Mycobacterium tuberculosis causes Tuberculosis (TB), which is a common but life‐debilitating disease. The continued development of resistance to frontline anti‐TB drugs such as isoniazid and rifampicin threatens the efficacy of currently available treatment procedures. This highlights the need to explore diverse approaches essential for drug development against multi‐drug‐resistant strains of tuberculosis. Drug development relies on the findings associated with novel protein targets, which play a crucial role in the disease life cycle. DprE1, an enzyme that plays a critical role in the cell wall synthesis of M. tuberculosis, has been recognized as a promising target for drug development. In the present study, based on previous experimental findings, seven mutant models of DprE1 involved in DprE1 resistance are predicted using homology modeling. Further, potential inhibitors are selected based on their efficacy and IC50 values. Shortlisted inhibitors are docked with the wild‐type and mutant structures of DprE1. The deduced inhibitor molecule (ZINC5) is found to possess high potential as a lead inhibitor for all the models of DprE1. It can be used to circumvent drug resistance in the current treatment regime.
{"title":"Computational approaches to identify novel inhibitors for the drug‐ resistant Mycobacterium tuberculosis DprE1 enzyme","authors":"Chaitali Dhande, Devanshi Mistry, Anandakrishnan Karthic, Rajshri Singh, Sagar Hindurao Barage","doi":"10.22146/ijbiotech.80145","DOIUrl":"https://doi.org/10.22146/ijbiotech.80145","url":null,"abstract":"Mycobacterium tuberculosis causes Tuberculosis (TB), which is a common but life‐debilitating disease. The continued development of resistance to frontline anti‐TB drugs such as isoniazid and rifampicin threatens the efficacy of currently available treatment procedures. This highlights the need to explore diverse approaches essential for drug development against multi‐drug‐resistant strains of tuberculosis. Drug development relies on the findings associated with novel protein targets, which play a crucial role in the disease life cycle. DprE1, an enzyme that plays a critical role in the cell wall synthesis of M. tuberculosis, has been recognized as a promising target for drug development. In the present study, based on previous experimental findings, seven mutant models of DprE1 involved in DprE1 resistance are predicted using homology modeling. Further, potential inhibitors are selected based on their efficacy and IC50 values. Shortlisted inhibitors are docked with the wild‐type and mutant structures of DprE1. The deduced inhibitor molecule (ZINC5) is found to possess high potential as a lead inhibitor for all the models of DprE1. It can be used to circumvent drug resistance in the current treatment regime.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135247101","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 : 2023-09-29DOI: 10.22146/ijbiotech.82760
Yeni Fatmawati, Ilyas Ilyas, Agus Budi Setiawan, Aziz Purwantoro, Dyah Weny Respatie, Chee How Teo
Mung bean (Vigna radiata L. Wilczek) is a self‐pollinating and indispensable pulse crop in Indonesia. While low yield productivity is a major concern, genetic improvement is possible through interspecific hybridization. However, interspecific hybridization is relatively infrequent and produces low recombination exchanges, significantly limiting crop breeding efficiency. Thus, a comprehensive study is needed of the selection and genetic diversity evaluation of progenies in advanced generations derived from interspecific hybridization using a specific molecular marker. This study aims to confirm the heterozygosity in the F2 population and assess the genetic diversity in F3 mung bean populations resulting from interspecific hybridization between the mung bean and common bean. We designed the retrotransposon‐based insertion polymorphism (RBIP) marker by identifying the syntenic regions in the flanking sequences of retrotransposon insertion in common bean and mung bean. The RBIP marker can be applied to distinguish the heterozygote progenies from the homozygote progenies. Six combinations of sequence‐related amplified polymorphism (SRAP) primers were used in the genotyping of F3 mung bean progenies. The SRAP marker showed a high degree of polymorphism of up to 100%, while high genetic variation was observed within the population (71%) of mung bean progenies. The F3.4 population had the greatest number of genotypes and displayed the highest number of effective alleles, private alleles, and percentage of polymorphic loci, suggesting the existence of high genetic diversity within this population. These genetic diversity data are exceptionally critical for future genetic research since it has potentially high yield production. The genomic and marker‐assisted selection studies will support the major goals of the mung bean breeding program.
