Pub Date : 2023-06-27DOI: 10.22146/ijbiotech.79105
M. Shafeeq
This study aims to establish an aqueous extract of Chlorella vulgaris as a green factory to manufacture titanium nanoparticles and to apply these nanoparticles to control the house flies (Musca domestica). Since the crystallite size of prepared titanium nanoparticles was 27.39 nm. Furthermore, the observed size for bulk particles ranged (from 92.33-249.6) nm through SEM. While for nanocrystalline the size ranged (from 9.395- 206) nm. Several phytochemicals were detected within algal extracts such as phenols, tannins, alkaloids, flavonoids, resins, and saponins. All these active compounds participated in nano-synthesis by acting as reducing and stabilizing agents. finally, titanium nanoparticles were used as a controlling agent against house flies (Musca domestica) and compared with traditional insecticides (Imidacloprid). High mortality percentages reached 100% against 1st larval stage, 70% against 3rd larval stage, and 93.3% in adult flies. These fatalities were higher after using Imidacloprid for all tested stages. Many phenotypic distortions were also caught in houseflies treated with TiO2 NPs prepared by Chlorella, such as; failure in pupal emergence and maturity, incomplete development in the head, legs, and wings, and disappearance in genital organs. It has shown that Chlorella Vulgaris is a good candidate for nanomanufacturing and a rich naturally derived Nanopesticide.
{"title":"Manufacturing of an effective, eco-friendly nano insecticide with aiding of green alga Chlorella vulgaris in contrast with the traditional insecticide.","authors":"M. Shafeeq","doi":"10.22146/ijbiotech.79105","DOIUrl":"https://doi.org/10.22146/ijbiotech.79105","url":null,"abstract":"This study aims to establish an aqueous extract of Chlorella vulgaris as a green factory to manufacture titanium nanoparticles and to apply these nanoparticles to control the house flies (Musca domestica). Since the crystallite size of prepared titanium nanoparticles was 27.39 nm. Furthermore, the observed size for bulk particles ranged (from 92.33-249.6) nm through SEM. While for nanocrystalline the size ranged (from 9.395- 206) nm. Several phytochemicals were detected within algal extracts such as phenols, tannins, alkaloids, flavonoids, resins, and saponins. All these active compounds participated in nano-synthesis by acting as reducing and stabilizing agents. finally, titanium nanoparticles were used as a controlling agent against house flies (Musca domestica) and compared with traditional insecticides (Imidacloprid). High mortality percentages reached 100% against 1st larval stage, 70% against 3rd larval stage, and 93.3% in adult flies. These fatalities were higher after using Imidacloprid for all tested stages. Many phenotypic distortions were also caught in houseflies treated with TiO2 NPs prepared by Chlorella, such as; failure in pupal emergence and maturity, incomplete development in the head, legs, and wings, and disappearance in genital organs. It has shown that Chlorella Vulgaris is a good candidate for nanomanufacturing and a rich naturally derived Nanopesticide.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41951588","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 : 2023-06-27DOI: 10.22146/ijbiotech.83595
A. Purwantoro, A. Setiawan, Rikcy Setiaji Nugraha, Sairoh Bisirotil Mujtaba, A. H. Setyadi
Dendrobium is the second largest genus in the Orchidaceae family. Dendrobium section Spatulata is widely cultivated in Indonesia due to its ease of cultivation, high economic value and adaptability, and extended flower shelf life. In this study, we have conducted a breeding program for developing new cultivar of Dendrobium section Spatulata through interspecific hybridization. This study is aimed to investigate the genetic variation and genomic constitution of the eight hybrids and their corresponding parental lines resulted from interspecific hybridization using SRAP markers. Dendrobium section Spatulata hybrids produced by interspecific hybridization are genuine hybrids with substantial genetic variability based on flower morphology, including labellum shapes and color intensities, as well as curly horn shapes and color intensities. The SRAP marker, which was utilized to genotype the hybrid and parental lines, exhibited a significant degree of polymorphism, and may be used to distinguish each accession. The UPGMA dendrogram and PCoA biplot showed that all the hybrids were grouped with their corresponding parental lines based on their genetic background and genomic constitution. These findings are critical for genetic improvement of the Spatulata orchid to develop novel varieties.
