Pub Date : 2021-03-30DOI: 10.22146/IJBIOTECH.62194
Mohammad Rizki Fadhil Pratama, H. Poerwono, Siswandono Siswodihardjo
Observation of molecular docking results was generally performed by analyzing the docking score and the interacting amino acid residues separately either in tables or graphs. Sometimes it was not easy to rank the tested ligands’ docking results, especially if there were many ligands. This study aims to introduce a new way to analyze docking results with a two‐dimensional graph between the difference in docking score and the similarity of ligand‐receptor interactions. Molecular docking was performed with one reference ligand and several test ligands. The docking score difference was obtained between the test and the reference ligands as the graph’s x‐axis. Meanwhile, the y‐axis contains the similarity of ligand‐receptor interactions, obtained from the ratio of amino acid residues and the types of interactions between the test and reference ligands. Docking result analysis was more straightforward because two critical parameters were presented in one graph. This graph could be used to support the analysis of the docking results.
{"title":"Introducing a two‐dimensional graph of docking score difference vs. similarity of ligand‐receptor interactions","authors":"Mohammad Rizki Fadhil Pratama, H. Poerwono, Siswandono Siswodihardjo","doi":"10.22146/IJBIOTECH.62194","DOIUrl":"https://doi.org/10.22146/IJBIOTECH.62194","url":null,"abstract":"Observation of molecular docking results was generally performed by analyzing the docking score and the interacting amino acid residues separately either in tables or graphs. Sometimes it was not easy to rank the tested ligands’ docking results, especially if there were many ligands. This study aims to introduce a new way to analyze docking results with a two‐dimensional graph between the difference in docking score and the similarity of ligand‐receptor interactions. Molecular docking was performed with one reference ligand and several test ligands. The docking score difference was obtained between the test and the reference ligands as the graph’s x‐axis. Meanwhile, the y‐axis contains the similarity of ligand‐receptor interactions, obtained from the ratio of amino acid residues and the types of interactions between the test and reference ligands. Docking result analysis was more straightforward because two critical parameters were presented in one graph. This graph could be used to support the analysis of the docking results.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":"26 1","pages":"54-60"},"PeriodicalIF":0.0,"publicationDate":"2021-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45367441","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}
Pub Date : 2021-03-30DOI: 10.22146/IJBIOTECH.54119
S. Gunawan, Nurul Rahmawati, R. B. Larasati, Ira Dwitasari, H. W. Aparamarta, T. Widjaja
One of the utilizations of bitter cassava is modified cassava flour (Mocaf) production using the fermentation process by Lactobacillus casei . The Mocaf has potential as the future of food security products. It has a characteristic property similar to wheat flour. Lactic acid was also produced as a by‐product during fermentation. After 40 h of fermentation, the proximate composition content of Mocaf was lactic acid content of 0.000928 g/L, hydrogen cyanide levels of 0.02 ppm, starch content of 59.13%, amylose content of 12.98% and amylopectin content of 46.15%. In the scaling‐up process from a laboratory scale to a pilot and industrial scale, modeling is needed. There are five equation models used to describe the kinetic reactions of lactic acid from bitter cassava starch: Monod, Moser, Powell, Blackman, and Product Inhibitor. Each parameter was being searched by a fitting curve using sigmaplot 12.0. The best result in terms of the highest R2 (0.65913) was obtained in the Powell equation with the value of µmax of 1.668/h, Ks of 123.4 g/L, and maintenance rate (m) of 4.672. The kinetic data obtained can be used to design biochemical reactors for industrial scale Mocaf flour production.