绿豆(Vigna radiata L. Wilczek)是印度尼西亚一种自花授粉的重要豆类作物。虽然低产量是主要问题，但通过种间杂交可以进行遗传改良。然而，种间杂交相对较少，重组交换较低，极大地限制了作物的育种效率。因此，需要利用特定的分子标记对种间杂交后代的选择和遗传多样性评价进行全面的研究。本研究旨在通过绿豆与普通豆的种间杂交，确定F2群体的杂合性，并评估F3绿豆群体的遗传多样性。我们通过对普通豆和绿豆的反转录转座子插入侧序列的同源区进行鉴定，设计了基于反转录转座子的插入多态性(RBIP)标记。RBIP标记可用于区分杂合子和纯合子。利用6个序列相关扩增多态性(SRAP)引物组合对F3绿豆后代进行基因分型。SRAP标记多态性高达100%，而绿豆后代群体内遗传变异较高(71%)。F3.4群体的基因型数量最多，有效等位基因数量、私有等位基因数量和多态性位点百分比最高，表明该群体具有较高的遗传多样性。这些遗传多样性数据对未来的遗传研究非常重要，因为它具有潜在的高产量。基因组学和标记辅助选择研究将支持绿豆育种计划的主要目标。
{"title":"Genetic evaluation of F2 and F3 interspecific hybrids of mung bean (Vigna radiata L. Wilczek) using retrotransposon‐based insertion polymorphism and sequence‐related amplified polymorphism markers","authors":"Yeni Fatmawati, Ilyas Ilyas, Agus Budi Setiawan, Aziz Purwantoro, Dyah Weny Respatie, Chee How Teo","doi":"10.22146/ijbiotech.82760","DOIUrl":"https://doi.org/10.22146/ijbiotech.82760","url":null,"abstract":"Mung bean (Vigna radiata L. Wilczek) is a self‐pollinating and indispensable pulse crop in Indonesia. While low yield productivity is a major concern, genetic improvement is possible through interspecific hybridization. However, interspecific hybridization is relatively infrequent and produces low recombination exchanges, significantly limiting crop breeding efficiency. Thus, a comprehensive study is needed of the selection and genetic diversity evaluation of progenies in advanced generations derived from interspecific hybridization using a specific molecular marker. This study aims to confirm the heterozygosity in the F2 population and assess the genetic diversity in F3 mung bean populations resulting from interspecific hybridization between the mung bean and common bean. We designed the retrotransposon‐based insertion polymorphism (RBIP) marker by identifying the syntenic regions in the flanking sequences of retrotransposon insertion in common bean and mung bean. The RBIP marker can be applied to distinguish the heterozygote progenies from the homozygote progenies. Six combinations of sequence‐related amplified polymorphism (SRAP) primers were used in the genotyping of F3 mung bean progenies. The SRAP marker showed a high degree of polymorphism of up to 100%, while high genetic variation was observed within the population (71%) of mung bean progenies. The F3.4 population had the greatest number of genotypes and displayed the highest number of effective alleles, private alleles, and percentage of polymorphic loci, suggesting the existence of high genetic diversity within this population. These genetic diversity data are exceptionally critical for future genetic research since it has potentially high yield production. The genomic and marker‐assisted selection studies will support the major goals of the mung bean breeding program.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135247352","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 : 2023-09-29DOI: 10.22146/ijbiotech.79677
James Setiabudi, Komang Mega Oka Sri Bintang, Stella Stacia Gani, Pissa Christanti, Evanie Noer Putri, Se Chan Kang, Johan Sukweenadhi
Korean Ginseng (Panax ginseng C.A. Meyer) is a high‐value herb with many pharmacological benefits due to its primary active compound, ginsenosides. The most ginsenosides are known to be thermolabile and susceptible to degradation at high‐temperature processing. Our previous studies revealed that the optimum parameters related to the P. ginseng tissue culture protocol, particularly for hairy root propagation of Cultured Roots of Mountain Ginseng (CRMG)‐88, was using a lab‐scale bioreactor. The next stage involves screening for a suitable post‐harvest treatment, i.e., drying, will be production of the best quality ginsenoside content. This study therefore aimed to examine the ginsenoside content by using a fluidised bed dryer (FBD) on the ginseng roots. Our results showed that FBD produced a significantly higher of total ginsenoside content (5.386 ± 1.167%), compared to control (3.750 ± 0.641%). FBD‐dried CRMG‐88 also appeared lighter in colour and more voluminous with a Loss on Drying (LOD) of 6.448 ± 1.900%. This study concluded that fluidised bed drying is superior in retaining ginsenoside content and has the potential for large‐scale application.