{"title":"Genetic Variation and Genomic Constitution in The Spatulata Orchid Hybrids (Dendrobium spp.) Derived from Interspecific Hybridization Using SRAP marker","authors":"A. Purwantoro, A. Setiawan, Rikcy Setiaji Nugraha, Sairoh Bisirotil Mujtaba, A. H. Setyadi","doi":"10.22146/ijbiotech.83595","DOIUrl":"https://doi.org/10.22146/ijbiotech.83595","url":null,"abstract":"Dendrobium is the second largest genus in the Orchidaceae family. Dendrobium section Spatulata is widely cultivated in Indonesia due to its ease of cultivation, high economic value and adaptability, and extended flower shelf life. In this study, we have conducted a breeding program for developing new cultivar of Dendrobium section Spatulata through interspecific hybridization. This study is aimed to investigate the genetic variation and genomic constitution of the eight hybrids and their corresponding parental lines resulted from interspecific hybridization using SRAP markers. Dendrobium section Spatulata hybrids produced by interspecific hybridization are genuine hybrids with substantial genetic variability based on flower morphology, including labellum shapes and color intensities, as well as curly horn shapes and color intensities. The SRAP marker, which was utilized to genotype the hybrid and parental lines, exhibited a significant degree of polymorphism, and may be used to distinguish each accession. The UPGMA dendrogram and PCoA biplot showed that all the hybrids were grouped with their corresponding parental lines based on their genetic background and genomic constitution. These findings are critical for genetic improvement of the Spatulata orchid to develop novel varieties.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43122674","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 : 2023-06-27DOI: 10.22146/ijbiotech.78420
Y. Manuhara, D. Y. Kusuma, A. Kristanti
Adventitious root culture and the development of a bioreactor are methods to obtain biomass and plant bioactive compounds in large quantities faster than conventional plant cultivation. These technologies provide an excellent opportunity to produce biomass and bioactive compounds from plants, especially Gynura procumbens. Previous reports mentioned a small-scale bioreactor could increase biomass and bioactive compounds of G. procumbens adventitious roots. Therefore, a larger bioreactor for adventitious root culture is necessary to develop. In this study, the development of the 19 L pilot bioreactor was successful. The optimal condition for bioreactor sterilization is 1.8 bar for 60 min using an autoclave. We found that G. procumbens adventitious roots culture in pilot bioreactors has resulted in optimal biomass using MS-Tek media (technical grade) compared to MS-PA (pro analyze) media after 35 d of the culture period. Although, higher productivity of total phenolics and total flavonoids in G. procumbens roots has been achieved from MS-PA media rather than MS-Tek media. In further study, it is necessary to evaluate the effect of technical-grade chemicals on kinetics root growth and chemical uptake. The hope is to obtain a suitable media formulation with affordable cost for adventitious root culture production.
