Pub Date : 2023-03-31DOI: 10.22146/ijbiotech.74104
Nurmalasari Darsono, W. D. Sawitri, Retnosari Apriasti, Agus Wahyudi, Putri Andreyna Saragi, Victorin Mega Putri, S. Sugiharto, W. Darmanto
Sugarcane Mosaic Virus (SCMV) infection is one of the most serious problems that can result in severe yield loss of sugarcane. Since the symptoms of SCMV infection are similar to other biotic and abiotic stress symptoms, the development of a rapid diagnostic with high precision is required. The use of laboratory animals such as rabbits is required for antibody production in immunoassay‐based detection. However, due to its many advantages, specific chicken egg yolk immunoglobulin (IgY) has received considerable attention as an alternative antibody production in immunodiagnostics for infectious diseases. In this study, IgY antibody against SCMV recombinant coat protein (CP) was successfully obtained from chicken blood serum and tested to compare its efficacy against antibody from rabbit (IgG) using immunocapture reverse transcription‐polymerase chain reaction (IC‐RT‐PCR). The result showed that IgY and IgG could detect 0.1 g SCMV infected leaves using 1000‐times‐diluted antibodies. The IgY antibody was also confirmed to be reproducible and potentially applicable in plant disease diagnostics using an antibody‐based detection.
甘蔗花叶病毒(SCMV)感染是导致甘蔗严重减产的最严重问题之一。由于SCMV感染的症状与其他生物和非生物应激症状相似，因此需要开发高精度的快速诊断方法。在基于免疫分析的检测中，抗体生产需要使用实验动物，如兔子。然而，特异性鸡卵黄免疫球蛋白(IgY)由于其诸多优点，作为一种替代抗体在传染病的免疫诊断中受到了广泛的关注。本研究成功地从鸡血清中获得了抗SCMV重组外壳蛋白(CP)的IgY抗体，并采用免疫捕获逆转录聚合酶链反应(IC‐RT‐PCR)对其抗兔抗体(IgG)的效果进行了比较。结果表明，IgY和IgG抗体稀释1000倍后可检测出0.1 g SCMV感染叶片。IgY抗体也被证实是可重复的，并有可能应用于基于抗体检测的植物疾病诊断。
{"title":"The efficacy of a chicken antibody for the development of immunoassay‐based rapid detection in sugarcane mosaic virus disease","authors":"Nurmalasari Darsono, W. D. Sawitri, Retnosari Apriasti, Agus Wahyudi, Putri Andreyna Saragi, Victorin Mega Putri, S. Sugiharto, W. Darmanto","doi":"10.22146/ijbiotech.74104","DOIUrl":"https://doi.org/10.22146/ijbiotech.74104","url":null,"abstract":"Sugarcane Mosaic Virus (SCMV) infection is one of the most serious problems that can result in severe yield loss of sugarcane. Since the symptoms of SCMV infection are similar to other biotic and abiotic stress symptoms, the development of a rapid diagnostic with high precision is required. The use of laboratory animals such as rabbits is required for antibody production in immunoassay‐based detection. However, due to its many advantages, specific chicken egg yolk immunoglobulin (IgY) has received considerable attention as an alternative antibody production in immunodiagnostics for infectious diseases. In this study, IgY antibody against SCMV recombinant coat protein (CP) was successfully obtained from chicken blood serum and tested to compare its efficacy against antibody from rabbit (IgG) using immunocapture reverse transcription‐polymerase chain reaction (IC‐RT‐PCR). The result showed that IgY and IgG could detect 0.1 g SCMV infected leaves using 1000‐times‐diluted antibodies. The IgY antibody was also confirmed to be reproducible and potentially applicable in plant disease diagnostics using an antibody‐based detection.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44118816","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 : 2022-12-30DOI: 10.22146/ijbiotech.63914
Adi Muradi Muhar, Faizal Mukharim, Dedy Hermansyah, A. Putra, Nurul Hidayah, N. Amalina, I. Alif
Full‐thickness wound healing is a complex process requiring a well‐orchestrated mechanism of various factors, including cytokines, particularly interleukin (IL)‐10 and transforming growth factor (TGF)‐β. IL‐10 and TGF‐β act as robust anti‐inflammatory cytokines in accelerating the wound healing process by regulating myofibroblasts. Hypoxic mesenchymal stem cell‐conditioned medium (hypMSC‐CM) containing cytokines potentially contribute to accelerate wound repair without scarring through the paracrine mechanism. This study aims to observe the role of hypMSC‐CM in controlling TGF‐β and IL‐10 levels to accelerate full‐thickness wound repair and regeneration. A total of 24 male Wistar rats were used in this study. Six healthy rats as a sham group and 18 rats were created as full‐thickness‐wound animal models using a 6 mm punch biopsy. The animals were randomly assigned into three groups (n = 6) consisting of two treatment groups treated with hypMSC‐CM at a low dose (200 µL hypMSC‐CM with 2 g water‐based gel added) and a high dose (400 µL hypMSC‐CM with 2 g water‐based gel added) and a control group (2 g water‐based gel only). The IL‐10 and TGF‐β levels were examined by ELISA. The results showed a significant increase in IL‐10 levels on day 3 after hypMSC‐CM treatment, followed by a decrease in platelet‐derived growth factor (PDGF) levels on days 6 and 9. In line with this finding, the TGF‐β levels also increased significantly on day 3 and then linearly decreased on days 6 and 9. HypMSC‐CM administra‐ tion may thus promote wound healing acceleration by controlling IL‐10 and TGF‐β levels in a full‐thickness‐wound rat model.
