Pub Date : 2021-01-01DOI: 10.22146/ijbiotech.67039
G. Ramadhan, S. Avivi, B. Sugiharto, Wahyu Indra Duwi Fanata
Plants activate the unfolded protein response as part of cellular adaptation, thereby maintaining the endoplasmic reticulum homeostasis during external stresses exposure. In this study, we examined the relationship between the degree of salt tolerance and unfolded protein response-related gene expression in India salt-tolerant Pokkali and INPARI 35 varieties compared to the Indica salt-sensitive counterpart IR64 and INPARI 4 varieties. Our result showed that the salt tolerance of Pokkali and INPARI 35 had been confirmed by their higher survival rate, higher chlorophyll content, lower electrolyte leakage, and lower H2O2 and malondialdehyde content under salt stress conditions. Furthermore, the expression of unfolded protein response genes was highest in INPARI 35, whereas IR64 and INPARI 4 exhibited low gene induction during endoplasmic reticulum stress conditions. Among the four examined varieties the salt tolerant Pokkali surprisingly showed the lowest induction of all examined unfolded protein response-related genes. These results indicated the possibility that unfolded protein response supports the rice plant for adapting to the saline environment.
{"title":"Unfolded protein response in rice (Oryza sativa L.) varieties with different level of salt stress tolerance","authors":"G. Ramadhan, S. Avivi, B. Sugiharto, Wahyu Indra Duwi Fanata","doi":"10.22146/ijbiotech.67039","DOIUrl":"https://doi.org/10.22146/ijbiotech.67039","url":null,"abstract":"Plants activate the unfolded protein response as part of cellular adaptation, thereby maintaining the endoplasmic reticulum homeostasis during external stresses exposure. In this study, we examined the relationship between the degree of salt tolerance and unfolded protein response-related gene expression in India salt-tolerant Pokkali and INPARI 35 varieties compared to the Indica salt-sensitive counterpart IR64 and INPARI 4 varieties. Our result showed that the salt tolerance of Pokkali and INPARI 35 had been confirmed by their higher survival rate, higher chlorophyll content, lower electrolyte leakage, and lower H2O2 and malondialdehyde content under salt stress conditions. Furthermore, the expression of unfolded protein response genes was highest in INPARI 35, whereas IR64 and INPARI 4 exhibited low gene induction during endoplasmic reticulum stress conditions. Among the four examined varieties the salt tolerant Pokkali surprisingly showed the lowest induction of all examined unfolded protein response-related genes. These results indicated the possibility that unfolded protein response supports the rice plant for adapting to the saline environment.","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":"68305847","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.62584
I. Gunam, T. Sone, Kozo Asano
Organosulfur compounds classified as dibenzothiophenes (DBTs) and their derivatives are contained in petroleum. When used as fuel, these substances release SOx emissions, thus contributing to air pollution, acid rain, and climate change. Therefore, it is necessary to reduce the content of these organic sulfur compounds in fuels and one way to achieve this is through bacterial desulfurization. This study reports the biodesulfurization process of a mixture of DBT, 4-hexyl DBT, 4,6-dibutyl DBT, and various organosulfur compounds in light gas oil (LGO). The experiment was conducted by treating 1 mL of aromatic organosulfur compounds with 100 mg/L in textit{n}-tetradecane or 1 mL LGO with 5 mL mineral salts in sulfur-free medium, incubated at 27 °C for 5 days with shaking at 273 rpm. Gas chromatography analyses revealed that the growing Sphingomonas subarctica T7b cells desulfurized and converted 88.29% of DBT to 2-hydroxybiphenyl as a metabolite while a mixture of DBT and 4,6-dibutyl DBT was desulfurized at 86.40% and 7.00%, respectively. Furthermore, the mixture of DBT, 4-hexyl DBT, and 4,6-dibutyl DBT had a desulfurization percentage of 84.40%, 41.00%, and 6.66%, respectively, after five days of incubation. The compounds were observed to desulfurize slightly better as single compounds compared to when mixed with other aromatic sulfur compounds.