{"title":"Reaction kinetics of lactic acid fermentation from bitter cassava (Manihot glaziovii) starch by Lactobacillus casei","authors":"S. Gunawan, Nurul Rahmawati, R. B. Larasati, Ira Dwitasari, H. W. Aparamarta, T. Widjaja","doi":"10.22146/IJBIOTECH.54119","DOIUrl":"https://doi.org/10.22146/IJBIOTECH.54119","url":null,"abstract":"One of the utilizations of bitter cassava is modified cassava flour (Mocaf) production using the fermentation process by Lactobacillus casei . The Mocaf has potential as the future of food security products. It has a characteristic property similar to wheat flour. Lactic acid was also produced as a by‐product during fermentation. After 40 h of fermentation, the proximate composition content of Mocaf was lactic acid content of 0.000928 g/L, hydrogen cyanide levels of 0.02 ppm, starch content of 59.13%, amylose content of 12.98% and amylopectin content of 46.15%. In the scaling‐up process from a laboratory scale to a pilot and industrial scale, modeling is needed. There are five equation models used to describe the kinetic reactions of lactic acid from bitter cassava starch: Monod, Moser, Powell, Blackman, and Product Inhibitor. Each parameter was being searched by a fitting curve using sigmaplot 12.0. The best result in terms of the highest R2 (0.65913) was obtained in the Powell equation with the value of µmax of 1.668/h, Ks of 123.4 g/L, and maintenance rate (m) of 4.672. The kinetic data obtained can be used to design biochemical reactors for industrial scale Mocaf flour production.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":"26 1","pages":"7-14"},"PeriodicalIF":0.0,"publicationDate":"2021-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41546362","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}
Pub Date : 2021-03-30DOI: 10.22146/IJBIOTECH.61682
Pasmawati Pasmawati, A. Tjahjoleksono, S. Suharsono
Bacterial wilt caused by Ralstonia solanacearum is one of the most important bacterial diseases in potato production. This study aimed to obtain the transgenic potato ( Solanum tuberosum L.) cultivar IPB CP3, containing LYZ‐C gene encoding for lysozyme type C, resistant to bacterial disease caused by R. solanacearum . Genetic transformation using Agrobacterium tumefaciens LBA4404 to 124 internode explants resulted in the transformation efficiency of about 47.58% with a regeneration efficiency of approximately 30.51%. Gene integration analysis showed that 16 clones were confirmed as transgenic clones containing the LYZ‐C gene. Analysis of resistance to R. solanacearum of three transgenic clones showed that all three transgenic clones were more resistant than a non‐transgenic one. This result showed that the LYZ‐C gene integrated in the genome of transgenic potato increased the resistance of potato plants to R. solanacearum . We obtained two transgenic clones considered resistant to bacterial wilt disease.
{"title":"Obtaining of transgenic potato (Solanum tuberosum L.) cultivar IPB CP3 containing LYZ‐C gene resistant to bacterial wilt disease","authors":"Pasmawati Pasmawati, A. Tjahjoleksono, S. Suharsono","doi":"10.22146/IJBIOTECH.61682","DOIUrl":"https://doi.org/10.22146/IJBIOTECH.61682","url":null,"abstract":"Bacterial wilt caused by Ralstonia solanacearum is one of the most important bacterial diseases in potato production. This study aimed to obtain the transgenic potato ( Solanum tuberosum L.) cultivar IPB CP3, containing LYZ‐C gene encoding for lysozyme type C, resistant to bacterial disease caused by R. solanacearum . Genetic transformation using Agrobacterium tumefaciens LBA4404 to 124 internode explants resulted in the transformation efficiency of about 47.58% with a regeneration efficiency of approximately 30.51%. Gene integration analysis showed that 16 clones were confirmed as transgenic clones containing the LYZ‐C gene. Analysis of resistance to R. solanacearum of three transgenic clones showed that all three transgenic clones were more resistant than a non‐transgenic one. This result showed that the LYZ‐C gene integrated in the genome of transgenic potato increased the resistance of potato plants to R. solanacearum . We obtained two transgenic clones considered resistant to bacterial wilt disease.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":"26 1","pages":"48-53"},"PeriodicalIF":0.0,"publicationDate":"2021-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49050572","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}
Pub Date : 2021-03-30DOI: 10.22146/IJBIOTECH.57701
Haniyya Haniyya, Lina Mulyawati, I. Helianti, Phitsanu Pinmanee, K. Kocharin, Duriya Cantasingh, Thidarat Nimchua