{"title":"Novel pilot bioreactor for scale up Gynura procumbens adventitious root culture","authors":"Y. Manuhara, D. Y. Kusuma, A. Kristanti","doi":"10.22146/ijbiotech.78420","DOIUrl":"https://doi.org/10.22146/ijbiotech.78420","url":null,"abstract":"Adventitious root culture and the development of a bioreactor are methods to obtain biomass and plant bioactive compounds in large quantities faster than conventional plant cultivation. These technologies provide an excellent opportunity to produce biomass and bioactive compounds from plants, especially Gynura procumbens. Previous reports mentioned a small-scale bioreactor could increase biomass and bioactive compounds of G. procumbens adventitious roots. Therefore, a larger bioreactor for adventitious root culture is necessary to develop. In this study, the development of the 19 L pilot bioreactor was successful. The optimal condition for bioreactor sterilization is 1.8 bar for 60 min using an autoclave. We found that G. procumbens adventitious roots culture in pilot bioreactors has resulted in optimal biomass using MS-Tek media (technical grade) compared to MS-PA (pro analyze) media after 35 d of the culture period. Although, higher productivity of total phenolics and total flavonoids in G. procumbens roots has been achieved from MS-PA media rather than MS-Tek media. In further study, it is necessary to evaluate the effect of technical-grade chemicals on kinetics root growth and chemical uptake. The hope is to obtain a suitable media formulation with affordable cost for adventitious root culture production.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47741451","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 : 2023-06-27DOI: 10.22146/ijbiotech.79642
Nisa Ul Hasanah, Ahmad Syauqy Tafrihani, Ummi Maryam Zulfin, D. Salsabila, Ratih Kurnia Wardani, Muthi’ Ikawati, E. Meiyanto, R. Jenie
Many chemotherapeutic agents cause various side effects, including nephrotoxicity. Doxorubicin, for example, increases the level of reactive oxygen species (ROS), leading to cell senescence in the kidneys. Cardamom essential oil (Amomum compactum Soland. ex Maton) contains compounds that exhibit antioxidant activity, such as 1.8-cineole, α-pinene, α-terpineol, and linalool. This study focused on exploring the potency of cardamom essential oil (CEO) as an anti-senescence induced by doxorubicin using Vero cells. CEO was obtained by steam distillation. The cytotoxic assay was carried out using trypan blue exclusion assay. We performed the 2',7'-dichlorodihydrofluorescein diacetate (DCFDA) staining and the senescence-associated beta-galactosidase (SA-β-gal) staining to measure the effect of CEO on intracellular ROS level and cell senescence, respectively. Analysis of the compounds with gas chromatography-mass spectrophotometry (GC-MS), revealed seven compounds with significant abundance, namely 1.8-cineole (50.82%), ß-pinene (12.43%), α-terpineol (8.50%), fenchone (4.10%), α-pinene (4.00%), sabinene (3.00%), and linalool (1.98%). The cytotoxicity assay of CEO on Vero cells showed an IC50 value of 178 μg/mL. Thus, the CEO is considered to be not cytotoxic and safe for normal kidney cells. Concentrations of 50 and 100 μg/mL reduced the senescence induced by doxorubicin. Therefore, the CEO has the potency as a nephroprotective agent in doxorubicin-induced senescence.
{"title":"Nephroprotective Effects of Cardamom Essential Oil (Amomum compactum Soland. Ex Maton) in Kidney Cells","authors":"Nisa Ul Hasanah, Ahmad Syauqy Tafrihani, Ummi Maryam Zulfin, D. Salsabila, Ratih Kurnia Wardani, Muthi’ Ikawati, E. Meiyanto, R. Jenie","doi":"10.22146/ijbiotech.79642","DOIUrl":"https://doi.org/10.22146/ijbiotech.79642","url":null,"abstract":"Many chemotherapeutic agents cause various side effects, including nephrotoxicity. Doxorubicin, for example, increases the level of reactive oxygen species (ROS), leading to cell senescence in the kidneys. Cardamom essential oil (Amomum compactum Soland. ex Maton) contains compounds that exhibit antioxidant activity, such as 1.8-cineole, α-pinene, α-terpineol, and linalool. This study