石油中含有被归类为二苯并噻吩(DBTs)及其衍生物的有机硫化合物。当用作燃料时，这些物质会释放出硫氧化物，从而造成空气污染、酸雨和气候变化。因此，有必要减少燃料中这些有机硫化合物的含量，实现这一目标的一种方法是通过细菌脱硫。本研究报道了DBT、4-己基DBT、4,6-二丁基DBT和多种有机硫化合物在轻油(LGO)中的生物脱硫过程。在无硫培养基中，用100 mg/L的textit{正}四烷溶液处理1 mL芳香烃有机硫化合物或用5 mL无机盐处理1 mL LGO，在27℃下孵育5天，以273 rpm振荡。气相色谱分析表明，生长中的亚北极鞘单胞菌T7b细胞脱硫转化88.29% of DBT to 2-hydroxybiphenyl as a metabolite while a mixture of DBT and 4,6-dibutyl DBT was desulfurized at 86.40% and 7.00%, respectively. Furthermore, the mixture of DBT, 4-hexyl DBT, and 4,6-dibutyl DBT had a desulfurization percentage of 84.40%, 41.00%, and 6.66%, respectively, after five days of incubation. The compounds were observed to desulfurize slightly better as single compounds compared to when mixed with other aromatic sulfur compounds.
{"title":"Biodesulfurization of the mixture of dibenzothiophene and its alkylated derivatives by Sphingomonas subarctica T7b","authors":"I. Gunam, T. Sone, Kozo Asano","doi":"10.22146/ijbiotech.62584","DOIUrl":"https://doi.org/10.22146/ijbiotech.62584","url":null,"abstract":"Organosulfur compounds classified as dibenzothiophenes (DBTs) and their derivatives are contained in petroleum. When used as fuel, these substances release SOx emissions, thus contributing to air pollution, acid rain, and climate change. Therefore, it is necessary to reduce the content of these organic sulfur compounds in fuels and one way to achieve this is through bacterial desulfurization. This study reports the biodesulfurization process of a mixture of DBT, 4-hexyl DBT, 4,6-dibutyl DBT, and various organosulfur compounds in light gas oil (LGO). The experiment was conducted by treating 1 mL of aromatic organosulfur compounds with 100 mg/L in textit{n}-tetradecane or 1 mL LGO with 5 mL mineral salts in sulfur-free medium, incubated at 27 °C for 5 days with shaking at 273 rpm. Gas chromatography analyses revealed that the growing Sphingomonas subarctica T7b cells desulfurized and converted 88.29% of DBT to 2-hydroxybiphenyl as a metabolite while a mixture of DBT and 4,6-dibutyl DBT was desulfurized at 86.40% and 7.00%, respectively. Furthermore, the mixture of DBT, 4-hexyl DBT, and 4,6-dibutyl DBT had a desulfurization percentage of 84.40%, 41.00%, and 6.66%, respectively, after five days of incubation. The compounds were observed to desulfurize slightly better as single compounds compared to when mixed with other aromatic sulfur compounds.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68306108","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 : 2020-12-11DOI: 10.22146/ijbiotech.53937
Imam Bagus Nugroho, F. Fahrurrozi
Theobroma cacao L. is an important Indonesian estate crop, which suffers from biotic and abiotic stresses. TcOSM , which encodes osmotin as a response to pathogens and environmental stresses, is, therefore, a focus of interest in this research, aiming to characterize TcOSM in an Indonesian local cacao cultivar. Bioinformatics queries for putative TcOSM were performed against the reference genome of a Criollo-type cacao cultivar. Based on nucleotide sequence determination, our results revealed two genes, TcOSM1 and TcOSM2 , which have the highest similarity (≥ 90%) to the cacao reference genes. Heterozygosity was detected in the TcOSM1 -encoding gene, which contained two overlapping peaks in Sanger-sequencing chromatograms. One of the alleles resulted from a single nucleotide change (G to A), leading to a same-sense mutation that did not substitute corresponding alanine residue. Homology modeling using Phyre2 and structural alignment (superimposition) was conducted to examine the influence of genetic variations in TcOSM sequences upon the global protein structures. The result showed no significant changes (RMSD ≤ 0.206 A, TM-score > 0.5) in tertiary protein structures. Altogether, this research succeeded in characterizing TcOSM while providing a fundamental study for future cacao biotechnology endeavors.