Thermoalkalophilic xylanases promise potential application in pulp biobleaching to reduce the use of toxic chlorinated chemical agents, which are harmful to the environment. In this study, a thermoalkalophilic endoxylanase gene ( bhxyn3 ) originating from Indonesian indigenous Bacillus halodurans CM1 was cloned into yeast expression vector pPICZα A and expressed in Pichia pastoris KM71 under the control of AOX1 promoter. Recombinant P. pastoris expressed the highest final level of xylanase (146 U/mL) on BMGY medium after five days of cultivation. Optimization of xylanase production on a small scale was carried out by varying the methanol concentrations and the optimal xylanase production by the recombinant P. pastoris was observed in the culture with 2% (v/v) methanol after four days of the induction phase. The recombinant xylanase (BHxyn3E) was thermotolerant and alkalophilic, with an optimal temperature at around 55‐65 °C and under pH 8.0. The enzyme activity was slightly induced by K+, Fe2+, and MoO42‐. Enzymatic bleaching of bagasse pulp with no prior pH adjustment (pH 9) using BHxyn3E at 200 U/g oven dried pulp increased the lightness index (L*) and changed substantially the color a index (a*); however, the treatments did not change the whiteness index in a significant way. Therefore, further optimization and assessment such as adjustment of incubation temperature and pH in biobleaching were needed to reduce the use of harmful chemical agents in industrial applications.
{"title":"Characterization of recombinant Bacillus halodurans CM1 xylanase produced by Pichia pastoris KM71 and its potential application in bleaching process of bagasse pulp","authors":"Haniyya Haniyya, Lina Mulyawati, I. Helianti, Phitsanu Pinmanee, K. Kocharin, Duriya Cantasingh, Thidarat Nimchua","doi":"10.22146/IJBIOTECH.57701","DOIUrl":"https://doi.org/10.22146/IJBIOTECH.57701","url":null,"abstract":"Thermoalkalophilic xylanases promise potential application in pulp biobleaching to reduce the use of toxic chlorinated chemical agents, which are harmful to the environment. In this study, a thermoalkalophilic endoxylanase gene ( bhxyn3 ) originating from Indonesian indigenous Bacillus halodurans CM1 was cloned into yeast expression vector pPICZα A and expressed in Pichia pastoris KM71 under the control of AOX1 promoter. Recombinant P. pastoris expressed the highest final level of xylanase (146 U/mL) on BMGY medium after five days of cultivation. Optimization of xylanase production on a small scale was carried out by varying the methanol concentrations and the optimal xylanase production by the recombinant P. pastoris was observed in the culture with 2% (v/v) methanol after four days of the induction phase. The recombinant xylanase (BHxyn3E) was thermotolerant and alkalophilic, with an optimal temperature at around 55‐65 °C and under pH 8.0. The enzyme activity was slightly induced by K+, Fe2+, and MoO42‐. Enzymatic bleaching of bagasse pulp with no prior pH adjustment (pH 9) using BHxyn3E at 200 U/g oven dried pulp increased the lightness index (L*) and changed substantially the color a index (a*); however, the treatments did not change the whiteness index in a significant way. Therefore, further optimization and assessment such as adjustment of incubation temperature and pH in biobleaching were needed to reduce the use of harmful chemical agents in industrial applications.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":"26 1","pages":"15-24"},"PeriodicalIF":0.0,"publicationDate":"2021-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42168422","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}
Pub Date : 2021-03-30DOI: 10.22146/IJBIOTECH.58554
Z. Zulkarnaini, P. S. Komala, A. Almi
The anaerobic ammonium oxidation (anammox) biofilm process commonly uses various inorganic carriers to enhance nitrogen removal under anaerobic conditions. This study aims to analyze the performance of nitrogen removal in anammox process using sugarcane bagasse as an organic carrier. The experiment was carried out by using an up‐flow anaerobic sludge blanket (UASB) reactor for treating artificial wastewater at room temperature. The reactor was fed with ammonium and nitrite with the concentrations of 70‐150 mg–N/L and variations in the hydraulic retention time of 24 and 12 h. The granular anammox belongs to the genus Candidatus Brocadia sinica that was added as an inoculum of the reactor operation. The experimental stoichiometric of anammox for ΔNO2‐–N: ΔNH4+–N and ΔNO3‐: ΔNH4+ were 1.24 and 0.18, respectively, which is similar to anammox stoichiometry. The maximum Nitrogen Removal Rate (NRR) has achieved 0.29 kg–N/m3.d at Nitrogen Loading Rate (NLR) 0.6 kg–N/m3.d. The highest ammonium conversion efficiency (ACE) and nitrogen removal efficiency (NRE) were 88% and 85%, respectively. Based on this results, it indicated that sugarcane bagasse as organic carriers could increase the amount of total nitrogen removal by provided of denitrification process but inhibited the anammox process at a certain COD concentration.