focused on exploring the potency of cardamom essential oil (CEO) as an anti-senescence induced by doxorubicin using Vero cells. CEO was obtained by steam distillation. The cytotoxic assay was carried out using trypan blue exclusion assay. We performed the 2',7'-dichlorodihydrofluorescein diacetate (DCFDA) staining and the senescence-associated beta-galactosidase (SA-β-gal) staining to measure the effect of CEO on intracellular ROS level and cell senescence, respectively. Analysis of the compounds with gas chromatography-mass spectrophotometry (GC-MS), revealed seven compounds with significant abundance, namely 1.8-cineole (50.82%), ß-pinene (12.43%), α-terpineol (8.50%), fenchone (4.10%), α-pinene (4.00%), sabinene (3.00%), and linalool (1.98%). The cytotoxicity assay of CEO on Vero cells showed an IC50 value of 178 μg/mL. Thus, the CEO is considered to be not cytotoxic and safe for normal kidney cells. Concentrations of 50 and 100 μg/mL reduced the senescence induced by doxorubicin. Therefore, the CEO has the potency as a nephroprotective agent in doxorubicin-induced senescence. ","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48985604","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 : 2023-03-31DOI: 10.22146/ijbiotech.73649
W. Dewatisari, L. Nugroho, E. Retnaningrum, Y. A. Purwestri
Sansevieria trifasciata is a plant that is commonly utilized in traditional medicine. The leaves of S. trifasciata show antibacterial properties against Pseudomonas aeruginosa. This bacterium is an opportunistic pathogen that can cause serious illness in humans and produce a variety of virulence factors responsible for bacterial pathogenesis with quorum sensing (QS) systems that mediate intracellular communication. Bacteria produce protease through a QS mechanism in which they express signaling molecules to become pathogens. Proteases are extracellular enzymes required for successful infection that mediate biofilm spread through QS and regulate a variety of cellular and physiological functions. This research aimed to evaluate the protease, and anti‐QS activities of the ethanolic extract from S. trifasciata leaves against P. aeruginosa and the expression of QS genes. An azocasein test was used to determine the protease activity in qualitative and quantitative methods. Using real‐time quantitative polymerase chain reaction, a study was conducted to investigate the effect of ethanolic extract from S. trifasciata leaves on selected QS‐regulatory genes at the transcriptional level. The results showed that the potential ethanolic extract from S. trifasciata leaves inhibited the protease enzyme activity by as much as 77.1%. The potential ethanolic extract from S. trifasciata leaves decreased the expressions of lasA, lasB, lasI, lasR, rhlI, and rhlR with 2‐ΔΔCt values of 0.81, 0.93, 0.76, 0.97, 0.90, and 0.55 respectively.
{"title":"Inhibition of protease activity and anti‐quorum sensing of the potential fraction of ethanolic extract from Sansevieria trifasciata Prain leaves against Pseudomonas aeruginosa","authors":"W. Dewatisari, L. Nugroho, E. Retnaningrum, Y. A. Purwestri","doi":"10.22146/ijbiotech.73649","DOIUrl":"https://doi.org/10.22146/ijbiotech.73649","url":null,"abstract":"Sansevieria trifasciata is a plant that is commonly utilized in traditional medicine. The leaves of S. trifasciata show antibacterial properties against Pseudomonas aeruginosa. This bacterium is an opportunistic pathogen that can cause serious illness in humans and produce a variety of virulence factors responsible for bacterial pathogenesis with quorum sensing (QS) systems that mediate intracellular communication. Bacteria produce protease through a QS mechanism in which they express signaling molecules to become pathogens. Proteases are extracellular enzymes required for successful infection that mediate biofilm spread through QS and regulate a variety of cellular and physiological functions. This research aimed to evaluate the protease, and anti‐QS activities of the ethanolic extract from S. trifasciata leaves against P. aeruginosa and the expression of QS genes. An azocasein test