{"title":"Cloning and in silico analysis revealed a genetic variation in osmotin-encoding genes in an Indonesian local cacao cultivar","authors":"Imam Bagus Nugroho, F. Fahrurrozi","doi":"10.22146/ijbiotech.53937","DOIUrl":"https://doi.org/10.22146/ijbiotech.53937","url":null,"abstract":"Theobroma cacao L. is an important Indonesian estate crop, which suffers from biotic and abiotic stresses. TcOSM , which encodes osmotin as a response to pathogens and environmental stresses, is, therefore, a focus of interest in this research, aiming to characterize TcOSM in an Indonesian local cacao cultivar. Bioinformatics queries for putative TcOSM were performed against the reference genome of a Criollo-type cacao cultivar. Based on nucleotide sequence determination, our results revealed two genes, TcOSM1 and TcOSM2 , which have the highest similarity (≥ 90%) to the cacao reference genes. Heterozygosity was detected in the TcOSM1 -encoding gene, which contained two overlapping peaks in Sanger-sequencing chromatograms. One of the alleles resulted from a single nucleotide change (G to A), leading to a same-sense mutation that did not substitute corresponding alanine residue. Homology modeling using Phyre2 and structural alignment (superimposition) was conducted to examine the influence of genetic variations in TcOSM sequences upon the global protein structures. The result showed no significant changes (RMSD ≤ 0.206 A, TM-score > 0.5) in tertiary protein structures. Altogether, this research succeeded in characterizing TcOSM while providing a fundamental study for future cacao biotechnology endeavors.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43909605","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 : 2020-12-02DOI: 10.22146/IJBIOTECH.55604
Kezia Abib Yerah Tjandra, K. Dewi, A. M. Fuad, T. Anindyawati
Trichoderma reesei is known to be one of the organisms capable for producing various types of cellulase in high concentrations. Among these cellulases, the highest catalytic efficiency of endoglucanases II (EGII, EC 3.2.1.4 ) are considered important for industrial application. The characterization of the EGII is necessary since it is widely used in high-temperature reactions in the industries. In this study, the recombinant EGII protein was expressed in Pichia pastoris and it has a molecular mass of approximately 52 kDa. Recombinant EGII was purified using Ni-NTA affinity chromatography and characterized by SDS-PAGE and western blot analyses. The enzyme activity of recombinant EGII was measured using the Nelson Somogyi method to determine its optimum pH and temperature. The result showed that the maximum EGII expression was achieved after 72 h of culture incubation. The crude enzyme has optimum activity at pH 5.0, resulting in 16.3 U/mL and 14.6 U/mL activity at 40 °C and 50 °C, respectively. While the purified enzyme gave the specific activity of 115.7 U/mg under the optimum condition. Finally, our study demonstrated that recombinant EGII could retain the endoglucanase activity for 89% and 80% at 40 °C and 50 °C, respectively.