{"title":"Hypoxic mesenchymal stem cell‐conditioned medium accelerates wound healing by regulating IL‐10 and TGF‐β levels in a full‐thickness‐wound rat model","authors":"Adi Muradi Muhar, Faizal Mukharim, Dedy Hermansyah, A. Putra, Nurul Hidayah, N. Amalina, I. Alif","doi":"10.22146/ijbiotech.63914","DOIUrl":"https://doi.org/10.22146/ijbiotech.63914","url":null,"abstract":"Full‐thickness wound healing is a complex process requiring a well‐orchestrated mechanism of various factors, including cytokines, particularly interleukin (IL)‐10 and transforming growth factor (TGF)‐β. IL‐10 and TGF‐β act as robust anti‐inflammatory cytokines in accelerating the wound healing process by regulating myofibroblasts. Hypoxic mesenchymal stem cell‐conditioned medium (hypMSC‐CM) containing cytokines potentially contribute to accelerate wound repair without scarring through the paracrine mechanism. This study aims to observe the role of hypMSC‐CM in controlling TGF‐β and IL‐10 levels to accelerate full‐thickness wound repair and regeneration. A total of 24 male Wistar rats were used in this study. Six healthy rats as a sham group and 18 rats were created as full‐thickness‐wound animal models using a 6 mm punch biopsy. The animals were randomly assigned into three groups (n = 6) consisting of two treatment groups treated with hypMSC‐CM at a low dose (200 µL hypMSC‐CM with 2 g water‐based gel added) and a high dose (400 µL hypMSC‐CM with 2 g water‐based gel added) and a control group (2 g water‐based gel only). The IL‐10 and TGF‐β levels were examined by ELISA. The results showed a significant increase in IL‐10 levels on day 3 after hypMSC‐CM treatment, followed by a decrease in platelet‐derived growth factor (PDGF) levels on days 6 and 9. In line with this finding, the TGF‐β levels also increased significantly on day 3 and then linearly decreased on days 6 and 9. HypMSC‐CM administra‐ tion may thus promote wound healing acceleration by controlling IL‐10 and TGF‐β levels in a full‐thickness‐wound rat model.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44183714","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 : 2022-12-30DOI: 10.22146/ijbiotech.73476
N. T. Mai, Thi Van Anh Le, B. C. Nguyen, Nguyen Ha Trang Le, Quang Minh Do
Hairy roots are widely known as a biological system for the production of highly diverse biomolecules. β‐carotene – a precursor for vitamin A – is known to be an anti‐oxidant and anti‐gastric cancer and protection agent against cardiovascular disease, heart disease and stroke. β‐carotene has been chemically synthesised and consumed by humans. However, the chemical process often produces a by‐product that may be harmful to human health. Therefore, this study established a protocol to induce hairy roots (HRs) from a Vietnamese carrot variety and produce natural β‐carotene. The Rhizobium rhizogenes ATCC15834 harbouring Ri plasmid and a Vietnamese carrot variety were used as materials for genetic transformation and HR induction studies. The result showed that approximately 50 HR lines were obtained. Culture medium supplemented with 30 mg/L of sucrose that gave the highest biomass of HR was shown in carrot HR line 30, which had a doubling time of 6.5 days. The highest content of β‐carotene extraction, at 128 mg/100g hairy roots, was achieved with a ratio volume (v/v) of 2‐propanol and plant samples of 20:1, followed by two hours’ incubation with 2‐propanol at 60 °C. Our study reveals a highly efficient protocol for Vietnamese carrot hairy root establishment and multiplication. A very efficient protocol for β‐carotene extraction from the hairy root was established to produce natural β‐carotene that achieves the same β‐carotene quantity as that produced by normal roots. This study provides new insight into the production of high‐content and natural β‐carotene for therapeutic application.