{"title":"Effect of fluidised bed drying on ginsenoside content in hairy root cultures of Panax ginseng C.A. Meyer","authors":"James Setiabudi, Komang Mega Oka Sri Bintang, Stella Stacia Gani, Pissa Christanti, Evanie Noer Putri, Se Chan Kang, Johan Sukweenadhi","doi":"10.22146/ijbiotech.79677","DOIUrl":"https://doi.org/10.22146/ijbiotech.79677","url":null,"abstract":"Korean Ginseng (Panax ginseng C.A. Meyer) is a high‐value herb with many pharmacological benefits due to its primary active compound, ginsenosides. The most ginsenosides are known to be thermolabile and susceptible to degradation at high‐temperature processing. Our previous studies revealed that the optimum parameters related to the P. ginseng tissue culture protocol, particularly for hairy root propagation of Cultured Roots of Mountain Ginseng (CRMG)‐88, was using a lab‐scale bioreactor. The next stage involves screening for a suitable post‐harvest treatment, i.e., drying, will be production of the best quality ginsenoside content. This study therefore aimed to examine the ginsenoside content by using a fluidised bed dryer (FBD) on the ginseng roots. Our results showed that FBD produced a significantly higher of total ginsenoside content (5.386 ± 1.167%), compared to control (3.750 ± 0.641%). FBD‐dried CRMG‐88 also appeared lighter in colour and more voluminous with a Loss on Drying (LOD) of 6.448 ± 1.900%. This study concluded that fluidised bed drying is superior in retaining ginsenoside content and has the potential for large‐scale application.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135247107","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 : 2023-09-29DOI: 10.22146/ijbiotech.73989
Hafeez Muhammad Yakasai, Faisal Muhammad, Mohd Yunus Shukor
Atrazine herbicide is known to disrupt the endocrine system and is potentially carcinogenic. Consumption of which is devastating. This research aimed to isolate and characterize bacteria with atrazine degrading ability. An enrichment method was adopted to isolate the bacteria on mineral salt media following serial dilution. The isolate was identified molecularly and characterized based on effects of temperature, pH, substrate concentration, incubation time, inoculum size and heavy metals. GC-MS analysis was performed to identify the metabolites and degradation efficiency. The isolate was identified as Bacillus safensis strain BUKˍBCHˍBTE6 based on 16S rRNA gene sequence and molecular phylogenetic analysis. Growth and degradation of atrazine by this bacterium was optimal at 35 °C, pH of 7.5, 400 mgL-1, inoculum size 600 µL after 48 h. The growth of the isolate was inhibited by 2 ppm Hg, Cd, Cr, Pb, Ar and Ni. The degradation efficiency after 120 h was 88.85%. GC-MS analysis detected the formation of Desethyldeisopropylatrazine, Deisopropylatrazine, N-Ethylammelide and Cyanuric acid as metabolites. This isolate can be efficient atrazine degrader, hence may be beneficial for bioremediation of atrazine polluted sites.
{"title":"Atrazine Degradation by Bacillus safensis Strain BUK_BCH_BTE6 Isolated from Agricultural Land in Northwestern Nigeria","authors":"Hafeez Muhammad Yakasai, Faisal Muhammad, Mohd Yunus Shukor","doi":"10.22146/ijbiotech.73989","DOIUrl":"https://doi.org/10.22146/ijbiotech.73989","url":null,"abstract":"Atrazine herbicide is known to disrupt the endocrine system and is potentially carcinogenic. Consumption of which is devastating. This research aimed to isolate and characterize bacteria with atrazine degrading ability. An enrichment method was adopted to isolate the bacteria on mineral salt media following serial dilution. The isolate was identified molecularly and characterized based on effects of temperature, pH, substrate concentration, incubation time, inoculum size and heavy metals. GC-MS analysis was performed to identify the metabolites and degradation efficiency. The isolate was identified as Bacillus safensis strain BUKˍBCHˍBTE6 based on 16S rRNA gene sequence and molecular phylogenetic analysis. Growth and degradation of atrazine by this bacterium was optimal at 35 °C, pH of 7.5, 400 mgL-1, inoculum size 600 µL after 48 h. The growth of the isolate was inhibited by 2 ppm Hg, Cd, Cr, Pb, Ar and Ni. The degradation efficiency after 120 h was 88.85%. GC-MS analysis detected the formation of Desethyldeisopropylatrazine, Deisopropylatrazine, N-Ethylammelide and Cyanuric acid as metabolites. This isolate can be efficient atrazine degrader, hence may be beneficial for bioremediation of atrazine polluted sites.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135247105","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 : 2023-09-29DOI: 10.22146/ijbiotech.83376