{"title":"Anammox biofilm process using sugarcane bagasse as an organic carrier","authors":"Z. Zulkarnaini, P. S. Komala, A. Almi","doi":"10.22146/IJBIOTECH.58554","DOIUrl":"https://doi.org/10.22146/IJBIOTECH.58554","url":null,"abstract":"The anaerobic ammonium oxidation (anammox) biofilm process commonly uses various inorganic carriers to enhance nitrogen removal under anaerobic conditions. This study aims to analyze the performance of nitrogen removal in anammox process using sugarcane bagasse as an organic carrier. The experiment was carried out by using an up‐flow anaerobic sludge blanket (UASB) reactor for treating artificial wastewater at room temperature. The reactor was fed with ammonium and nitrite with the concentrations of 70‐150 mg–N/L and variations in the hydraulic retention time of 24 and 12 h. The granular anammox belongs to the genus Candidatus Brocadia sinica that was added as an inoculum of the reactor operation. The experimental stoichiometric of anammox for ΔNO2‐–N: ΔNH4+–N and ΔNO3‐: ΔNH4+ were 1.24 and 0.18, respectively, which is similar to anammox stoichiometry. The maximum Nitrogen Removal Rate (NRR) has achieved 0.29 kg–N/m3.d at Nitrogen Loading Rate (NLR) 0.6 kg–N/m3.d. The highest ammonium conversion efficiency (ACE) and nitrogen removal efficiency (NRE) were 88% and 85%, respectively. Based on this results, it indicated that sugarcane bagasse as organic carriers could increase the amount of total nitrogen removal by provided of denitrification process but inhibited the anammox process at a certain COD concentration.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":"26 1","pages":"25-32"},"PeriodicalIF":0.0,"publicationDate":"2021-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44998481","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}
Pub Date : 2021-03-30DOI: 10.22146/IJBIOTECH.54611
D. Savitri, I. Putri, W. P. Nugrahani, M. Purwaningrum, A. Haryanto
Sex identification of endangered and protected birds in captivity is very important for conservation programs. Half of the world’s bird species are monomorphic, where male and female are difficult to distinguished morphologically, including cockatoos. Sex identification using molecular bird sexing is more accurate and applicable because it directly targets the sex chromosomes. The purpose of this study was to determine the sex of Sulphur‐crested cockatoo ( Cacatua galerita ) by detecting differences in the intron size of the chromodomain helicase DNA‐binding 1 (CHD1) gene on the Z and W chromosomes by polymerase chain reaction (PCR) method and to compare of plucked feathers and blood samples as DNA sources for molecular bird sexing. DNA was extracted from feather and blood samples from four C. galerita . Extracted DNA was amplified on the CHD1 gene by PCR method with P2, MP, and NP primers, which were visualized using agarose gel 1.5% under UV transilluminator with a wavelength of 280 nm. The resulting PCR product was detected at 392 bp for the CHD1 Z gene segment and 297 bp for CHD1 W gene segments, where males showed a single DNA band (ZZ) and females showed a double DNA band (ZW). Four C. galerita were 100% successfully determined, consisting of one female and three males. Electrophoresis results showed DNA bands from blood samples were thicker and brighter than DNA bands from feather samples.