{"title":"Carrot hairy roots (Daucus carota L.) characterisation and optimisation for high β‐carotene extraction","authors":"N. T. Mai, Thi Van Anh Le, B. C. Nguyen, Nguyen Ha Trang Le, Quang Minh Do","doi":"10.22146/ijbiotech.73476","DOIUrl":"https://doi.org/10.22146/ijbiotech.73476","url":null,"abstract":"Hairy roots are widely known as a biological system for the production of highly diverse biomolecules. β‐carotene – a precursor for vitamin A – is known to be an anti‐oxidant and anti‐gastric cancer and protection agent against cardiovascular disease, heart disease and stroke. β‐carotene has been chemically synthesised and consumed by humans. However, the chemical process often produces a by‐product that may be harmful to human health. Therefore, this study established a protocol to induce hairy roots (HRs) from a Vietnamese carrot variety and produce natural β‐carotene. The Rhizobium rhizogenes ATCC15834 harbouring Ri plasmid and a Vietnamese carrot variety were used as materials for genetic transformation and HR induction studies. The result showed that approximately 50 HR lines were obtained. Culture medium supplemented with 30 mg/L of sucrose that gave the highest biomass of HR was shown in carrot HR line 30, which had a doubling time of 6.5 days. The highest content of β‐carotene extraction, at 128 mg/100g hairy roots, was achieved with a ratio volume (v/v) of 2‐propanol and plant samples of 20:1, followed by two hours’ incubation with 2‐propanol at 60 °C. Our study reveals a highly efficient protocol for Vietnamese carrot hairy root establishment and multiplication. A very efficient protocol for β‐carotene extraction from the hairy root was established to produce natural β‐carotene that achieves the same β‐carotene quantity as that produced by normal roots. This study provides new insight into the production of high‐content and natural β‐carotene for therapeutic application.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45089616","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 : 2022-12-30DOI: 10.22146/ijbiotech.66680
D. R. A. Daning, Budi Prasetyo Widyobroto, L. M. Yusiati, C. Hanim
The study aimed to evaluate the effect of administering galangal essential oil (EO) on the abundance of rumen bacteria using the 16s rRNA method. The treatments included a control (no EO addition), galangal EO (30, 60, 120 µL), and cineole (5 µL). The treatments were assessed using a 48‐hour in vitro batch culture of rumen fluid containing a 60:40 ratio of forage to concentrate. For amplification of the prokaryotes (bacteria and archaea) in region V4, 16s rRNA primer 5’GTGCCAGCMGCCGCGTAA, GGACTACHVGGGTWTCTAAT3’ was employed. The data for rumen microbial abundance were analysed descriptively, while the data for rumen microbial diversity were obtained from the report on the Next Generation Sequencing Method. The microbial composition of each sample was tested for operational taxonomic units (OTUs) with a 97% identity rate on a valid label. The 16S rRNA gene sequencing yielded a total of 3,977 OTUs. Adding galangal and cineole EOs resulted in the same variation of the Shannon index. The population index (chao1 index) was highest when 60 µL of galangal EO was added, compared to 30 and 120 µL of galangal EO and cineole. In addition, providing 60 µL of galangal EO decreased the abundance of Prevotella ruminicola compared to the control and cineole doses. The addition of galangal EO also led to a decline in the number of Methanobacteriales. The population of the fibre‐degrading bacteria group (Ruminococcus albus and Ruminococcus flavefaciens) was higher in a dose of galangal EO than the control and cineole. Therefore, it can be concluded that the effective dose of galangal EO, i.e. 60 µL/300 mg (DM feed) in vitro, can reduce the abundance of Prevotella bacteria and methanogens.
