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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 8 Documents

Search results for , issue "Vol 22, No 2 (2017)" : 8 Documents clear

Allelic diversity of butyrophilin (BTN1A1) gene in Indian bovines Manoj Kumar; Poonam Ratwan; Ramendra Das; Alka Chopra; Vikas Vohra
Indonesian Journal of Biotechnology Vol 22, No 2 (2017)
Publisher : Universitas Gadjah Mada

Indian milch bovines comprises of 58.56% of total livestock population (512.05 million) in the country and primarily includes native and crossbred cattle (37.28%) and water buffaloes (21.28%). Milk and milk products are essential food items of Indian diet especially in children, old and senile. Milk fat is an important constituent of milk and has an economic value and its percentage in milk varies betweem species and breeds within species. Butyrophilin (BTN1A1) a membrane protein regulates secretion of lipids and size of a fat globule in milk. Present study was conducted in 538 bovines of 11 breeds/populations adapted to different parts of India, with an aim to screen and determine the major allele of BTN1A1 gene using PCR-RFLP based test. Results indicate that exon 8 of BTN1A1 gene is polymorphic in Tharparkar, Sahiwal, Jhari and Belahi populations of native cattle and Holstein Friesian and Jersey crossbreds where as the same exon was monomorphic in Murrah, Chilika, Gojri, Chhattisgarhi and Bargur populations of water buffalo. We conclude that variations in BTN1A1 gene can serve as an excellent genetic marker while selecting cows for higher milk fat and can be applied while formulating their breeding plans.

Generation of recombinant scFv antibody against Ochratoxin A (OTA) Ranya Pranomphon; Witsanu Srila; Montarop Yamabhai
Indonesian Journal of Biotechnology Vol 22, No 2 (2017)
Publisher : Universitas Gadjah Mada

Ochratoxin A (OTA) is a mycotoxin commonly found in agricultural products and can accumulate in the blood and tissues after that consuming contaminated food. Recombinant single-chain antibody fragments (scFv) against OTA were selected from phage display libraries. After of one round of biopanning against BSA-conjugated OTA (OTA-BSA), 52 and 6 phage clones displaying scFv antibodies were isolated from human (Yamo I.3) and rabbit (Bozmix I.2) libraries. Two phage clones (one from each libraries, i.e., yOTA1e3 and bOTA2a9) showed binding to free toxin by competitive ELISA. The soluble scFv antibodies were produced by superinfecting phage clones into E. coli suppressor strain HB2151. The scFv genes from these two phage clones were sub-cloned into pKP300ΔIII vectors to generate scFv-AP fusions. The binding affinity (IC50) of antibody derived from human library was higher than those from rabbit library. The binding property of recombinant antibody in the form of scFv-AP was better than those of soluble scFv form. Cross-reactivity analysis indicated that the two recombinant antibodies did not cross-react with other soluble toxins, namely AFB1, DON, ZEN and FB. The ability to use the recombinant scFv-AP to detect contaminated toxins in agricultural product (corn) was demonstrated.

NMR metabolite comparison of local pigmented rice in Yogyakarta Dio N. Wijaya; Febri Adi Susanto; Yekti Asih Purwestri; Dyah Ismoyowati; Tri Rini Nuringtyas
Indonesian Journal of Biotechnology Vol 22, No 2 (2017)
Publisher : Universitas Gadjah Mada

Pigmented rice may have a black or red color due to higher anthocyanin content in its grain. A natural antioxidant, many studies on anthocyanin have reported its positive effects on human health. This fact has spurred the development of pigmented rice as a functional food. This study aimed to compare the metabolite profiles of black and red rice. Three black rice cultivars, namely Melik, Pari Ireng, and Cempo Ireng Sleman, and two red rice cultivars, Inpari 24 and RC 204, were used. After husk removal, grain samples were ground in liquid nitrogen and dried with a freeze dryer. The dried samples were extracted using 50% MeOD4 (in a D2O phosphate buffer pH 6 containing 0.01% TSP as an internal standard). Metabolomic analysis was performed using 500 MHz NMR followed by multivariate data analysis. An orthogonal partial least squares-discriminant analysis (OPLS-DA) model ađer PCA was constructed to discriminate between the five different cultivars. The resulting OPLS-DA score plot revealed a clear separation between black rice and red rice. The metabolites that could influence the separation of red rice and black rice were valine, threonine, alanine, glutamate, galactinol, β-glucose, α-glucose, raffinose, and fumaric acid.

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.

Gelatin extraction from the indigenous Pangasius catfish bone using pineapple liquid waste Yoni Atma; Hisworo Ramdhani
Indonesian Journal of Biotechnology Vol 22, No 2 (2017)
Publisher : Universitas Gadjah Mada

Gelatin extraction from fish bone has traditionally involved hydrogen chloride and/or sodium hydroxide during pre-treatment. However, these chemicals have begun to be abandoned because of their associated safety and environmental issues. Several studies have looked at the use of citric acid as a safer alternative in fish bone gelatin extraction. The aim of this research was to extract gelatin from the bone of Pangasius catfish with pineapple liquid waste. The extraction was performed in two steps: pre-treatment followed by main extraction at various times (24–56 h) and temperatures (45–75°C). Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) was used as a confirmation test and showed a band for gelatin at ~120 kDa. Gelatin yields were calculated as the ratio of weight of dried gelatin to the total weight of fish ossein. The results indicated that pineapple liquid waste can be used for fish bone gelatin extraction. The recommended conditions for extraction of fish bone gelatin using pineapple liquid waste are 56 h of pre-treatment and 5 h of main extraction at a temperature of 75°C. The gelatin yield was 6.12% and the protein concentration 4.00 g/100 g.