{"title":"Expression and characterization of Trichoderma reesei endoglucanase II in Pichia pastoris under the regulation of the GAP promoter","authors":"Kezia Abib Yerah Tjandra, K. Dewi, A. M. Fuad, T. Anindyawati","doi":"10.22146/IJBIOTECH.55604","DOIUrl":"https://doi.org/10.22146/IJBIOTECH.55604","url":null,"abstract":"Trichoderma reesei is known to be one of the organisms capable for producing various types of cellulase in high concentrations. Among these cellulases, the highest catalytic efficiency of endoglucanases II (EGII, EC 3.2.1.4 ) are considered important for industrial application. The characterization of the EGII is necessary since it is widely used in high-temperature reactions in the industries. In this study, the recombinant EGII protein was expressed in Pichia pastoris and it has a molecular mass of approximately 52 kDa. Recombinant EGII was purified using Ni-NTA affinity chromatography and characterized by SDS-PAGE and western blot analyses. The enzyme activity of recombinant EGII was measured using the Nelson Somogyi method to determine its optimum pH and temperature. The result showed that the maximum EGII expression was achieved after 72 h of culture incubation. The crude enzyme has optimum activity at pH 5.0, resulting in 16.3 U/mL and 14.6 U/mL activity at 40 °C and 50 °C, respectively. While the purified enzyme gave the specific activity of 115.7 U/mg under the optimum condition. Finally, our study demonstrated that recombinant EGII could retain the endoglucanase activity for 89% and 80% at 40 °C and 50 °C, respectively.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46311778","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 : 2020-12-02DOI: 10.22146/IJBIOTECH.54111
S. H. Irianingsih, B. Poermadjaja, H. Wuryastuti, R. Wasito
The bovine viral diarrhea virus (BVDV) is a major viral pathogen in cattle worldwide. In Indonesia, diversity in subgenotypes of BVDV-1 has been observed, with the highest proportion of subgenotype -1a, followed by -1c, -1b, and -1d. So far, phylogenetic analysis of BVDV-1 is based on nucleotide sequences of the 5′ UTR and partial NS5B regions. Accuracy in identifying the subgenotype and antigenic type is critical for vaccine development and effective vaccination. The aim of this study was to determine genetic recombination of BVDV through phylogenetic analysis of five different regions (5′ UTR, NPro, E2, NS3, and NS5B) of BVDV in persistently infected dairy cattle. Five isolates were sequenced using next-generation sequencing, and data were analyzed with the CLC Genomic Workbench 9.0 and MEGA-X programs. Phylogenetic analysis based on the 5′ UTR (275 nt), NPro (504 nt), E2 (1,122 nt), NS3 (2,049 nt), and NS5B (2,157 nt) regions indicated that one BVDV isolate from Banyumas, Central Java, could be classified into different subgenotypes based on the E2 region (-1c), but the same subgenotype based on the other four regions (-1a), suggesting the presence of genetic recombination of the BVDV subgenotypes -1a and -1c in persistently infected dairy cattle.
{"title":"Genetic recombination of bovine viral diarrhea virus subgenotype -1a and -1c in persistently infected dairy cattle","authors":"S. H. Irianingsih, B. Poermadjaja, H. Wuryastuti, R. Wasito","doi":"10.22146/IJBIOTECH.54111","DOIUrl":"https://doi.org/10.22146/IJBIOTECH.54111","url":null,"abstract":"The bovine viral diarrhea virus (BVDV) is a major viral pathogen in cattle worldwide. In Indonesia, diversity in subgenotypes of BVDV-1 has been observed, with the highest proportion of subgenotype -1a, followed by -1c, -1b, and -1d. So far, phylogenetic analysis of BVDV-1 is based on nucleotide sequences of the 5′ UTR and partial NS5B regions. Accuracy in identifying the subgenotype and antigenic type is critical for vaccine development and effective vaccination. The aim of this study was to determine genetic recombination of BVDV through phylogenetic analysis of five different regions (5′ UTR, NPro, E2, NS3, and NS5B) of BVDV in persistently infected dairy cattle. Five isolates were sequenced using next-generation sequencing, and data were analyzed with the CLC Genomic Workbench 9.0 and MEGA-X programs. Phylogenetic analysis based on the 5′ UTR (275 nt), NPro (504 nt), E2 (1,122 nt), NS3 (2,049 nt), and NS5B (2,157 nt) regions indicated that one BVDV isolate from Banyumas, Central Java, could be classified into different subgenotypes based on the E2 region (-1c), but the same subgenotype based on the other four regions (-1a), suggesting the presence of genetic recombination of the BVDV subgenotypes -1a and -1c in persistently infected dairy cattle.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43594177","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 : 2020-12-02DOI: 10.22146/IJBIOTECH.53936