{"title":"Effect of galangal essential oils on rumen microbial population and biodiversity on in vitro rumen fermentation","authors":"D. R. A. Daning, Budi Prasetyo Widyobroto, L. M. Yusiati, C. Hanim","doi":"10.22146/ijbiotech.66680","DOIUrl":"https://doi.org/10.22146/ijbiotech.66680","url":null,"abstract":"The study aimed to evaluate the effect of administering galangal essential oil (EO) on the abundance of rumen bacteria using the 16s rRNA method. The treatments included a control (no EO addition), galangal EO (30, 60, 120 µL), and cineole (5 µL). The treatments were assessed using a 48‐hour in vitro batch culture of rumen fluid containing a 60:40 ratio of forage to concentrate. For amplification of the prokaryotes (bacteria and archaea) in region V4, 16s rRNA primer 5’GTGCCAGCMGCCGCGTAA, GGACTACHVGGGTWTCTAAT3’ was employed. The data for rumen microbial abundance were analysed descriptively, while the data for rumen microbial diversity were obtained from the report on the Next Generation Sequencing Method. The microbial composition of each sample was tested for operational taxonomic units (OTUs) with a 97% identity rate on a valid label. The 16S rRNA gene sequencing yielded a total of 3,977 OTUs. Adding galangal and cineole EOs resulted in the same variation of the Shannon index. The population index (chao1 index) was highest when 60 µL of galangal EO was added, compared to 30 and 120 µL of galangal EO and cineole. In addition, providing 60 µL of galangal EO decreased the abundance of Prevotella ruminicola compared to the control and cineole doses. The addition of galangal EO also led to a decline in the number of Methanobacteriales. The population of the fibre‐degrading bacteria group (Ruminococcus albus and Ruminococcus flavefaciens) was higher in a dose of galangal EO than the control and cineole. Therefore, it can be concluded that the effective dose of galangal EO, i.e. 60 µL/300 mg (DM feed) in vitro, can reduce the abundance of Prevotella bacteria and methanogens.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44318660","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 : 2022-12-30DOI: 10.22146/ijbiotech.68800
Novi Tri Astuti, P. Novitasari, R. Tjandrawinata, A. Nugroho, S. Pramono
Andrographolide has been shown to have a pharmacological effect as an antidiabetic. Nevertheless, the comprehensive mechanism of action has yet to be determined. Andrographolide is a primary component of the sambiloto herb (Andrographis paniculata (Burm.f.) Nees), in which a simple isolation process can obtain high yields. This study aimed to explain the anti‐diabetic effect of andrographolide compared to pioglitazone (a positive control) on glucose uptake by measuring the expression levels of peroxisome proliferator‐activated receptor gamma (PPARγ) and glucose transporter type 4 (GLUT‐4) genes in 3T3‐LI mouse adipocytes as an in vitro model. The differentiation of mature adipocytes from 3T3‐L1 fibroblasts was induced with 3‐isobutyl‐1‐methylxanthine, dexamethasone, and insulin. Andrographolide was provided through direct isolation from A. paniculata herbs. The gene expression was detected using the reverse transcription‐polymerase chain reaction (RT‐PCR). Pioglitazone and andrographolide significantly increased glucose uptake capability. Andrographolide was able to increase the mRNA levels of PPARγ and GLUT‐4 compared to pioglitazone with the best concentration at 5.6 µM. In conclusion, andrographolide can improve glucose uptake by increasing mRNA levels of PPARγ and GLUT‐4 that encodes protein, which are key factors for glucose homeostasis. Therefore, this finding further establishes the potency of andrographolide from A. paniculata as an antidiabetic.