Riswanto Napitupulu, Is Helianti, Maimunah Maimunah, Fairuz Andini Fatiningtyas, Amarila Malik
The SARS‐CoV‐2 outbreak caused a global pandemic, claiming numerous lives and becoming this century’s most widespread life‐threatening disease. The virus relies on two specific enzymes to facilitate replication, 3‐Chymotrypsin‐like protease (3CLPro) and Papain‐like‐protease (PLpro). These enzymes are crucial in breaking down nonstructural polypeptides into functional proteins. PLpro with LXGG↓X recognition and cleavage sites also play a role in deubiquitylase (DUB) and delSGylase by cleaving after the double glycine residue of ubiquitin (Ub) and ISG15 as a mechanism to suppress the host’s innate immune response. Despite its important role in the viral infection cycle and the potential for drug discovery, no antivirals have been approved as PLpro inhibitors. Therefore, this review focuses on PLpro protein, its recombinant product development and purification, and its application as a protein target in drug discovery for COVID‐19 screening to develop effective COVID‐19 drugs.
{"title":"The development of papain‐like protease from SARS‐CoV‐2, a potential drug target for antiviral screening: A review","authors":"Riswanto Napitupulu, Is Helianti, Maimunah Maimunah, Fairuz Andini Fatiningtyas, Amarila Malik","doi":"10.22146/ijbiotech.83376","DOIUrl":"https://doi.org/10.22146/ijbiotech.83376","url":null,"abstract":"The SARS‐CoV‐2 outbreak caused a global pandemic, claiming numerous lives and becoming this century’s most widespread life‐threatening disease. The virus relies on two specific enzymes to facilitate replication, 3‐Chymotrypsin‐like protease (3CLPro) and Papain‐like‐protease (PLpro). These enzymes are crucial in breaking down nonstructural polypeptides into functional proteins. PLpro with LXGG↓X recognition and cleavage sites also play a role in deubiquitylase (DUB) and delSGylase by cleaving after the double glycine residue of ubiquitin (Ub) and ISG15 as a mechanism to suppress the host’s innate immune response. Despite its important role in the viral infection cycle and the potential for drug discovery, no antivirals have been approved as PLpro inhibitors. Therefore, this review focuses on PLpro protein, its recombinant product development and purification, and its application as a protein target in drug discovery for COVID‐19 screening to develop effective COVID‐19 drugs.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135247104","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 : 2023-09-29DOI: 10.22146/ijbiotech.82159
Gracia Christine Lembong Purwanto, Fedric Intan Damai, Dian Fitria Agustiyanti, Popi Hadi Wisnuwardhani, Alfi Taufik Fathurahman, Yana Rubiyana, Ratna Dwi Ramadani, Muhammad Khairul Lisan Sidqi, Pekik Wiji Prasetyaningrum, Endah Puji Septisetyani, Dadang Supriatna, Ratih Asmana Ningrum, Wien Kusharyoto, Ihsan Tria Pramanda, Andri Wardiana
The COVID‐19 pandemic threatened public health around the world at the same time as highlighting the urgency of vaccine development. Subunit vaccines are safe and effective vaccine types that utilize parts of viruses to trigger the body’s immune response. Previous research has shown that fusion of the spike protein with the foldon domain (fd) achieved the trimeric form to increase the protein stability of the recombinant subunit protein spike from SARS‐CoV and MERS‐CoV, thus exceeding the immune response in the body. The study aims to observe the expression of RBD‐fd and S1‐fd recombinant proteins from the spike protein of SARS‐CoV‐2 in CHO‐K1 mammalian cells and investigate the binding activity of those proteins with hACE2 receptors, expressed in HEK293T cells using immunofluorescence staining. The plasmids were transiently transfected into the cells, followed by antibiotic selection using G418 as an initial stage to select the positive stable transformants. Protein expression was confirmed by Western blotting and showed an estimated size for monomeric RBD‐fd of 35 kDa and S1‐fd of 55 kDa. However, the trimeric form of the proteins was not observed. In addition, immunofluorescence staining showed the binding activity between the RBD‐fd and S1‐fd proteins and hACE2 expressing cell line, revealing binding and an internalization process.