R. Susanti, A. Yuniastuti, Fitri Arum Sasi, M. Dafip
The diversity of intestinal bacteria in geese correlates with environmental conditions, rearing methods, and consumed feeds. The intestinal bacteria composition is useful for the absorption of nutrition, improving the metabolism, and may be related to the immune system. This study was conducted to examine the intestinal bacteria composition and the diversity of maintained goose in aviaries and barns. This research was an observational exploratory. Five geese were taken purposively from local breeders in Gunungpati District, Semarang City. A total of 5 g of intestinal contents from each sample was used for microbial genome isolation. Then, the genome was amplified to collect 16S rRNA gene region V3-V4. The amplicons were then sequenced using the next generation sequencing (NGS) method (Illumina high-throughput sequencing; paired-end reads) and analyzed using QIIME2 to identify bacterial species. In addition, GC-MS was performed to identify and measure fatty acid contents in the intestinal. The results showed that both rearing and caged goose contained nine phyla of intestinal bacteria. The number of intestinal bacteria of barn geese (SU) reached 32,748 Operational Taxonomy Units (OTU); higher than aviary geese (SK), which was 11,646 OTU. The intestinal bacteria community in barn geese was approved by Phylum TM7 ( Saccharibacteria candidate ) (53.18%), followed by Firmicutes (32.51%) and Bacteriodetes (5.42%). Whereas on SK Firmicutes was compiled 49.3 4% of total OTU, TM7 ( S. candidate ) up to 21.17%, and Actinobacteria up to 15.99 %. The abundance of TM7 may contribute to high 9,12-octadecadienoic acid production, while Firmicutes was related to the high production of oleic acid. Based on these data, the reared geese had a more abundant diversity of bacteria than the caged one.
{"title":"Metagenomic analysis of intestinal microbiota in geese from different farming systems in Gunungpati, Semarang","authors":"R. Susanti, A. Yuniastuti, Fitri Arum Sasi, M. Dafip","doi":"10.22146/IJBIOTECH.53936","DOIUrl":"https://doi.org/10.22146/IJBIOTECH.53936","url":null,"abstract":"The diversity of intestinal bacteria in geese correlates with environmental conditions, rearing methods, and consumed feeds. The intestinal bacteria composition is useful for the absorption of nutrition, improving the metabolism, and may be related to the immune system. This study was conducted to examine the intestinal bacteria composition and the diversity of maintained goose in aviaries and barns. This research was an observational exploratory. Five geese were taken purposively from local breeders in Gunungpati District, Semarang City. A total of 5 g of intestinal contents from each sample was used for microbial genome isolation. Then, the genome was amplified to collect 16S rRNA gene region V3-V4. The amplicons were then sequenced using the next generation sequencing (NGS) method (Illumina high-throughput sequencing; paired-end reads) and analyzed using QIIME2 to identify bacterial species. In addition, GC-MS was performed to identify and measure fatty acid contents in the intestinal. The results showed that both rearing and caged goose contained nine phyla of intestinal bacteria. The number of intestinal bacteria of barn geese (SU) reached 32,748 Operational Taxonomy Units (OTU); higher than aviary geese (SK), which was 11,646 OTU. The intestinal bacteria community in barn geese was approved by Phylum TM7 ( Saccharibacteria candidate ) (53.18%), followed by Firmicutes (32.51%) and Bacteriodetes (5.42%). Whereas on SK Firmicutes was compiled 49.3 4% of total OTU, TM7 ( S. candidate ) up to 21.17%, and Actinobacteria up to 15.99 %. The abundance of TM7 may contribute to high 9,12-octadecadienoic acid production, while Firmicutes was related to the high production of oleic acid. Based on these data, the reared geese had a more abundant diversity of bacteria than the caged one.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44244765","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 : 2020-12-02DOI: 10.22146/IJBIOTECH.55631
Jeremias Ivan, Rizky Nurdiansyah, A. A. Parikesit