{"title":"Anti‐diabetic effect of andrographolide from Sambiloto herbs (Andrographis paniculata (Burm.f.) Nees) through the expression of PPARγ and GLUT‐4 in adipocytes","authors":"Novi Tri Astuti, P. Novitasari, R. Tjandrawinata, A. Nugroho, S. Pramono","doi":"10.22146/ijbiotech.68800","DOIUrl":"https://doi.org/10.22146/ijbiotech.68800","url":null,"abstract":"Andrographolide has been shown to have a pharmacological effect as an antidiabetic. Nevertheless, the comprehensive mechanism of action has yet to be determined. Andrographolide is a primary component of the sambiloto herb (Andrographis paniculata (Burm.f.) Nees), in which a simple isolation process can obtain high yields. This study aimed to explain the anti‐diabetic effect of andrographolide compared to pioglitazone (a positive control) on glucose uptake by measuring the expression levels of peroxisome proliferator‐activated receptor gamma (PPARγ) and glucose transporter type 4 (GLUT‐4) genes in 3T3‐LI mouse adipocytes as an in vitro model. The differentiation of mature adipocytes from 3T3‐L1 fibroblasts was induced with 3‐isobutyl‐1‐methylxanthine, dexamethasone, and insulin. Andrographolide was provided through direct isolation from A. paniculata herbs. The gene expression was detected using the reverse transcription‐polymerase chain reaction (RT‐PCR). Pioglitazone and andrographolide significantly increased glucose uptake capability. Andrographolide was able to increase the mRNA levels of PPARγ and GLUT‐4 compared to pioglitazone with the best concentration at 5.6 µM. In conclusion, andrographolide can improve glucose uptake by increasing mRNA levels of PPARγ and GLUT‐4 that encodes protein, which are key factors for glucose homeostasis. Therefore, this finding further establishes the potency of andrographolide from A. paniculata as an antidiabetic.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44546373","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 : 2022-12-30DOI: 10.22146/ijbiotech.73930
A. Kadi, U. Bagale, I. Potoroko
Many earlier studies have documented pasteurization problems in the dairy industry. As a result, ultrasonic processing has been researched as a non‐heat alternative to pasteurization. In this study, milk‐based soft cheese was treated using various sonication times (0, 1, and 3 min) at a set frequency (22 kHz) with an amplitude of 60% of 630 W and different ripening periods (0, 15, 30, and 60 days) in brine (15%), stored at 4 °C, to reduce heat treatment and increase yield. The physicochemical parameters of white cheeses were examined over next 60 days and compared with a control cheese. The result showed that ultrasound had no significant effect on the cheeses in terms of their fat and protein content on storage. Compared to the control sample, ultrasound treatment improved the taste and aroma ratings due to increased lipolysis and proteolysis. In terms of overall acceptability, the ultra‐filtrate cheese sonicated for 3 min received the highest marks compared to the control. Sonication for 3 min treated fresh milk showed the maximum yield (190.5 g/L milk) compared to untreated raw milk yields (150.32 g/L).
{"title":"The effect of ultrasonic processing on physical and chemical properties of milk‐based soft, brine cheese","authors":"A. Kadi, U. Bagale, I. Potoroko","doi":"10.22146/ijbiotech.73930","DOIUrl":"https://doi.org/10.22146/ijbiotech.73930","url":null,"abstract":"Many earlier studies have documented pasteurization problems in the dairy industry. As a result, ultrasonic processing has been researched as a non‐heat alternative to pasteurization. In this study, milk‐based soft cheese was treated using various sonication times (0, 1, and 3 min) at a set frequency (22 kHz) with an amplitude of 60% of 630 W and different ripening periods (0, 15, 30, and 60 days) in brine (15%), stored at 4 °C, to reduce heat treatment and increase yield. The physicochemical parameters of white cheeses were examined over next 60 days and compared with a control cheese. The result showed that ultrasound had no significant effect on the cheeses in terms of their fat and protein content on storage. Compared to the control sample, ultrasound treatment improved the taste and aroma ratings due to increased lipolysis and proteolysis. In terms of overall acceptability, the ultra‐filtrate cheese sonicated for 3 min received the highest marks compared to the control. Sonication for 3 min treated fresh milk showed the maximum yield (190.5 g/L milk) compared to untreated raw milk yields (150.32 g/L).","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48437940","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 : 2022-12-30DOI: 10.22146/ijbiotech.66103
Wahyu Irawati, C. Tahya, Greisnaningsi Greisnaningsi
Copper pollution in Cisadane is a serious environmental issue that needs to be resolved immediately due to its negative impacts on river ecosystems. Bioremediation utilising indigenous bacteria offers excellent potential to restore copper‐contaminated river water. This study aimed to obtain indigenous copper‐resistant bacteria isolated from the Cisadane River as copper bioremediation agents. Bacteria from Cisadane River water samples were isolated by the spread plate method on Luria Bertani medium containing 3 mM CuSO4. Resistance was determined based on the minimum inhibitory concentration value, while copper concentration was measured using an atomic absorption spec‐ trophotometer. The results presented a total of 13 bacterial isolates with a minimum inhibitory concentration of up to 8 mM CuSO4. Sequence alignment analysis was performed on three selected copper‐resistant bacteria, i.e. isolate IrCis1, IrCis4 and IrCis13, which were identified as Pantoea agglomerans, Klebsiella pneumoniae and Shigella flexneri based on 16S rRNA, respectively. Each isolate accumulated copper at 1.19 mg, 1.34 mg and 0.92 mg/g DW of cells, with copper biosorption potentials of 73.74%, 70.17% and 67.73%, respectively. In conclusion, P. agglomerans strain IrCis1, K. pneu‐ moniae strain IrCis4 and S. flexneri strain IrCis5 isolated from the Cisadane River can be used as copper bioremediation agents.