{"title":"Foldon fusion of RBD and S1 fragments of SARS‐CoV‐2 to stabilize the structure of subunit protein as a vaccine candidate","authors":"Gracia Christine Lembong Purwanto, Fedric Intan Damai, Dian Fitria Agustiyanti, Popi Hadi Wisnuwardhani, Alfi Taufik Fathurahman, Yana Rubiyana, Ratna Dwi Ramadani, Muhammad Khairul Lisan Sidqi, Pekik Wiji Prasetyaningrum, Endah Puji Septisetyani, Dadang Supriatna, Ratih Asmana Ningrum, Wien Kusharyoto, Ihsan Tria Pramanda, Andri Wardiana","doi":"10.22146/ijbiotech.82159","DOIUrl":"https://doi.org/10.22146/ijbiotech.82159","url":null,"abstract":"The COVID‐19 pandemic threatened public health around the world at the same time as highlighting the urgency of vaccine development. Subunit vaccines are safe and effective vaccine types that utilize parts of viruses to trigger the body’s immune response. Previous research has shown that fusion of the spike protein with the foldon domain (fd) achieved the trimeric form to increase the protein stability of the recombinant subunit protein spike from SARS‐CoV and MERS‐CoV, thus exceeding the immune response in the body. The study aims to observe the expression of RBD‐fd and S1‐fd recombinant proteins from the spike protein of SARS‐CoV‐2 in CHO‐K1 mammalian cells and investigate the binding activity of those proteins with hACE2 receptors, expressed in HEK293T cells using immunofluorescence staining. The plasmids were transiently transfected into the cells, followed by antibiotic selection using G418 as an initial stage to select the positive stable transformants. Protein expression was confirmed by Western blotting and showed an estimated size for monomeric RBD‐fd of 35 kDa and S1‐fd of 55 kDa. However, the trimeric form of the proteins was not observed. In addition, immunofluorescence staining showed the binding activity between the RBD‐fd and S1‐fd proteins and hACE2 expressing cell line, revealing binding and an internalization process.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135247106","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 : 2023-09-29DOI: 10.22146/ijbiotech.80853
Nisa Ihsani
The transformed plant tissue sections through the agroinfiltration method are difficult to be observed under a fluorescent microscope. It is due to the softness of the post-transformation explant. This research was conducted to optimize the sectioning of the transformed plant using the agarose embedding technique. The optimization method was carried out in various agarose concentrations: 2%, 4%, and 6%, followed by five minutes of incubation in various temperatures: -80 oC, 4 oC, and 25 oC. The results showed that the embedding method using 6% agarose produced a transformed plant section was better than 2% and 4% agarose. Meanwhile, the incubation method at 25 oC was more suitable for the transformed plant tissue than 4 oC and -80 oC. Green Fluorescent Protein (GFP) could be determined using these methods under a fluorescent microscope. Thus, the optimum method for making sections of transformed plants by embedding was using 6% agarose then incubating at 25 oC for 5 minutes.
{"title":"A Simple Method of Plant Sectioning Using Agarose Embedding Technique for Screening Intracellular Green Fluorescent Protein","authors":"Nisa Ihsani","doi":"10.22146/ijbiotech.80853","DOIUrl":"https://doi.org/10.22146/ijbiotech.80853","url":null,"abstract":"The transformed plant tissue sections through the agroinfiltration method are difficult to be observed under a fluorescent microscope. It is due to the softness of the post-transformation explant. This research was conducted to optimize the sectioning of the transformed plant using the agarose embedding technique. The optimization method was carried out in various agarose concentrations: 2%, 4%, and 6%, followed by five minutes of incubation in various temperatures: -80 oC, 4 oC, and 25 oC. The results showed that the embedding method using 6% agarose produced a transformed plant section was better than 2% and 4% agarose. Meanwhile, the incubation method at 25 oC was more suitable for the transformed plant tissue than 4 oC and -80 oC. Green Fluorescent Protein (GFP) could be determined using these methods under a fluorescent microscope. Thus, the optimum method for making sections of transformed plants by embedding was using 6% agarose then incubating at 25 oC for 5 minutes.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135247102","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.72550
Angelia Wattimury, D. Suroto, Tyas Utami, R. Wikandari, E. Rahayu
Previous studies found that antibiotics resistance genes on plasmids in Lactobacillus make them unsafe for food purposes due to the capability of genes to transfer to pathogenic microorganisms. In contrast, Lactobacillus is widely used as a probiotic. This study assessed the antibiotics susceptibility of Lactobacillus plantarum Kita-3 isolated from Halloumi cheese using eight antibiotics. Genome sequencing was performed using the NovaSeq 6000 sequencing platform to detect the presence of antibiotics resistance genes on chromosomes and plasmids. L. plantarum Kita-3 was resistant to clindamycin, streptomycin, chloramphenicol and susceptible to tetracycline, ampicillin, kanamycin, erythromycin, ciprofloxacin. Genome sequencing of the L. plantarum Kita-3 verified the presence of the tetracycline, fluoroquinolones, β-lactamase resistance genes, and multidrug resistance efflux. Kita-3 did not have transposable elements, gene transfer agents, and plasmid-related functions. Overall, this study resulted in the antibiotics resistance profile of L. plantarumKita-3 to assess the risk of antibiotics resistance genes transfer to other bacteria. This study can provide essential data on the safe use of Lactobacillus plantarum Kita-3 as probiotics.