Inhibition of ADP-ribosylation factor 6 messenger RNA (ARF6 mRNA) by microRNA-145 (miR-145), mediated by Argonaute (AGO) protein, has been found to play essential roles in several types of cancer and cellular processes. This study aimed to model the molecular interaction between miR-145 and ARF6 mRNA with AGO protein. The sequences of miR-145 and the 3’ untranslated region (UTR) of ARF6 mRNA were retrieved from miRTarBase, followed by miRNA target-site and structure predictions were done using RNAhybrid, RNAfold, and simRNAweb, respectively. The interaction between the miRNA-mRNA duplex and AGO was further assessed via molecular docking, interaction analysis, and dynamics, using PatchDock Server, PLIP, and VMD/NAMD, respectively. The models between miR-145, predicted target site of ARF6 mRNA, and AGO protein returned stable thermodynamic variables with negative free energy. Specifically, the RNA duplex had an energy of -19.80 kcal/mol, while the docking had -84.58 atomic contact energy supported by 70 hydrogen bonds and 14 hydrophobic interactions. However, the stability of the RMSD plot was still unclear due to limited computational resources. Nevertheless, these results computationally confirm favorable interaction of the three molecules, which can be utilized for further transcriptomics-based drugs or treatments.
{"title":"Computational modeling of AGO-mediated molecular inhibition of ARF6 by miR-145","authors":"Jeremias Ivan, Rizky Nurdiansyah, A. A. Parikesit","doi":"10.22146/IJBIOTECH.55631","DOIUrl":"https://doi.org/10.22146/IJBIOTECH.55631","url":null,"abstract":"Inhibition of ADP-ribosylation factor 6 messenger RNA (ARF6 mRNA) by microRNA-145 (miR-145), mediated by Argonaute (AGO) protein, has been found to play essential roles in several types of cancer and cellular processes. This study aimed to model the molecular interaction between miR-145 and ARF6 mRNA with AGO protein. The sequences of miR-145 and the 3’ untranslated region (UTR) of ARF6 mRNA were retrieved from miRTarBase, followed by miRNA target-site and structure predictions were done using RNAhybrid, RNAfold, and simRNAweb, respectively. The interaction between the miRNA-mRNA duplex and AGO was further assessed via molecular docking, interaction analysis, and dynamics, using PatchDock Server, PLIP, and VMD/NAMD, respectively. The models between miR-145, predicted target site of ARF6 mRNA, and AGO protein returned stable thermodynamic variables with negative free energy. Specifically, the RNA duplex had an energy of -19.80 kcal/mol, while the docking had -84.58 atomic contact energy supported by 70 hydrogen bonds and 14 hydrophobic interactions. However, the stability of the RMSD plot was still unclear due to limited computational resources. Nevertheless, these results computationally confirm favorable interaction of the three molecules, which can be utilized for further transcriptomics-based drugs or treatments.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43120206","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 : 2020-11-24DOI: 10.22146/IJBIOTECH.50750
Fihiruddin Fihiruddin, W. Artama, B. Widartono
Toxoplasmosis is an obligate intracellular zoonotic parasite caused by T oxoplasma gondii that can infect all warm-blooded animals including humans. Prevalence of toxoplasmosis varies depending on climate, geography, and the presence of cats in an area. This study aimed to identify the prevalence and distribution of toxoplasmosis in Sleman, Yogyakarta through EcoHealth approaches. A total of 385 blood samples were collected from residents in the district of Sleman. Seven people from 55 villages were selected for blood sampling using a cluster method. The collected serums were tested by ELISA using recombinant Granule 1 protein (GRA-1) as coated antigen. Data on altitude and coordinates of sampling sites were collected using GPS. instruments, soil surface temperature in Sleman was obtained by satellite imagery, and cat population in residential areas was determined by questionnaire. The prevalence of toxoplasmosis in Sleman was 58%, of which distributed around rivers and in cattle pens. Based on altitude and temperature, toxoplasmosis cases were found the highest at 0-150 m (66.3%) and at temperatures of 26-30°C (66.4%). Areas with large numbers of cats had toxoplasmosis prevalence of 75.8% while areas with moderate and few cats were 56.5% and 49.0%, respectively. Thus, differences in the prevalence of toxoplasmosis at settlement were found based on altitude, soil surface temperature, and cat populations.