{"title":"Pantoea agglomerans, Klebsiella pneumoniae, and Shigella flexneri isolated from the Cisadane River as multiresistant bacteria to copper and dyes","authors":"Wahyu Irawati, C. Tahya, Greisnaningsi Greisnaningsi","doi":"10.22146/ijbiotech.66103","DOIUrl":"https://doi.org/10.22146/ijbiotech.66103","url":null,"abstract":"Copper pollution in Cisadane is a serious environmental issue that needs to be resolved immediately due to its negative impacts on river ecosystems. Bioremediation utilising indigenous bacteria offers excellent potential to restore copper‐contaminated river water. This study aimed to obtain indigenous copper‐resistant bacteria isolated from the Cisadane River as copper bioremediation agents. Bacteria from Cisadane River water samples were isolated by the spread plate method on Luria Bertani medium containing 3 mM CuSO4. Resistance was determined based on the minimum inhibitory concentration value, while copper concentration was measured using an atomic absorption spec‐ trophotometer. The results presented a total of 13 bacterial isolates with a minimum inhibitory concentration of up to 8 mM CuSO4. Sequence alignment analysis was performed on three selected copper‐resistant bacteria, i.e. isolate IrCis1, IrCis4 and IrCis13, which were identified as Pantoea agglomerans, Klebsiella pneumoniae and Shigella flexneri based on 16S rRNA, respectively. Each isolate accumulated copper at 1.19 mg, 1.34 mg and 0.92 mg/g DW of cells, with copper biosorption potentials of 73.74%, 70.17% and 67.73%, respectively. In conclusion, P. agglomerans strain IrCis1, K. pneu‐ moniae strain IrCis4 and S. flexneri strain IrCis5 isolated from the Cisadane River can be used as copper bioremediation agents.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46742589","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 : 2022-12-30DOI: 10.22146/ijbiotech.71643
Deasy Widiana, Sotharith Phon, A. Ningrum, L. D. Witasari
Amylases are considered the most essential enzymes in biotechnology since they are widely utilized in the textile, food processing, and detergent industries. It is necessary to explore extracellular enzymatic activity in several microorganisms to discover a new potential application from amylases. In a previous study, thermophilic bacteria Geobacillus sp. DS3 isolated from Sikidang Crater, Dieng Plateau, Central Java, Indonesia showed amylase activity in starch medium at 70 °C. This study aimed to purify and characterize the thermostable alpha‐amylase from Geobacillus sp. DS3. The alpha‐amylase was produced and purified using ammonium sulfate and DEAE Sephadex A‐25 column. The enzyme activity was determined using the 3,5‐dinitrosalicylic acid (DNS) method. Geobacillus sp. DS3 optimally produced the alpha‐amylase at 60 °C for 15 h. The alpha‐amylase exhibited high enzymatic activity in 40–60% saturated ammonium sulfate extract. The molecular weight of the enzyme was estimated to be 58 kDa. The thermostable alpha‐amylase showed activity at the optimum temperature of 50 °C in 200 mM sodium phosphate buffer pH 7.0. The enzyme was inhibited by EDTA, PMSF, 2‐ME, and mostly by HgCl2. The Km and Vmax of the pure enzyme were 235.43 mM and 1428.57 U/mL, respectively. The result suggested that the purified thermostable alpha‐amylase from Geobacillus sp. DS3 offers potential application in areas of the food industry, such as the bakery industry.