was used to determine the protease activity in qualitative and quantitative methods. Using real‐time quantitative polymerase chain reaction, a study was conducted to investigate the effect of ethanolic extract from S. trifasciata leaves on selected QS‐regulatory genes at the transcriptional level. The results showed that the potential ethanolic extract from S. trifasciata leaves inhibited the protease enzyme activity by as much as 77.1%. The potential ethanolic extract from S. trifasciata leaves decreased the expressions of lasA, lasB, lasI, lasR, rhlI, and rhlR with 2‐ΔΔCt values of 0.81, 0.93, 0.76, 0.97, 0.90, and 0.55 respectively.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48950765","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 : 2023-03-31DOI: 10.22146/ijbiotech.77137
N‐acetylglucosamine (NAG) is the monomer product of chitin, which has been widely used as a bioactive com‐ pound in applications such as anti‐tumor, anti‐microbial, and antioxidant activities. In production, biological processes using enzymes are preferable to chemicals due to environmental issues. This study aims to determine the activity, purity level, and molecular weight of purified chitinase from Micromonospora sp. AR17 determines the concentration of NAG produced by purified chitinase that has been characterized. Chitinase was produced by fermentation in colloidal chitin broth at 40 °C, pH 7, for 7 days, while chitinase activity was checked every 24 h. The optimal fermentation time was used to produce chitinase for a further purification step. Enzyme purification was carried out by ultrafiltration, ammonium sulfate precipitation, ion exchange chromatography (Q Sepharose Fast Flow), and gel filtration (Sephacryl S‐300). The purified enzyme was then char‐ acterized for optimum time, pH, and temperature to produce NAG. The results suggested that the fourth day was the optimal time for chitinase production, with chitinase activity of 0.0040 U/mL and a NAG concentration of 7.62 µg/mL. The purifica‐ tion step successfully increased the purity by 6.82 times with chitinase‐specific activity at 1.4648 U/mg. Production of NAG with purified chitinase produced a NAG concentration of 32.472 µg/mL with an incubation time of 30 min at 40 °C and pH 7.
N-乙酰葡糖胺（NAG）是几丁质的单体产物，作为一种生物活性化合物，在抗肿瘤、抗微生物和抗氧化等方面得到了广泛应用。在生产中，由于环境问题，使用酶的生物工艺比化学工艺更可取。本研究旨在确定小单孢菌纯化几丁质酶的活性、纯度水平和分子量。AR17确定了纯化几丁质酶产生的NAG的浓度，该浓度已被表征。通过在40°C、pH 7的胶体几丁质肉汤中发酵7天来生产几丁质酶，同时每24小时检查一次几丁质酶活性。使用最佳发酵时间生产几丁质酶以进行进一步纯化步骤。通过超滤、硫酸铵沉淀、离子交换色谱（Q Sepharose Fast Flow）和凝胶过滤（Sephacryl S‐300）进行酶纯化。然后将纯化的酶在最佳时间、pH和温度下进行表征，以产生NAG。结果表明，第四天是产几丁质酶的最佳时间，几丁质酶活性为0.0040 U/mL，NAG浓度为7.62µg/mL。纯化步骤成功地将纯度提高了6.82倍，几丁质酶比活性为1.4648U/mg。用纯化的几丁质酶生产NAG产生的NAG浓度为32.472µg/mL，在40°C和pH 7下孵育30分钟。
{"title":"Production, purification and characterization of chitinase from Micromonospora sp. AR17","authors":"","doi":"10.22146/ijbiotech.77137","DOIUrl":"https://doi.org/10.22146/ijbiotech.77137","url":null,"abstract":"N‐acetylglucosamine (NAG) is the monomer product of chitin, which has been widely used as a bioactive com‐ pound in applications such as anti‐tumor, anti‐microbial, and antioxidant activities. In production, biological processes using enzymes are preferable to chemicals due to environmental issues. This study aims to determine the activity, purity level, and molecular weight of purified chitinase from Micromonospora sp. AR17 determines the concentration of NAG produced by purified chitinase that has been characterized. Chitinase was produced by fermentation in colloidal chitin broth at 40 °C, pH 7, for 7 days, while chitinase activity was checked every 24 h. The optimal fermentation time was used to produce chitinase for a further purification step. Enzyme purification was carried out by ultrafiltration, ammonium sulfate precipitation, ion exchange chromatography (Q Sepharose Fast Flow), and gel filtration (Sephacryl S‐300). The purified enzyme was then char‐ acterized for optimum time, pH, and temperature to produce NAG. The results suggested that the fourth day was the optimal time for chitinase production, with chitinase activity of 0.0040 U/mL and a NAG concentration of 7.62 µg/mL. The purifica‐ tion step successfully increased the purity by 6.82 times with chitinase‐specific activity at 1.4648 U/mg. Production of NAG with purified chitinase produced a NAG concentration of 32.472 µg/mL with an incubation time of 30 min at 40 °C and pH 7.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43292836","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 : 2023-03-31DOI: 10.22146/ijbiotech.75783