{"title":"Spatial analysis of toxoplasmosis through EcoHealth approaches using GRA-1 recombinant: case in Sleman, Yogyakarta","authors":"Fihiruddin Fihiruddin, W. Artama, B. Widartono","doi":"10.22146/IJBIOTECH.50750","DOIUrl":"https://doi.org/10.22146/IJBIOTECH.50750","url":null,"abstract":"Toxoplasmosis is an obligate intracellular zoonotic parasite caused by T oxoplasma gondii that can infect all warm-blooded animals including humans. Prevalence of toxoplasmosis varies depending on climate, geography, and the presence of cats in an area. This study aimed to identify the prevalence and distribution of toxoplasmosis in Sleman, Yogyakarta through EcoHealth approaches. A total of 385 blood samples were collected from residents in the district of Sleman. Seven people from 55 villages were selected for blood sampling using a cluster method. The collected serums were tested by ELISA using recombinant Granule 1 protein (GRA-1) as coated antigen. Data on altitude and coordinates of sampling sites were collected using GPS. instruments, soil surface temperature in Sleman was obtained by satellite imagery, and cat population in residential areas was determined by questionnaire. The prevalence of toxoplasmosis in Sleman was 58%, of which distributed around rivers and in cattle pens. Based on altitude and temperature, toxoplasmosis cases were found the highest at 0-150 m (66.3%) and at temperatures of 26-30°C (66.4%). Areas with large numbers of cats had toxoplasmosis prevalence of 75.8% while areas with moderate and few cats were 56.5% and 49.0%, respectively. Thus, differences in the prevalence of toxoplasmosis at settlement were found based on altitude, soil surface temperature, and cat populations.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41757576","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 : 2020-11-10DOI: 10.22146/IJBIOTECH.54092
A. Tharek, S. E. Mohamad, K. Iwamoto, I. Suzuki, H. Hara, R. Dolah, S. Yoshizaki, H. Jamaluddin, M. Salleh, A. Yahya
Microalgae are known to be a potential resource of high-value metabolites that can be used in the growing field of biotechnology. These metabolites constitute valuable compounds with a wide range of applications that strongly enhance a bio-based economy. Among these metabolites, astaxanthin is considered the most important secondary metabolite, having superior antioxidant properties. For commercial feasibility, microalgae with enhanced astaxanthin production need to be developed. In this study, the tropical green microalgae strain, Coelastrum sp., isolated from the environment in Malaysia, was incubated with methyl viologen, a reactive oxygen species (ROS) reagent that generates superoxide anion radicals (O 2 - ) as an enhancer to improve the accumulation of astaxanthin. The effect of different concentrations of methyl viologen on astaxanthin accumulation was investigated. The results suggested that the supplementation of methyl viologen at low concentration (0.001 mM) was successfully used as a ROS reagent in facilitating and thereby increasing the production of astaxanthin in Coelastrum sp. at a rate 1.3 times higher than in the control.