{"title":"Purification and characterization of thermostable alpha‐amylase from Geobacillus sp. DS3 from Sikidang Crater, Central Java, Indonesia","authors":"Deasy Widiana, Sotharith Phon, A. Ningrum, L. D. Witasari","doi":"10.22146/ijbiotech.71643","DOIUrl":"https://doi.org/10.22146/ijbiotech.71643","url":null,"abstract":"Amylases are considered the most essential enzymes in biotechnology since they are widely utilized in the textile, food processing, and detergent industries. It is necessary to explore extracellular enzymatic activity in several microorganisms to discover a new potential application from amylases. In a previous study, thermophilic bacteria Geobacillus sp. DS3 isolated from Sikidang Crater, Dieng Plateau, Central Java, Indonesia showed amylase activity in starch medium at 70 °C. This study aimed to purify and characterize the thermostable alpha‐amylase from Geobacillus sp. DS3. The alpha‐amylase was produced and purified using ammonium sulfate and DEAE Sephadex A‐25 column. The enzyme activity was determined using the 3,5‐dinitrosalicylic acid (DNS) method. Geobacillus sp. DS3 optimally produced the alpha‐amylase at 60 °C for 15 h. The alpha‐amylase exhibited high enzymatic activity in 40–60% saturated ammonium sulfate extract. The molecular weight of the enzyme was estimated to be 58 kDa. The thermostable alpha‐amylase showed activity at the optimum temperature of 50 °C in 200 mM sodium phosphate buffer pH 7.0. The enzyme was inhibited by EDTA, PMSF, 2‐ME, and mostly by HgCl2. The Km and Vmax of the pure enzyme were 235.43 mM and 1428.57 U/mL, respectively. The result suggested that the purified thermostable alpha‐amylase from Geobacillus sp. DS3 offers potential application in areas of the food industry, such as the bakery industry.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47002909","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 : 2022-09-30DOI: 10.22146/ijbiotech.69212
F. Nadifah, W. Artama, B. Daryono, E. Retnaningrum
Standard microbiological culture techniques can only identify a fraction of the urogenital microbiome. Meanwhile, identifying and characterizing infectious microorganisms are very important for the success of diagnosis and treatments, especially for Urinary Tract Infection (UTI) patients. This study aimed to characterize the urogenital microbiome of UTI patients using 16S rRNA gene sequencing. We sequenced two pooled DNA samples from voided urine of UTI patients (21 females and 13 males). To determine the structure and composition of taxa in the samples, 16S rRNA gene sequencing was performed using the Illumina Mi‐Seq paired‐end platform. The most abundant genera were Burkholderia‐Caballeronia‐Paraburkholderia (71%) followed by Prevotella (33%), Escherichia‐Shigella (24%), Klebsiella (23%) and Sneathia (10%). The female microbiome was dominated by Prevotella bivia (28%), Escherichia coli (24%), Sneathia sanguinegens (7%) and Klebsiella pneumoniae (4%). On the other hand, the male microbiome was dominated by K. pneumoniae (23%) and E. coli (2%). K. pneumoniae and E. coli were the most abundant species found in both microbiomes. The 16S rRNA gene sequencing used in this study successfully uncovered the composition of the urogenital microbiome, which might not have been possible with conventional culture methods.
标准的微生物培养技术只能识别一小部分的泌尿生殖微生物组。同时，感染微生物的识别和表征对诊断和治疗的成功至关重要，特别是对尿路感染(UTI)患者。本研究旨在利用16S rRNA基因测序来表征尿路感染患者的泌尿生殖微生物组。我们对来自尿路感染患者(21名女性和13名男性)的两份合并DNA样本进行了测序。为了确定样品中分类群的结构和组成，使用Illumina Mi - Seq配对端平台进行16S rRNA基因测序。最丰富的属为伯克霍尔德菌属-卡瓦隆菌属-副伯克霍尔德菌属(71%)，其次为普雷沃氏菌属(33%)、埃希氏菌属-志贺氏菌属(24%)、克雷伯氏菌属(23%)和Sneathia属(10%)。雌性微生物群以毕氏普雷沃氏菌(28%)、大肠杆菌(24%)、血奈瑟菌(7%)和肺炎克雷伯菌(4%)为主。另一方面，男性微生物组以肺炎克雷伯菌(23%)和大肠杆菌(2%)为主。肺炎克雷伯菌和大肠杆菌是两个微生物组中最丰富的物种。本研究中使用的16S rRNA基因测序成功地揭示了泌尿生殖微生物组的组成，这可能是传统培养方法无法实现的。