Adinda Fitri Salsabila, Abidah Tauchid, M. S. Rohman, D. Widianto, S. Margino
We noticed that the Priestia megaterium genome contains five Luciferase‐like monooxygenase (LLM) encoding genes, however, their functions are unknown. The objective of this work was to characterize the biophysical properties of the recombinant LLM2 from Priestia megaterium PSA10 through in vitro and in silico approaches. We successfully cloned into the pET vector system and expressed the recombinant LLM2 in Escherichia coli BL21(DE3). The recombinant LLM2 was overproduced and purified in the form of an inclusion body with a molecular weight of ±39.5 kDa when it was analyzed in 15% SDS‐PAGE. The inclusion body of recombinant LLM2 was then refolded and characterized for its biophysical properties by measuring the UV spectrum of 200 to 250 nm wavelength and determining the change of enthalpy (ΔH) and entropy (ΔS) at the melting temperature. The refolded recombinant LLM2 exhibited a strong spectrum at 205 nm, while the unfolded recombinant LLM2 did not. The Tm, ΔHTm, and ΔSTm values of the refolded recombinant LLM2 were determined to be 318.31±4.4 K, 11.76±1.3 kJ.mol‐1, and (3.74±0.48)x10‐2 kJ.mol‐1.K‐1, respectively. The predicted 3D structure of LLM2 showed that the protein contains the TIM‐barrel, resembling the common global fold of bacterial luciferases. Determination of the cofactor preference suggested that the LLM2 preferred FAD for its cofactor.
{"title":"Biophysical characterization of folded state type II luciferase‐like monooxygenase","authors":"Adinda Fitri Salsabila, Abidah Tauchid, M. S. Rohman, D. Widianto, S. Margino","doi":"10.22146/ijbiotech.75783","DOIUrl":"https://doi.org/10.22146/ijbiotech.75783","url":null,"abstract":"We noticed that the Priestia megaterium genome contains five Luciferase‐like monooxygenase (LLM) encoding genes, however, their functions are unknown. The objective of this work was to characterize the biophysical properties of the recombinant LLM2 from Priestia megaterium PSA10 through in vitro and in silico approaches. We successfully cloned into the pET vector system and expressed the recombinant LLM2 in Escherichia coli BL21(DE3). The recombinant LLM2 was overproduced and purified in the form of an inclusion body with a molecular weight of ±39.5 kDa when it was analyzed in 15% SDS‐PAGE. The inclusion body of recombinant LLM2 was then refolded and characterized for its biophysical properties by measuring the UV spectrum of 200 to 250 nm wavelength and determining the change of enthalpy (ΔH) and entropy (ΔS) at the melting temperature. The refolded recombinant LLM2 exhibited a strong spectrum at 205 nm, while the unfolded recombinant LLM2 did not. The Tm, ΔHTm, and ΔSTm values of the refolded recombinant LLM2 were determined to be 318.31±4.4 K, 11.76±1.3 kJ.mol‐1, and (3.74±0.48)x10‐2 kJ.mol‐1.K‐1, respectively. The predicted 3D structure of LLM2 showed that the protein contains the TIM‐barrel, resembling the common global fold of bacterial luciferases. Determination of the cofactor preference suggested that the LLM2 preferred FAD for its cofactor.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46277651","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 : 2023-03-31DOI: 10.22146/ijbiotech.49368
Audie Masola Putra, H. Nugrahapraja, F. Dwivany