{"title":"In Silico Analysis of Antibiotics Resistance Genes in Lactobacillus plantarum Kita-3 isolated from Halloumi Cheese","authors":"Angelia Wattimury, D. Suroto, Tyas Utami, R. Wikandari, E. Rahayu","doi":"10.22146/ijbiotech.72550","DOIUrl":"https://doi.org/10.22146/ijbiotech.72550","url":null,"abstract":"Previous studies found that antibiotics resistance genes on plasmids in Lactobacillus make them unsafe for food purposes due to the capability of genes to transfer to pathogenic microorganisms. In contrast, Lactobacillus is widely used as a probiotic. This study assessed the antibiotics susceptibility of Lactobacillus plantarum Kita-3 isolated from Halloumi cheese using eight antibiotics. Genome sequencing was performed using the NovaSeq 6000 sequencing platform to detect the presence of antibiotics resistance genes on chromosomes and plasmids. L. plantarum Kita-3 was resistant to clindamycin, streptomycin, chloramphenicol and susceptible to tetracycline, ampicillin, kanamycin, erythromycin, ciprofloxacin. Genome sequencing of the L. plantarum Kita-3 verified the presence of the tetracycline, fluoroquinolones, β-lactamase resistance genes, and multidrug resistance efflux. Kita-3 did not have transposable elements, gene transfer agents, and plasmid-related functions. Overall, this study resulted in the antibiotics resistance profile of L. plantarumKita-3 to assess the risk of antibiotics resistance genes transfer to other bacteria. This study can provide essential data on the safe use of Lactobacillus plantarum Kita-3 as probiotics.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44781985","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.76257
Gurushankar Krishnamoorthy, K. Chinnaiah, K. Kannan, V. Maik, V. Potemkin, M. Grishina, S. Christopher Jeyaseelan, A. Muthuvel, D. Gnanasangeetha
Here in we report, silver nanoparticles (Ag NPs) prepared from leaf extract of Datura metel L. via green synthesis method. Datura metel L. is an herbal medicinal plant of solanaceae family. The as - prepared Ag NPs characterized employing UV-Vis spectrometer, X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy and scanning electron microscopy (SEM) with energy dispersive X-ray analysis (EDAX) techniques. The appearance of Surface Plasmon Resonance (SPR) peak at 415 nm suggested that creation of Ag NPs in UV-Vis spectrum. XRD pattern showed face centered cubic crystal structure of Ag NPs with organometallic complex phase. Peaks in FTIR spectrum reveal the existence of biomolecules. SEM image illustrate their clastic rock morphology and EDAX profile authenticate the company of Ag and plant trace element. The Cyclic voltammetry (CV), Choronopotentiometry, and Electrochemical impedance spectroscopy (EIS) analysis were performed as prepared Ag electrode. The specific capacitance of 267.59 F/g at 0.5 A/g and cyclic retention of 83.7% after charge-discharge 5000 cycles are obtained. Hence this material could be utilized as Supercapacitor energy storage devices.
