Indonesian Journal of Biotechnology最新文献

Computational approaches to identify novel inhibitors for the drug‐ resistant Mycobacterium tuberculosis DprE1 enzyme 确定耐药结核分枝杆菌DprE1酶新抑制剂的计算方法

Indonesian Journal of Biotechnology Pub Date : 2023-09-29 DOI: 10.22146/ijbiotech.80145

Chaitali Dhande, Devanshi Mistry, Anandakrishnan Karthic, Rajshri Singh, Sagar Hindurao Barage

{"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}

引用次数: 0

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 利用反转录转座子插入多态性和序列相关扩增多态性标记对绿豆(Vigna radiata L. Wilczek) F2和F3种间杂种进行遗传评价

Indonesian Journal of Biotechnology Pub Date : 2023-09-29 DOI: 10.22146/ijbiotech.82760

Yeni Fatmawati, Ilyas Ilyas, Agus Budi Setiawan, Aziz Purwantoro, Dyah Weny Respatie, Chee How Teo

{"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}

引用次数: 0

Effect of fluidised bed drying on ginsenoside content in hairy root cultures of Panax ginseng C.A. Meyer 流化床干燥对人参毛状根培养物人参皂苷含量的影响

Indonesian Journal of Biotechnology Pub Date : 2023-09-29 DOI: 10.22146/ijbiotech.79677

James Setiabudi, Komang Mega Oka Sri Bintang, Stella Stacia Gani, Pissa Christanti, Evanie Noer Putri, Se Chan Kang, Johan Sukweenadhi

{"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}

引用次数: 0

Atrazine Degradation by Bacillus safensis Strain BUK_BCH_BTE6 Isolated from Agricultural Land in Northwestern Nigeria 尼日利亚西北部农田中分离的萨菲芽孢杆菌BUK_BCH_BTE6菌株降解阿特拉津的研究

Indonesian Journal of Biotechnology Pub Date : 2023-09-29 DOI: 10.22146/ijbiotech.73989

Hafeez Muhammad Yakasai, Faisal Muhammad, Mohd Yunus Shukor

{"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}

引用次数: 1

The development of papain‐like protease from SARS‐CoV‐2, a potential drug target for antiviral screening: A review 从SARS - CoV - 2中提取木瓜蛋白酶样蛋白酶，作为抗病毒筛选的潜在药物靶点:综述

Indonesian Journal of Biotechnology Pub Date : 2023-09-29 DOI: 10.22146/ijbiotech.83376

Riswanto Napitupulu, Is Helianti, Maimunah Maimunah, Fairuz Andini Fatiningtyas, Amarila Malik

引用次数: 0

Foldon fusion of RBD and S1 fragments of SARS‐CoV‐2 to stabilize the structure of subunit protein as a vaccine candidate SARS - CoV - 2 RBD和S1片段的折叠融合以稳定亚基蛋白结构作为候选疫苗

Indonesian Journal of Biotechnology Pub Date : 2023-09-29 DOI: 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

{"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}

引用次数: 0

A Simple Method of Plant Sectioning Using Agarose Embedding Technique for Screening Intracellular Green Fluorescent Protein 琼脂糖包埋技术筛选细胞内绿色荧光蛋白的简易植物切片方法

Indonesian Journal of Biotechnology Pub Date : 2023-09-29 DOI: 10.22146/ijbiotech.80853

Nisa Ihsani

引用次数: 0

In Silico Analysis of Antibiotics Resistance Genes in Lactobacillus plantarum Kita-3 isolated from Halloumi Cheese Halloumi奶酪植物乳杆菌Kita-3耐药基因的硅晶分析

Indonesian Journal of Biotechnology Pub Date : 2023-06-27 DOI: 10.22146/ijbiotech.72550

Angelia Wattimury, D. Suroto, Tyas Utami, R. Wikandari, E. Rahayu

{"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}

引用次数: 0

Spectroscopic analysis of plant trace element incorporated silver nanoparticles synthesis from Datura metel l. 曼陀罗合成植物微量元素含银纳米颗粒的光谱分析。

Indonesian Journal of Biotechnology Pub Date : 2023-06-27 DOI: 10.22146/ijbiotech.76257

Gurushankar Krishnamoorthy, K. Chinnaiah, K. Kannan, V. Maik, V. Potemkin, M. Grishina, S. Christopher Jeyaseelan, A. Muthuvel, D. Gnanasangeetha

{"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}

引用次数: 1

Antibacterial Activity of Bioactive Compound Produces by Endophtic Fungi Isolated from Mangifera casturi Kosterm Endemic Plant from South Kalimantan, Indonesia 南加里曼丹芒果特有植物内生真菌产生物活性化合物的抗菌活性研究

Indonesian Journal of Biotechnology Pub Date : 2023-06-27 DOI: 10.22146/ijbiotech.71150

Fatia Rizki Nuraini

{"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}

引用次数: 0