{"title":"Molecular bird sexing of sulphur‐crested cockatoo (Cacatua galerita) by poly","authors":"D. Savitri, I. Putri, W. P. Nugrahani, M. Purwaningrum, A. Haryanto","doi":"10.22146/IJBIOTECH.54611","DOIUrl":"https://doi.org/10.22146/IJBIOTECH.54611","url":null,"abstract":"Sex identification of endangered and protected birds in captivity is very important for conservation programs. Half of the world’s bird species are monomorphic, where male and female are difficult to distinguished morphologically, including cockatoos. Sex identification using molecular bird sexing is more accurate and applicable because it directly targets the sex chromosomes. The purpose of this study was to determine the sex of Sulphur‐crested cockatoo ( Cacatua galerita ) by detecting differences in the intron size of the chromodomain helicase DNA‐binding 1 (CHD1) gene on the Z and W chromosomes by polymerase chain reaction (PCR) method and to compare of plucked feathers and blood samples as DNA sources for molecular bird sexing. DNA was extracted from feather and blood samples from four C. galerita . Extracted DNA was amplified on the CHD1 gene by PCR method with P2, MP, and NP primers, which were visualized using agarose gel 1.5% under UV transilluminator with a wavelength of 280 nm. The resulting PCR product was detected at 392 bp for the CHD1 Z gene segment and 297 bp for CHD1 W gene segments, where males showed a single DNA band (ZZ) and females showed a double DNA band (ZW). Four C. galerita were 100% successfully determined, consisting of one female and three males. Electrophoresis results showed DNA bands from blood samples were thicker and brighter than DNA bands from feather samples.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":"26 1","pages":"1-6"},"PeriodicalIF":0.0,"publicationDate":"2021-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43788341","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}
Pub Date : 2021-03-30DOI: 10.22146/IJBIOTECH.57561
Andhi Sukma, H. Oktavianty, S. Sumardiono
Enhancement of crude protein content in rice bran with the solid‐state fermentation method in tray bioreactor using Rhizopus oryzae FNCC 6011 has been investigated. This research aimed to optimize the fermentation condition using the response surface methodology (RSM). The central composite design (CCD) with three independent variables, including substrate thickness (1 to 3 cm), fermentation temperature (28 to 32 °C), and nutrient concentration of KH2PO4 (2 to 6 g/L) used to determine the crude protein enrichment. The quadratic model has successfully described the effect of variable interactions on responses very well as indicated by the F value and p‐value are 11.20 and 0.0041, respectively. The multiple correlation coefficients (R2) of 0.9438 indicated that 94.38% of the model data has approached the actual data with a deviation of 5.62%. The interaction between the variable substrate thickness and the fermentation temperature is the most influential variable on the crude protein enrichment of rice bran, indicated by the highest F value of 24.08 and the lowest p‐value of 0.0027. The highest protein increase of 62.51% was obtained at 2 cm substrate thickness, fermentation temperature of 30 °C, and KH2PO4 concentration of 4 g/L.