{"title":"Spectroscopic analysis of plant trace element incorporated silver nanoparticles synthesis from Datura metel l.","authors":"Gurushankar Krishnamoorthy, K. Chinnaiah, K. Kannan, V. Maik, V. Potemkin, M. Grishina, S. Christopher Jeyaseelan, A. Muthuvel, D. Gnanasangeetha","doi":"10.22146/ijbiotech.76257","DOIUrl":"https://doi.org/10.22146/ijbiotech.76257","url":null,"abstract":"Here in we report, silver nanoparticles (Ag NPs) prepared from leaf extract of Datura metel L. via green synthesis method. Datura metel L. is an herbal medicinal plant of solanaceae family. The as - prepared Ag NPs characterized employing UV-Vis spectrometer, X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy and scanning electron microscopy (SEM) with energy dispersive X-ray analysis (EDAX) techniques. The appearance of Surface Plasmon Resonance (SPR) peak at 415 nm suggested that creation of Ag NPs in UV-Vis spectrum. XRD pattern showed face centered cubic crystal structure of Ag NPs with organometallic complex phase. Peaks in FTIR spectrum reveal the existence of biomolecules. SEM image illustrate their clastic rock morphology and EDAX profile authenticate the company of Ag and plant trace element. The Cyclic voltammetry (CV), Choronopotentiometry, and Electrochemical impedance spectroscopy (EIS) analysis were performed as prepared Ag electrode. The specific capacitance of 267.59 F/g at 0.5 A/g and cyclic retention of 83.7% after charge-discharge 5000 cycles are obtained. Hence this material could be utilized as Supercapacitor energy storage devices.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44986034","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.71150
Fatia Rizki Nuraini
One of promising bio-prospect as producer of an antibacterial compound is endophytic fungi that live in endemic plants. This research is aimed to evaluate the endophytic fungi antibacterial compound from Mangifera casturi, an South Kalimantan endemic plant that has ethnobotanical utilisation in the pharmaceutical field. The bioactive compounds of 13 endophytic fungi were extracted using ethyl acetate and evaluated for antibacterial activity using disc diffusion assay. The minimum inhibitory concentration (MIC) was measured by the serial broth dilution method. Scanning Electron Microscopy (SEM) was used to examine cell damage due to the effect of the extract. The antibacterial compounds then were detected using GC-MS analysis. The endophytic fungi were identified morphologically and molecularly based on ITS rDNA sequence. Among 13 isolates, endophytic fungi identified as Botryosphaeria rhodina AK32 able to produce antibacterial compounds that exhibited the highest activity and have a broad spectrum, moreover capable against resistant bacteria (MRSA) with 1.56% of MIC value for all of the test bacteria. AK32 ethyl acetate extract was inhibiting the cell wall synthesis and penetrate the outer membrane of bacteria. Based on GC-MS, antibacterial compounds of AK32 ethyl acetate extract were di-n-octylphthalate, phenol, 2-methyl-, 4-pentadecyne, 15-chloro-, benzeneacetonitrile, and benztriazole.
{"title":"Antibacterial Activity of Bioactive Compound Produces by Endophtic Fungi Isolated from Mangifera casturi Kosterm Endemic Plant from South Kalimantan, Indonesia","authors":"Fatia Rizki Nuraini","doi":"10.22146/ijbiotech.71150","DOIUrl":"https://doi.org/10.22146/ijbiotech.71150","url":null,"abstract":"One of promising bio-prospect as producer of an antibacterial compound is endophytic fungi that live in endemic plants. This research is aimed to evaluate the endophytic fungi antibacterial compound from Mangifera casturi, an South Kalimantan endemic plant that has ethnobotanical utilisation in the pharmaceutical field. The bioactive compounds of 13 endophytic fungi were extracted using ethyl acetate and evaluated for antibacterial activity using disc diffusion assay. The minimum inhibitory concentration (MIC) was measured by the serial broth dilution method. Scanning Electron Microscopy (SEM) was used to examine cell damage due to the effect of the extract. The antibacterial compounds then were detected using GC-MS analysis. The endophytic fungi were identified morphologically and molecularly based on ITS rDNA sequence. Among 13 isolates, endophytic fungi identified as Botryosphaeria rhodina AK32 able to produce antibacterial compounds that exhibited the highest activity and have a broad spectrum, moreover capable against resistant bacteria (MRSA) with 1.56% of MIC value for all of the test bacteria. AK32 ethyl acetate extract was inhibiting the cell wall synthesis and penetrate the outer membrane of bacteria. Based on GC-MS, antibacterial compounds of AK32 ethyl acetate extract were di-n-octylphthalate, phenol, 2-methyl-, 4-pentadecyne, 15-chloro-, benzeneacetonitrile, and benztriazole.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44767357","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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