Banana (Musa spp.) is one of the most widely consumed fruits in the world. Unfortunately, the plants are at risk from many disease problems, which mainly derive from microorganism. It is a little known about the relationship between disease‐inducing microorganisms and plants, particularly at the molecular level. This research aimed to characterize long non‐coding RNA (lncRNA) from bananas that may have roles in regulating gene expression related to the disease response mechanism in banana derived from transcriptomic libraries. Furthermore, the detected transcripts were analyzed to identify the endogenous target mimics (eTMs) interaction between lncRNA and microRNA (miRNA) using computational approaches. Data from Cavendish banana (AAA group), Berangan (AAA group), Yunnan Banana (Itinerans), Dajiao (ABB group), and Klutuk (BB group) were used in this research. We found that lncRNA tends to be unsustainable, and most sizes are below 1000 bp (≥ 75%). Based on this result, we investigated the eTMs to determine lncRNA transcripts and miRNA, such as miR397 in Cavendish and miR444 in Klutuk. This transcript would be regulated following exposure to extreme temperatures and disease, indicating the possibility of disease‐specific interaction between bananas and their environment at the molecular level.
{"title":"Revealing disease‐specific endogenous target mimic of microRNA from long non‐coding RNA identification and characterization in Musa spp.","authors":"Audie Masola Putra, H. Nugrahapraja, F. Dwivany","doi":"10.22146/ijbiotech.49368","DOIUrl":"https://doi.org/10.22146/ijbiotech.49368","url":null,"abstract":"Banana (Musa spp.) is one of the most widely consumed fruits in the world. Unfortunately, the plants are at risk from many disease problems, which mainly derive from microorganism. It is a little known about the relationship between disease‐inducing microorganisms and plants, particularly at the molecular level. This research aimed to characterize long non‐coding RNA (lncRNA) from bananas that may have roles in regulating gene expression related to the disease response mechanism in banana derived from transcriptomic libraries. Furthermore, the detected transcripts were analyzed to identify the endogenous target mimics (eTMs) interaction between lncRNA and microRNA (miRNA) using computational approaches. Data from Cavendish banana (AAA group), Berangan (AAA group), Yunnan Banana (Itinerans), Dajiao (ABB group), and Klutuk (BB group) were used in this research. We found that lncRNA tends to be unsustainable, and most sizes are below 1000 bp (≥ 75%). Based on this result, we investigated the eTMs to determine lncRNA transcripts and miRNA, such as miR397 in Cavendish and miR444 in Klutuk. This transcript would be regulated following exposure to extreme temperatures and disease, indicating the possibility of disease‐specific interaction between bananas and their environment at the molecular level.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42412914","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 : 2023-03-31DOI: 10.22146/ijbiotech.69073
Diego Mauricio Cano-Reinoso, Y. Purwanto, I. Budiastra, S. Kuroki, S. Sutrisno, S. Widodo
This study aimed to evaluate the aromatic characteristic of patchouli essential oil (Pogostemon cablin Benth.) by near‐infrared spectroscopy combined with chemometric treatments. The study used 84 oil samples collected from around Indonesia, namely in Konawe, Kolaka, Bogor, Garut, Aceh, Jambi, and Masamba. Several pretreatments were used to process the spectral data, together with the application of partial least squares. The spectrum wavelength applied was between 1000 and 2500 nm. The spectra data were separated to develop two models based on their physical and chemical properties (Bogor, Garut, Konawe, and Kolaka in the first model; Aceh, Jambi, and Masamba in the second one). Liquid chromatography‐mass spectrometry (LC‐MS) was used as a reference method. Patchouli alcohol was established as the main chemical compound of this aromatic oil. The best calibration for the first model was that with mean center normalization as a data pretreatment, while for the second model, it was the one using the second derivative. Both models had a correlation coefficient higher than 0.90 and a coefficient of variation lower than 2.98%. In conclusion, near‐infrared spectroscopy can be employed as an accurate tool to determine the characteristic of patchouli oil.