{"title":"Characterization of the urogenital microbiome in patients with urinary tract infections","authors":"F. Nadifah, W. Artama, B. Daryono, E. Retnaningrum","doi":"10.22146/ijbiotech.69212","DOIUrl":"https://doi.org/10.22146/ijbiotech.69212","url":null,"abstract":"Standard microbiological culture techniques can only identify a fraction of the urogenital microbiome. Meanwhile, identifying and characterizing infectious microorganisms are very important for the success of diagnosis and treatments, especially for Urinary Tract Infection (UTI) patients. This study aimed to characterize the urogenital microbiome of UTI patients using 16S rRNA gene sequencing. We sequenced two pooled DNA samples from voided urine of UTI patients (21 females and 13 males). To determine the structure and composition of taxa in the samples, 16S rRNA gene sequencing was performed using the Illumina Mi‐Seq paired‐end platform. The most abundant genera were Burkholderia‐Caballeronia‐Paraburkholderia (71%) followed by Prevotella (33%), Escherichia‐Shigella (24%), Klebsiella (23%) and Sneathia (10%). The female microbiome was dominated by Prevotella bivia (28%), Escherichia coli (24%), Sneathia sanguinegens (7%) and Klebsiella pneumoniae (4%). On the other hand, the male microbiome was dominated by K. pneumoniae (23%) and E. coli (2%). K. pneumoniae and E. coli were the most abundant species found in both microbiomes. The 16S rRNA gene sequencing used in this study successfully uncovered the composition of the urogenital microbiome, which might not have been possible with conventional culture methods.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42812115","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 : 2022-09-30DOI: 10.22146/ijbiotech.68040
Musawira Musawira, S. Suharsono, M. Miftahudin, A. Tjahjoleksono
Potato ( Solanum tuberosum L.) cultivar IPB CP1 is suitable as a raw material for the potato chip industry. Potato plants are sensitive to various abiotic stresses such as drought, aluminium and salinity, which induce reactive oxygen species (ROS). ROS is very toxic to plant cells. Superoxide dismutase (SOD) is one of the enzymes that catalyse ROS to H2O2 and O2. This study aimed to establish transgenic potato cv. IPB CP1 plants containing the MmCuZn‐SOD gene that are tolerant to various abiotic stresses. Genetic transformation using internodes without buds as explants produced putative transgenic potato with a transformation efficiency of 51.25% and a regeneration efficiency of 38.87%. Integration analysis of the MmCuZn‐SOD transgene in putative transgenic plants by polymerase chain reaction (PCR) with a set of specific primers showed that eight plants contained the MmCuZn‐SOD gene under the control of the 35S CaMV promoter. In vitro salinity stress, aluminium stress, and drought stress assays showed that transgenic plants had a higher number of roots and total root length than non‐transgenic ones. These results indicate that transgenic potato cv. IPB CP1 plants are more tolerant to abiotic stresses than non‐transgenic ones.
{"title":"Establishment of transgenic potato cultivar IPB CP1 plants containing gene encoding for superoxide dismutase to increase the abiotic stress tolerance","authors":"Musawira Musawira, S. Suharsono, M. Miftahudin, A. Tjahjoleksono","doi":"10.22146/ijbiotech.68040","DOIUrl":"https://doi.org/10.22146/ijbiotech.68040","url":null,"abstract":"Potato ( Solanum tuberosum L.) cultivar IPB CP1 is suitable as a raw material for the potato chip industry. Potato plants are sensitive to various abiotic stresses such as drought, aluminium and salinity, which induce reactive oxygen species (ROS). ROS is very toxic to plant cells. Superoxide dismutase (SOD) is one of the enzymes that catalyse ROS to H2O2 and O2. This study aimed to establish transgenic potato cv. IPB CP1 plants containing the MmCuZn‐SOD gene that are tolerant to various abiotic stresses. Genetic transformation using internodes without buds as explants produced putative transgenic potato with a transformation efficiency of 51.25% and a regeneration efficiency of 38.87%. Integration analysis of the MmCuZn‐SOD transgene in putative transgenic plants by polymerase chain reaction (PCR) with a set of specific primers showed that eight plants contained the MmCuZn‐SOD gene under the control of the 35S CaMV promoter. In vitro salinity stress, aluminium stress, and drought stress assays showed that transgenic plants had a higher number of roots and total root length than non‐transgenic ones. These results indicate that transgenic potato cv. IPB CP1 plants are more tolerant to abiotic stresses than non‐transgenic ones.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48355535","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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