{"title":"Enhanced astaxanthin production by oxidative stress using methyl viologen as a reactive oxygen species (ROS) reagent in green microalgae Coelastrum sp.","authors":"A. Tharek, S. E. Mohamad, K. Iwamoto, I. Suzuki, H. Hara, R. Dolah, S. Yoshizaki, H. Jamaluddin, M. Salleh, A. Yahya","doi":"10.22146/IJBIOTECH.54092","DOIUrl":"https://doi.org/10.22146/IJBIOTECH.54092","url":null,"abstract":"Microalgae are known to be a potential resource of high-value metabolites that can be used in the growing field of biotechnology. These metabolites constitute valuable compounds with a wide range of applications that strongly enhance a bio-based economy. Among these metabolites, astaxanthin is considered the most important secondary metabolite, having superior antioxidant properties. For commercial feasibility, microalgae with enhanced astaxanthin production need to be developed. In this study, the tropical green microalgae strain, Coelastrum sp., isolated from the environment in Malaysia, was incubated with methyl viologen, a reactive oxygen species (ROS) reagent that generates superoxide anion radicals (O 2 - ) as an enhancer to improve the accumulation of astaxanthin. The effect of different concentrations of methyl viologen on astaxanthin accumulation was investigated. The results suggested that the supplementation of methyl viologen at low concentration (0.001 mM) was successfully used as a ROS reagent in facilitating and thereby increasing the production of astaxanthin in Coelastrum sp. at a rate 1.3 times higher than in the control.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":"25 1","pages":"95-101"},"PeriodicalIF":0.0,"publicationDate":"2020-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46881708","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 : 2020-11-10DOI: 10.22146/IJBIOTECH.54703
A. Haryanto, H. Wihadmadyatami, N. Wijayanti
The aim of this work was the in vitro expression of the recombinant fusion (F) protein of Newcastle disease virus (NDV). The pBT7-N-His-Fusion-NDV expression plasmid which carries the recombinant F protein encoding gene from local Indonesian isolates, was prepared and transformed into E. coli BL21 (DE3). To detect bacterial colonies carrying the recombinant plasmid, a restriction endonuclease analysis was performed using the EcoRI restriction endonuclease. These results showed that the pBT-N-His-Fusion-NDV plasmid was successfully isolated with a size of 4.601 bp, and three recombinant plasmids carrying the gene coding for the recombinant F protein of NDV were obtained. Selected recombinant plasmids were then in vitro by using a cell-free protein expression system followed by visualization of the recombinant F protein on a 12% SDS-PAGE gel both by Coomassie Brilliant Blue staining and Western blotting. Recombinant F protein was successfully in vitro expressed by using a cell-free protein expression system as indicated by a specific single protein band with a molecular mass of 25.6 kDa.
{"title":"In vitro expression of the recombinant fusion protein of Newcastle disease virus from local Indonesian isolates by using a cell-free protein expression system","authors":"A. Haryanto, H. Wihadmadyatami, N. Wijayanti","doi":"10.22146/IJBIOTECH.54703","DOIUrl":"https://doi.org/10.22146/IJBIOTECH.54703","url":null,"abstract":"The aim of this work was the in vitro expression of the recombinant fusion (F) protein of Newcastle disease virus (NDV). The pBT7-N-His-Fusion-NDV expression plasmid which carries the recombinant F protein encoding gene from local Indonesian isolates, was prepared and transformed into E. coli BL21 (DE3). To detect bacterial colonies carrying the recombinant plasmid, a restriction endonuclease analysis was performed using the EcoRI restriction endonuclease. These results showed that the pBT-N-His-Fusion-NDV plasmid was successfully isolated with a size of 4.601 bp, and three recombinant plasmids carrying the gene coding for the recombinant F protein of NDV were obtained. Selected recombinant plasmids were then in vitro by using a cell-free protein expression system followed by visualization of the recombinant F protein on a 12% SDS-PAGE gel both by Coomassie Brilliant Blue staining and Western blotting. Recombinant F protein was successfully in vitro expressed by using a cell-free protein expression system as indicated by a specific single protein band with a molecular mass of 25.6 kDa.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48999470","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}
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