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INDONESIA
Indonesian Journal of Biotechnology
Published by Universitas Gadjah Mada
ISSN : 08538654     EISSN : 20892241     DOI : -
Core Subject : Science,
Biochemistry, Genetics & Molecular Biology Immunology & microbiology Materials Science & Nanotechnology
The Indonesian Journal of Biotechnology (IJBiotech) is an open access, peer-reviewed, multidisciplinary journal dedicated to the publication of novel research in all aspects of biotechnology, with particular attention paid to the exploration and development of natural products derived from tropical—and especially Indonesian—biodiversity. IJBiotech is published biannually and accepts original research articles featuring well-designed studies with clearly analyzed and logically interpreted results. A strong preference is given to research that has the potential to make significant contributions to both the field of biotechnology and society in general.
Arjuna Subject : -
Articles 7 Documents
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Search results for , issue "Vol 28, No 3 (2023)" : 7 Documents clear
Atrazine degradation by Bacillus safensis strain BUK_BCH_BTE6 isolated from agricultural land in northwestern Nigeria Faisal Muhammad; Hafeez Muhammad Yakasai; Mohd Yunus Shukor
Indonesian Journal of Biotechnology Vol 28, No 3 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.73989

Abstract

Atrazine herbicide is known to disrupt the endocrine system and is potentially carcinogenic. Its continual application leads to high residue levels in soil, causing water pollution, which when consumed is associated with devastating health effects. This research reported the isolation and characterization of a new bacterial strains from active agricultural soil with the potential to biodegrade atrazine as a sole carbon source. An enrichment method was utilized to isolate the bacteria (A1, A2, B1, B2, C1 and C2) on mineral salt media (MSM) following serial dilution. Six isolates were screened for their tolerance to various concentrations of atrazine (500 to 1500 mg∙L‐1), and only isolate B1 tolerated up to 1500 mg∙L‐1 atrazine. The isolate was identified molecularly as Bacillus safensis strain BUK_BCH_BTE6 based on 16S rRNA gene sequencing and molecular phylogenetic analysis. Characterization of the isolate based on the effects of temperature, pH, substrate concentration, incubation time, inoculum size, and heavy metals revealed optimum growth and atrazine degradation at 35 °C, a pH of 7.5, 400 mg∙L‐1, at 48 h, and inoculum size of 600 µL, respectively. The growth of the isolate was inhibited by 2 ppm Hg, Cd, Cr, Pb, Ar, and Ni, while Fe, Cu, and Zn stimulated it. GC‐MS analysis revealed a degradation efficiency of 88.85% within 120 h, while metabolites such as desethyldeisopropylatrazine, deisopropylatrazine, N‐ethylammelide, and cyanuric acid were also detected. This isolate is a highly atrazine‐tolerant and efficient atrazine degrader that could be employed for bioremediation of atrazine‐polluted sites.
Effect of fluidised bed drying on ginsenoside content in hairy root cultures of Panax ginseng C.A. Meyer James Setiabudi; Komang Mega Oka Sri Bintang; Stella Stacia Gani; Pissa Christanti; Evanie Noer Putri; Se Chan Kang; Johan Sukweenadhi
Indonesian Journal of Biotechnology Vol 28, No 3 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.79677

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.
Computational approaches to identify novel inhibitors for the drug‐resistant Mycobacterium tuberculosis DprE1 enzyme Chaitali Dhande; Devanshi Mistry; Anandakrishnan Karthic; Rajshri Singh; Sagar Hindurao Barage
Indonesian Journal of Biotechnology Vol 28, No 3 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.80145

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.
A simple method of plant sectioning using the agarose embedding technique for screening intracellular green fluorescent protein Nisa Ihsani; Fenny Martha Dwivany; Sony Suhandono
Indonesian Journal of Biotechnology Vol 28, No 3 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.80853

Abstract

It is difficult to observe plant tissue sections transformed using the agroinfiltration method under a fluorescent microscope. This is due to the softness of the post‐transformation plant. This research was conducted to optimize the sectioning of tobacco stems transformed through the agarose embedding technique. Optimization was conducted at various agarose concentrations: 2%, 4%, and 6%, followed by five minutes of incubation at various temperatures: –80 °C, 4 °C, and 25 °C. The stems were then cut using a scalpel and examined under a fluorescence microscope. The results showed that the embedding method using 6% agarose was more effective at producing a tobacco stem section than 2% or 4% agarose. Meanwhile, incubation at 25 °C was better suited to the transformed tobacco stems than at 4 °C or –80 °C. Green Fluorescent Protein (GFP) could be determined under a fluorescent microscope when using the optimum method. Thus, the optimum method for creating sections of transformed tobacco stems by embedding was to use 6% agarose followed by incubation at 25 °C for 5 min. The optimum result can be applied to obtain a slight section of tobacco stem in order to observe a recombinant protein or other anatomical structures.
Foldon fusion of RBD and S1 fragments of SARS‐CoV‐2 to stabilize the structure of subunit protein as a vaccine candidate 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
Indonesian Journal of Biotechnology Vol 28, No 3 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.82159

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 receptor, 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.
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 Yeni Fatmawati; Ilyas Ilyas; Agus Budi Setiawan; Aziz Purwantoro; Dyah Weny Respatie; Chee How Teo
Indonesian Journal of Biotechnology Vol 28, No 3 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.82760

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.
The development of papain‐like protease from SARS‐CoV‐2, a potential drug target for antiviral screening: A review Riswanto Napitupulu; Is Helianti; Maimunah Maimunah; Fairuz Andini Fatiningtyas; Amarila Malik
Indonesian Journal of Biotechnology Vol 28, No 3 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.83376

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.

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