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The SARS‐CoV‐2 virus has been the cause of the global pandemic since the end of 2019. Since then, the virus has mutated to create different types of variants with numerous effects on those infected. This has complicated human intervention for prevention. Indonesia was heavily affected by the pandemic, specifically from May to August 2021, and as a country has recorded many distinct isolates. Thus, characterization of the virus strains from Indonesia is important. GISAID, NCBI BLAST, and MAFFT version 7 were used. There were 9,488 isolates in Indonesia as of November 2021, with the majority including the Delta variant. While most of the isolates have mutations common to those from other countries, there are some atypical ones, such as mutation V1264L in the Delta variant that was suspected to play a role in worsening the pandemic. The Delta variant had the most mutations in the spike protein when compared to the Alpha and Beta variants, giving it important roles in infectivity and vigorous entry into cells, with some general clinical manifestations like fever and sore throat; however, the severity of the Delta variant is attributable to its rapid growth. This is why, from May to November 2021 in Indonesia, cases of the Delta variant rocketed, unlike the other variants.
自2019年底以来，SARS - CoV - 2病毒一直是全球大流行的原因。从那以后，病毒发生了变异，产生了不同类型的变体，对感染者产生了多种影响。这使得人为干预预防变得复杂。印度尼西亚受到大流行的严重影响，特别是在2021年5月至8月期间，作为一个国家，印度尼西亚记录了许多不同的分离病例。因此，确定来自印度尼西亚的病毒株的特征是很重要的。使用GISAID、NCBI BLAST和matfft version 7。截至2021年11月，印度尼西亚有9488株分离株，其中大多数包括Delta变体。虽然大多数分离株具有与来自其他国家的分离株相同的突变，但也有一些非典型的突变，例如Delta变体中的V1264L突变，该突变被怀疑在大流行恶化中发挥了作用。与α和β变体相比，δ变体在刺突蛋白中突变最多，这使得它在感染性和快速进入细胞方面发挥了重要作用，并有一些一般的临床表现，如发烧和喉咙痛;然而，Delta变体的严重性归因于其快速增长。这就是为什么从2021年5月到11月，在印度尼西亚，Delta型的病例激增，而不像其他型号。
{"title":"Whole genome sequence analyses of Indonesian isolates SARS‐CoV‐2 variants and their clinical manifestations","authors":"Elnora Listianto Lie, Tedi Dwi Fauzi Hermawan, Kholis Abdurachim Audah","doi":"10.22146/ijbiotech.73783","DOIUrl":"https://doi.org/10.22146/ijbiotech.73783","url":null,"abstract":"The SARS‐CoV‐2 virus has been the cause of the global pandemic since the end of 2019. Since then, the virus has mutated to create different types of variants with numerous effects on those infected. This has complicated human intervention for prevention. Indonesia was heavily affected by the pandemic, specifically from May to August 2021, and as a country has recorded many distinct isolates. Thus, characterization of the virus strains from Indonesia is important. GISAID, NCBI BLAST, and MAFFT version 7 were used. There were 9,488 isolates in Indonesia as of November 2021, with the majority including the Delta variant. While most of the isolates have mutations common to those from other countries, there are some atypical ones, such as mutation V1264L in the Delta variant that was suspected to play a role in worsening the pandemic. The Delta variant had the most mutations in the spike protein when compared to the Alpha and Beta variants, giving it important roles in infectivity and vigorous entry into cells, with some general clinical manifestations like fever and sore throat; however, the severity of the Delta variant is attributable to its rapid growth. This is why, from May to November 2021 in Indonesia, cases of the Delta variant rocketed, unlike the other variants.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":"98 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135733142","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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