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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 518 Documents
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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.
Cloning and characterization of bgl6111 gene encoding β‐glucosidase from bagasse metagenome Fitra Adi Prayogo; Benjarat Bunterngsook; Pattanop Kanokratana; Hermin Pancasakti Kusumaningrum; Dyah Wulandari; Anto Budiharjo
Indonesian Journal of Biotechnology Vol 28, No 4 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.81536

Abstract

β‐Glucosidase (BGL) is an essential enzyme for the hydrolysis of cellulose in industrial processes, but natural BGL enzymes are poorly understood. Metagenomics is a robust tool for bioprospecting in the search for novel enzymes from the entire community’s genomic DNA present in nature. The metagenomics approach simplifies the process of searching for new BGL enzymes by extracting DNA and retrieving its gene information through a series of bioinformatic analyses. In this study, we report the gene cloning, heterologous expression of the bgl6111 gene (accession number MW221260) in Pichia pastoris KM71, and the biochemical characterization of the recombinant enzyme. We successfully identified the bgl6111 sequence of 2,520 bp and 839 amino acids with a molecular size of 89.4 kDa. The amino acid sequence of the bgl6111 gene showed 67.61% similarity to BGL from an uncultured bacterium (ABB51613.1). The BGL product has the highest activity on the third day at 1.210 U/mL, categorized as low production. The enzymatic activity could enhance up to 539.8% of 7.742 U/mL by using the ultrafiltration method. Our findings provide insightful information that bgl6111 obtained from bagasse metagenome could be an alternative candidate for industrial applications in the future.
Chitosan Xylotrupes gideon encapsulated lemongrass leaf ethanol extract reduce H2O2‐induced oxidative stress in human dermal fibroblast Komariah Komariah; Pretty Trisfilha; Rahman Wahyudi; Nada Erica; Didi Nugroho; Yessy Ariesanti; Sarat Kumar Swain
Indonesian Journal of Biotechnology Vol 28, No 4 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.81544

Abstract

During phagocytosis, phagocyte cells discharge reactive oxygen species referred to as respiratory bursts, inducing a rise in pro‐oxidants and subjecting the cell to oxidative stress. Such stress is a biological mechanism related to an imbalance in pro‐oxidant/antioxidant homeostasis, which generates toxic reactive oxygen. Encapsulation is a coating process to improve the stability of bioactive compounds from lemongrass extract. Therefore, this study aims to determine the encapsulation activity of lemongrass leaf extract with chitosan X. gideon (LEChXg) to reduce the oxidative stress of fibroblasts. The research used the human dermal fibroblast (HDF) cell line, comprising negative and positive controls and use of LEChXg 100, 200, 300, 400, and 500 µg/mL. HDF cell migration was evaluated by employing the scratch wound healing method and the wound closure was oberseved at 0, 2, 4, 6, and 24 h intervals. The cell proliferation was observed at 24, 48, and 72 h using CCK‐8 at a 450 nm wavelength. The results showed that the observations at 0, 2, and 4 h did not demonstrate any significant difference on the cell migration (p > 0.05) among the groups. However, the wound closure at 4 and 6 h showed a significant difference (p < 0.05) with LEChXg 300 µg/mL. Despite the lack of any significant variation observed up to 24 h, fibroblast subjected to the stressor did not achieve complete closure. The groups treated with LEChXg were more stable in maintaining fibroblast proliferation up to the end of the observation than those with stressors at 24, 48, and 72 h. Fibroblast induced with a stressor was also more stable in maintaining migration and proliferation in groups receiving LEChXg 300 µg/mL.
A response surface methodology for the use of MIL‐101 as a catalyst for the one‐step synthesis of lactide Clara Novia; Catia Angli Curie; Misri Gozan
Indonesian Journal of Biotechnology Vol 28, No 4 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.82387

Abstract

Lactide is a vital monomer for producing high molecular weight polylactic acid (PLA) through ring‐opening polymerization. This study synthesized crude lactide from L‐lactic acid with MIL‐101 as the catalyst. MIL‐101 is a metal‐based catalyst with organic ligands (MOF) that was prepared by reacting Cr(NO3)3.9H2O with terephthalic acid (BDC). The formation of MIL‐101 was confirmed from Fourier‐transform infrared (FTIR) analysis. The role of MIL‐101 and the effect of temperature, time, and MIL‐101 loading, as well as their interactions in the conversion of lactic acid to crude lactide, were then investigated using the response surface method (RSM). Crude lactide was analyzed using 1H‐nuclear magnetic resonance (NMR) spectroscopy to confirm the presence of lactide. The RSM results indicated that the highest conversion of 22.84% can be obtained using a temperature of 175 °C, 1.5% w/w MIL‐101 loading, and a reaction time of 5 h. The RSM model showed that the interaction of MIL‐101 loading and reaction time strongly affected the conversion of lactic acid to lactide, with a P‐value of 0.0021 and an F‐value of 50.45. In contrast, the interaction of catalyst loading and temperature did not significantly affect the conversion of lactic acid to lactide, with a P‐value of 0.2565 and an F‐value of 1.75.
Thrombolytic protease characterization from leaves and fruit flesh of the jernang rattan plant (Daemonorops draco) Urbanus Yustus Lebuan; Roga Florida Kembaren; Merry Meryam Martgrita; Cut Rizlani Kholibrina
Indonesian Journal of Biotechnology Vol 28, No 4 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.82390