Agrobacterium tumefaciens-mediated transformation of Jatropha curcas L. with a polyhydroxyalkanoate gene (phaC) Chesara Novatiano; Adi Pancoro; Erly Marwani
Indonesian Journal of Biotechnology Vol 22, No 2 (2017)
Publisher : Universitas Gadjah Mada

Polyhydroxybutyrate is a component of bioplastics that is synthesized under the control of enzymes encoded by pha multigenes. The genes are naturally present in Ralstonia eutropha. However, the production of bioplastics in bacteria is inefficient because the bacterial biomass is relatively small compared with plants or fungi. As such, engineering techniques have been developed that enable pha genes to be inserted into plant biomass, and then be expressed in the biomass of the plant to produce polyhydroxybutyrate. The objectives of this study were to transform the tissue of Jatropha curcas using the phaC gene (a pha gene), to regenerate the transformed plant, and to confirm the presence of the inserted genes with PCR. The genetic transformation of J. curcas was mediated by Agrobacterium tumefaciens strain GV3101 containing pARTC by dipping the cotyledon tissue of J. curcas in a suspension of the bacterium for 30 min, followed by cocultivation for 3 d on Murashige and Skoog (MS) medium. The tissue was then placed on a selection medium, i.e. MS medium containing 13.3 µM BAP and 0.05 µM IBA with the addition of 20 mg/L kanamycin. The results showed that 12.35% of the tissue survived and regenerated into a shoot after 1–2 months. Molecular analysis of the transformed tissue was performed using phaC and nptII primers, in order to detect the presence of the phaC and nptII genes. Specific bands were detected at 659 bp and 700 bp, corresponding to the nptII primer and phaC primer, respectively.

Cloning and expression of haloacid dehalogenase gene from Bacillus cereus IndB1 Enny Ratnaningsih; Idris Idris
Indonesian Journal of Biotechnology Vol 22, No 2 (2017)
Publisher : Universitas Gadjah Mada

Organohalogen compounds, widely used as pesticides in agriculture and solvents in the industrial sector, cause environmental pollution and health problems due to their toxicity and persistence. Numerous studies have been conducted on the biodegradation of organohalogen compounds, with many focusing on the use of dehalogenase from bacteria. Haloacid dehalogenase is a group of enzymes that cleaves the carbon-halogen bond in halogenated aliphatic acids. In a previous study, the bcfd1 gene encoded haloacid dehalogenase from Bacillus cereus IndB1 was successfully isolated and characterized. This research aimed to create an expression system of the bcfd1 gene by subcloning this gene into pET expression vector and to overexpress the gene in Escherichia coli BL21 (DE3). In addition, the recombinant protein was characterized to gain a better understanding of the catalytic action of this enzyme. A high expression of bcfd1 was obtained by inducing the culture at OD550 0.8–1.0 using 0.01 mM IPTG as determined by SDS-PAGE. Zymogram analysis proved that the recombinant protein possessed dehalogenase activity. Bcfd1 activity toward monochloroacetic acid (MCA) showed specific activity of 37 U/mg at 30°C, pH 9. The predicted tertiary structure of Bcfd1 was estimated has conserved α/ß hydrolase folding motif for haloacid dehalogenase superfamily.

The expression of growth factor signaling genes in co-culture IVM Erif Maha Nugraha Setiawan; Hyun Ju Oh; Min Jung Kim; Geon A Kim; Seok Hee Lee; Yoo Bin Choi; Ki Hae Ra; Byeong Chun Lee
Indonesian Journal of Biotechnology Vol 22, No 2 (2017)
Publisher : Universitas Gadjah Mada

The objective of this study was to determine the expression of growth factor signaling genes in human adiposederived stem cells (ASCs), porcine oocytes, and cumulus during in vitro maturation (IVM). The human ASCs (from 2 young and 2 old donors) were used for the co-culture IVM system. The maturation rate was examined based on polar body extrusion. The expression of the growth factor signaling genes from ASCs, oocytes, and cumulus were measured using qPCR. All data were analyzed using ANOVA followed by Tukey’s test. The expression of the h-IGF1 signaling genes from human ASCs cells showed similar values in all groups and the h-FGF2 expressions were higher in the young donors than the old ones. The p-FGF2, p-FGFR2, and p-TGFβ1 expressions in the oocytes as well as p-IGFR in the cumulus that were co-cultured from the young donors showed higher values than the old and control groups. The apoptotic ratio (p-BAX/p-BCL2) from the oocytes and cumulus in both co-culture groups also showed lower levels than the control (P<0.05). Oocyte maturation rates were significantly increased in all co-cultured groups (Y1 (85.9 ± 2.2%), Y2 (91.2 ± 1.1%), O1 (86.3 ± 1.5%), and O2 (86.5 ± 2.3%)) compared with the control (76.7 ± 1.1%; P<0.05). Although the expression of growth factor signaling genes was varied, young donors’ ASCs might support in vitro maturation beħer than those from old donors.

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