{"title":"Optimization of solid‐state fermentation condition for crude protein enrichment of rice bran using Rhizopus oryzae in tray bioreactor","authors":"Andhi Sukma, H. Oktavianty, S. Sumardiono","doi":"10.22146/IJBIOTECH.57561","DOIUrl":"https://doi.org/10.22146/IJBIOTECH.57561","url":null,"abstract":"Enhancement of crude protein content in rice bran with the solid‐state fermentation method in tray bioreactor using Rhizopus oryzae FNCC 6011 has been investigated. This research aimed to optimize the fermentation condition using the response surface methodology (RSM). The central composite design (CCD) with three independent variables, including substrate thickness (1 to 3 cm), fermentation temperature (28 to 32 °C), and nutrient concentration of KH2PO4 (2 to 6 g/L) used to determine the crude protein enrichment. The quadratic model has successfully described the effect of variable interactions on responses very well as indicated by the F value and p‐value are 11.20 and 0.0041, respectively. The multiple correlation coefficients (R2) of 0.9438 indicated that 94.38% of the model data has approached the actual data with a deviation of 5.62%. The interaction between the variable substrate thickness and the fermentation temperature is the most influential variable on the crude protein enrichment of rice bran, indicated by the highest F value of 24.08 and the lowest p‐value of 0.0027. The highest protein increase of 62.51% was obtained at 2 cm substrate thickness, fermentation temperature of 30 °C, and KH2PO4 concentration of 4 g/L.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":"26 1","pages":"33-40"},"PeriodicalIF":0.0,"publicationDate":"2021-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48496857","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}
Pub Date : 2021-01-01DOI: 10.22146/ijbiotech.61164
C. U. Wirawati, M. Sudarwanto, D. Lukman, I. Wientarsih, E. A. Srihanto
The diversity of lactic acid bacteria (LAB) present during the manufacture of traditional fermented buffalo milk from West Sumatra, known as dadih, was studied via a culture-independent approach using terminal-restriction fragment length polymorphism (T-RFLP) to compare the dynamic diversity in back-slopping and spontaneous fermentation methods. Total LAB and pH were measured in freshly prepared buffalo milk and in textit{dadih} fermented for 24 and 48 hours. The results indicated significant differences between the fermentation methods, with higher total LAB, and greater phylotype richness and relative abundance being identified in the back-slopping method. Terminal fragment lengths (TRFs) of 68 and 310 bp were common to both techniques, similar to those of Lactobacillus fermentum, Fructobacillus pseudoficulneus, Leuconostoc citreum, Leuconostoc kimchii, and Leuconostoc sp. The changes in phylotype number (species number) and relative abundances of LAB communities identified are expected to produce data needed to formulate the best fermentation process for dadih manufacturing. A 24-hour back-slopping fermentation method is recommended, as fermentation time of longer than 24 hours reduced viable LAB significantly. Our results also indicated that the T-RFLP technique is not only clearly sensitive enough and adequate for segregating LAB diversity in both fermentation methods, but that it also provides good information regarding the structure of microbial communities and their composition change during the fermentation process.
{"title":"Comparative lactic acid bacteria (LAB) profiles during dadih fermentation with spontaneous and back-slopping methods, as identified by terminal-restriction fragment length polymorphism (T-RFLP)","authors":"C. U. Wirawati, M. Sudarwanto, D. Lukman, I. Wientarsih, E. A. Srihanto","doi":"10.22146/ijbiotech.61164","DOIUrl":"https://doi.org/10.22146/ijbiotech.61164","url":null,"abstract":"The diversity of lactic acid bacteria (LAB) present during the manufacture of traditional fermented buffalo milk from West Sumatra, known as dadih, was studied via a culture-independent approach using terminal-restriction fragment length polymorphism (T-RFLP) to compare the dynamic diversity in back-slopping and spontaneous fermentation methods. Total LAB and pH were measured in freshly prepared buffalo milk and in textit{dadih} fermented for 24 and 48 hours. The results indicated significant differences between the fermentation methods, with higher total LAB, and greater phylotype richness and relative abundance being identified in the back-slopping method. Terminal fragment lengths (TRFs) of 68 and 310 bp were common to both techniques, similar to those of Lactobacillus fermentum, Fructobacillus pseudoficulneus, Leuconostoc citreum, Leuconostoc kimchii, and Leuconostoc sp. The changes in phylotype number (species number) and relative abundances of LAB communities identified are expected to produce data needed to formulate the best fermentation process for dadih manufacturing. A 24-hour back-slopping fermentation method is recommended, as fermentation time of longer than 24 hours reduced viable LAB significantly. Our results also indicated that the T-RFLP technique is not only clearly sensitive enough and adequate for segregating LAB diversity in both fermentation methods, but that it also provides good information regarding the structure of microbial communities and their composition change during the fermentation process.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68306046","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}
Pub Date : 2021-01-01DOI: 10.22146/ijbiotech.63472
M. Cahyadi, Nurahmahdiani Fauziah, Imam Tubagus Suwarto, W. Boonsupthip
The rise of beef consumption in Indonesia opens an opportunity for “rogue” suppliers to mix beef with other meat species that are relatively cheaper, such as pork, chicken, etc. The aim of this study was to identify pig and chicken meat in raw, cooked, and processed meat products using multiplex-PCR of mitochondrial DNA Cytochrome b gene, which is maternally inherited and widely used for forensic studies. A total of 90 samples-33 raw meats, 33 cooked meats, and 24 meatballs-were used in this study. Each sample was extracted to obtain the DNA genome and this was then amplified using multiplex-PCR. The PCR products were visualized using 2% agarose gel electrophoresis. The results showed that species contained in raw, cooked, and processed meat samples could be identified as indicated by DNA bands at 398, 274, 227, and 157 bp for pig, cattle, chicken, and goat species respectively. This study concluded that species substitution in raw, cooked, and processed meats could be detected using the Cytochrome b gene as a genetic marker through multiplex-PCR assay.
