contributors were not always originated from the vicinity of the female parents.Key words: isozyme markers, paternity analysis, tea

The synthesis of polymeric dual-functional antimicrobial surface based on poly(2-methyl-2-oxazoline) Bidhari Pidhatika; Ekaterina Rakhmatullina
Indonesian Journal of Biotechnology Vol 19, No 1 (2014)
Publisher : Universitas Gadjah Mada

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.

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