Indonesian Journal of Biotechnology最新文献

{"title":"Amylolytic ability of bacteria isolated from termite (Coptotermes sp.) gut","authors":"P. Mulyani, Radhiyah Mardhiyah Hamid, Rifqi Zahroh Janatunaim, Y. A. Purwestri","doi":"10.22146/IJBIOTECH.32445","DOIUrl":"https://doi.org/10.22146/IJBIOTECH.32445","url":null,"abstract":"BSR 2, BSR 3, BSR 8, and BSR 9, different bacteria isolated from the termite gut, have been shown to possess cellulolytic activities, but their amylolytic ability has heretofore been unknown. This study attempted to fill in this knowledge gap. The formation of a clear zone using the iodine test showed that the bacteria were able to produce and secrete amylase. Based on the results, the best cultivation times for strains BSR 2, BSR 3, BSR 8, and BSR 9 were 6, 3, 2, and 2 d, respectively, yielding amylase activities of 2.59 ± 0.13 U/mg, 2.00 ± 0.08 U/mg, 1.67 ± 0.10 U/mg, and 1.55 ± 0.12 U/mg, respectively. BSR 2 had the highest amylase activity compared with the other bacterial isolates. The optimum ph for bacterial amylase activity of BSR 2 was 7.0, and the optimum temperature was 40°C. The molecular characterization of isolates BSR 2, BSR 3, BSR 8, and BSR 9 was based on 16S rRNA gene sequences. Isolates BSR 8 and BSR 9 were thus identified as Brevibacillus parabrevis and Brevibacillus sp. With similarities amounting to 92.48% and 95.91%, while the BSR 3 isolate was identified as Pseudomonas alcaligenes with a similarity of 94.29%, and the BSR 2 isolate could not be identified yet.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":"223 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41270484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gelatin extraction from the indigenous Pangasius catfish bone using pineapple liquid waste","authors":"Y. Atma, Hisworo Ramdhani","doi":"10.22146/IJBIOTECH.32472","DOIUrl":"https://doi.org/10.22146/IJBIOTECH.32472","url":null,"abstract":"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.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":"22 1","pages":"86-91"},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48789174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Allelic diversity of butyrophilin (BTN1A1) gene in Indian bovines","authors":"Manoj Kumar, P. Ratwan, Ramendra Das, A. Chopra, V. Vohra","doi":"10.22146/IJBIOTECH.30332","DOIUrl":"https://doi.org/10.22146/IJBIOTECH.30332","url":null,"abstract":"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.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":"22 1","pages":"92-97"},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49205996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of N-benzoylthiourea derivatives as possible analgesic agents by predicting their physicochemical and pharmacokinetic properties, toxicity, and analgesic activity","authors":"Suko Hardjono, S. Siswandono, Rina Andayani","doi":"10.22146/IJBIOTECH.27171","DOIUrl":"https://doi.org/10.22146/IJBIOTECH.27171","url":null,"abstract":"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.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":"22 1","pages":"76-85"},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43893040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"NMR metabolite comparison of local pigmented rice in Yogyakarta","authors":"D. N. Wijaya, F. Susanto, Y. A. Purwestri, D. Ismoyowati, T. R. Nuringtyas","doi":"10.22146/IJBIOTECH.27308","DOIUrl":"https://doi.org/10.22146/IJBIOTECH.27308","url":null,"abstract":"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 D 2 O 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.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":"22 1","pages":"68-75"},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48845771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The expression of growth factor signaling genes in co-culture IVM","authors":"E.M.N Setiawan, H. Oh, Min Jung Kim, Geon A Kim, Seok Hee Lee, Yoo-Bin Choi, Kihae Ra, Byeong-chun Lee","doi":"10.22146/IJBIOTECH.27309","DOIUrl":"https://doi.org/10.22146/IJBIOTECH.27309","url":null,"abstract":"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.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":"22 1","pages":"98-106"},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46820624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cloning and expression of haloacid dehalogenase gene from Bacillus cereus IndB1","authors":"E. Ratnaningsih, I. Idris","doi":"10.22146/IJBIOTECH.27338","DOIUrl":"https://doi.org/10.22146/IJBIOTECH.27338","url":null,"abstract":"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 OD 550 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/s hydrolase folding motif for haloacid dehalogenase superfamily. Normal 0 false false false IN X-NONE X-NONE /* Style Definitions */ \u0000 table.MsoNormalTable \u0000 {mso-style-name:\"Table Normal\"; \u0000 