{"title":"Detection of species substitution in raw, cooked, and processed meats utilizing multiplex-PCR assay","authors":"M. Cahyadi, Nurahmahdiani Fauziah, Imam Tubagus Suwarto, W. Boonsupthip","doi":"10.22146/ijbiotech.63472","DOIUrl":"https://doi.org/10.22146/ijbiotech.63472","url":null,"abstract":"The rise of beef consumption in Indonesia opens an opportunity for “rogue” suppliers to mix beef with other meat species that are relatively cheaper, such as pork, chicken, etc. The aim of this study was to identify pig and chicken meat in raw, cooked, and processed meat products using multiplex-PCR of mitochondrial DNA Cytochrome b gene, which is maternally inherited and widely used for forensic studies. A total of 90 samples-33 raw meats, 33 cooked meats, and 24 meatballs-were used in this study. Each sample was extracted to obtain the DNA genome and this was then amplified using multiplex-PCR. The PCR products were visualized using 2% agarose gel electrophoresis. The results showed that species contained in raw, cooked, and processed meat samples could be identified as indicated by DNA bands at 398, 274, 227, and 157 bp for pig, cattle, chicken, and goat species respectively. This study concluded that species substitution in raw, cooked, and processed meats could be detected using the Cytochrome b gene as a genetic marker through multiplex-PCR assay.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68306170","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}
Pub Date : 2021-01-01DOI: 10.22146/ijbiotech.63510
Dhania Novitasari, Laeli Muntafiah, N. Sari, E. Meiyanto, A. Hermawan
One of the mechanisms of cancer cell resistance toward chemotherapy is through cancer stem cells (CSCs), which are characterized by excessive activation of regulator proteins such as human epidermal receptor 2 (HER2). Sappan wood (Caesalpinia sappan L.) contains brazilin and brazilein that exhibit cytotoxic effects on several cancer cell lines. We aimed to explore the potency of the ethanolic extract of sappan (EES) in CSCs through bioinformatic analyses and by using a three-dimensional (3D) breast cancer stem cells (BCSCs) for in vitro assay with two different models (i.e., BCSCs and HER2-BCSCs) in order to identify the potential therapeutic targets of genes (PTTGs). Bioinformatic analyses identified PTTGs, which were further analyzed by gene ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, protein-protein interaction (PPI) networks, and hub protein selection. Mammospheres were cultured under conditioned media. The cytotoxic effects of EES were then measured by direct counting and based on the mammosphere-forming potential (MFP). Bioinformatic analysis disclosed PIK3CA and TP53 as PTTGs in BCSCs and HER2-BCSCs, respectively. In addition, the KEGG pathway analyses also demonstrated that PTTGs could regulate the ERBB pathway. EES thus demonstrated cytotoxicity and inhibited the formation of mammospheres. Collectively, EES exhibited excellent potential for further development as an inhibitor of cancer stem cells in breast cancer.
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