mso-tstyle-rowband-size:0; \u0000 mso-tstyle-colband-size:0; \u0000 mso-style-noshow:yes; \u0000 mso-style-priority:99; \u0000 mso-style-parent:\"\"; \u0000 mso-padding-alt:0mm 5.4pt 0mm 5.4pt; \u0000 mso-para-margin-top:0mm; \u0000 mso-para-margin-right:0mm; \u0000 mso-para-margin-bottom:8.0pt; \u0000 mso-para-margin-left:0mm; \u0000 line-height:107%; \u0000 mso-pagination:widow-orphan; \u0000 font-size:11.0pt; \u0000 font-family:\"Calibri\",sans-serif; \u0000 mso-ascii-font-family:Calibri; \u0000 mso-ascii-theme-font:minor-latin; \u0000 mso-hansi-font-family:Calibri; \u0000 mso-hansi-theme-font:minor-latin; \u0000 mso-bidi-font-family:\"Times New Roman\"; \u0000 mso-bidi-theme-font:minor-bidi; \u0000 mso-ansi-language:IN;}","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":"22 1","pages":"55-60"},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45815367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Generation of recombinant scFv antibody against Ochratoxin A (OTA)","authors":"Ranya Pranomphon, W. Srila, M. Yamabhai","doi":"10.22146/IJBIOTECH.31121","DOIUrl":"https://doi.org/10.22146/IJBIOTECH.31121","url":null,"abstract":"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 (IC 50 ) 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.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":"22 1","pages":"107-113"},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46928616","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Anthocyanin, nutrient contents, and antioxidant activity of black rice bran of Oryza sativa L. ‘Cempo Ireng’ from Sleman, Yogyakarta, Indonesia","authors":"P. Apridamayanti, R. Pratiwi, Y. A. Purwestri, Woro Anindito Sri Tunjung, R. Rumiyati","doi":"10.22146/IJBIOTECH.26401","DOIUrl":"https://doi.org/10.22146/IJBIOTECH.26401","url":null,"abstract":"The chemical contents and health benefits of black rice bran of some rice cultivars have been investigated. However, there has been little research on the ‘Cempo Ireng’ cultivar from Sleman, Yogyakarta. The aim of this present study was to determine the anthocyanin, antioxidant activity, and macro- and micronutrients contents of black rice bran from this local cultivar. The anthocyanin in the black rice bran was extracted using the maceration method with methanol as a solvent. The extract obtained was separated through a preparative thin layer chromatography (TLC) of silica GF254 and a mobile phase composed of n-butanol, acetic acid, and water. Two fractions were collected and analyzed for the anthocyanin content. The preparative TLC spots were separated for further detection and measurement of cyanidin 3-O-glucoside using HPLC followed by LC-MS. The antioxidant activity of the fractions were measured using the DPPH free radical scavenging method. The results showed that the anthocyanin in fraction 1 was identified as cyanidin 3-O-glucoside (66.1 ± 10.6 µg/g). The IC 50 of fractions 1 and 2 were 200.96 and 218.36 µg/mL, respectively. Analysis of the macro- and micronutrients revealed that the black rice bran of ‘Cempo Ireng’ had nutrient contents comparable with other rice cultivars. Therefore, this local black rice bran can be used as a source of antioxidants and macro-- and micronutrients.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":"22 1","pages":"49-54"},"PeriodicalIF":0.0,"publicationDate":"2018-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45762861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bioactivity and genetic screening of marine actinobacteria associated with red algae Gelidiella acerosa","authors":"M. Ulfah, N. Kasanah, N. Handayani","doi":"10.22146/IJBIOTECH.25920","DOIUrl":"https://doi.org/10.22146/IJBIOTECH.25920","url":null,"abstract":"Bacterial resistance to existing antibiotics has driven a search for new antibiotics from marine actinobacteria. Bioactivity and genetic screening of actinobacteria associated with red algae Gelidiella acerosa were conducted to discover new antibacterial compounds against Vibrio alginolyticus . A total of 14 actinobacteria isolates were obtained from G. acerosa . The isolates were subjected to genetic screening for nrps (non-ribosomal peptide synthetase) and FADH 2 -dependent halogenase genes. The isolates’ ability to produce secondary metabolites was examined by fermentation in various media in a six-well mini plate. The bioactivity of the secondary metabolites was screened using a microtiter assay and the agar overlay method. The results showed that all 14 isolates had the nrps gene, whereas none had the halogenase gene. Meanwhile, eight of the actinobacteria isolates showed antibacterial activity against V. alginolyticus .","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":"22 1","pages":"13-21"},"PeriodicalIF":0.0,"publicationDate":"2018-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45559519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}