Abstract

Thrombolytic agents are used for thrombolytic therapy to dissolve blood clots that form in a blood vessel. All currently used thrombolytic agents have unfavorable shortcomings, such as gastrointestinal bleeding, allergic reactions, and thrombolytic agent resistance, treatment for some of which can be quite expensive. As a result, the search for thrombolytic agents derived from plants is currently taking place. Some plants have been discovered to contain protease enzymes with thrombolytic activity; pharmaceuticals derived from plants are believed to be safer. Jernang rattan (Daemonorops draco) is a plant of the Arecaceae family and is known to produce resin. Jernang rattan resin is also known to have antioxidant, antiseptic, antitumor, antimicrobial, and cytotoxic activity, but very limited information on proteolytic activity of the protease from this plant. This research aims to isolate proteases from the leaves and fruit flesh of the rattan jernang plant (D. draco) and to investigate the proteolytic activity of the isolated proteases. The protease was isolated from the leaves and the fruit flesh, and then partially purified by ammonium sulfate precipitation. The radial caseinolytic assay showed that protease in a 60% ammonium sulfate fraction gave a clear zone, with diameters of 1.4 cm and 1.8 cm for the protease isolated from leaves and fruit flesh, respectively. A Folin‐Ciocalteau assay showed that the enzymes isolated were able to hydrolyze casein and release L‐tyrosine, with activity of 0.158 U/mL and 0.174 U/mL for the protease from the leaves and fruit flesh, respectively. A fibrinogenolytic assay showed that the protease from the fruit flesh hydrolyzed the A‐α, B‐β and the γ chain of human fibrinogen, while the protease from the leaves hydrolyzed the A‐α and γ chain. Both proteases were inhibited by 56% by phenylmethylsulfonyl fluoride (PMSF), indicating that the enzymes are serine proteases. Based on the assay results obtained, it can be concluded that proteases isolated from the leaves and fruit flesh have potential as thrombolytic proteases.
Fermentation medium optimization of Streptomyces sp. as an antifungal agent against the Ganoderma boninensis pathogen in oil palm Syamsika Tahir; Widya Dwi Rukmi Putri; Agustin Krisna Wardani; Rofiq Sunaryanto
Indonesian Journal of Biotechnology Vol 28, No 4 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.82396

Abstract

Ganoderma boninensis is the most common fungus which attacks oil palm trees. However, a significant percentage of inhibition to the problem is found through the use of Streptomyces sp. The optimization of the Streptomyces sp. fermentation medium growth factors affects the secondary metabolites production. This study aimed to identify the best formulation of carbon and nitrogen sources and the optimum concentration of Streptomyces sp. fermentation medium for antifungal compound production. The results showed that the best sources of carbon and nitrogen were liquid glucose and monosodium glutamate in the inhibition zones of 16.7 mm and 6.3 mm, while the best concentration levels were 20 g/L and 14.19 g/L, respectively. The results of the first optimization showed an inhibition zone response and area (%) of the optimum high‐performance liquid chromatography (HPLC) chromatogram of 24.39 mm and 62.68 percent, respectively. Taking the suggestion of the first optimization, the second optimization produced 15.2 g/L and 8.3 g/L. The predicted value of the inhibition zone was 21.47 mm, and the area (%) of the HPLC chromatogram was 53.44 percent. The validation results showed an inhibition zone response of 22.01 mm and an HPLC chromatogram area (%) of 54.86 percent. The difference between the predicted and validation values was less than 5 percent; the validation value was thus in line with the value predicted by Design Expert 10.0.7. The chemical formula of the probable active compound is that of the cyclo(phenylalanyl‐prolyl) compound.
Kinetic modeling, optimization of biomass and astaxanthin production in Spirogyra sp. under nitrogen and phosphorus deficiency Nadia Delfi Zafira; Malvin Yulius Christian Pakpahan; I Putu Ikrar Satyadharma; Khairul Hadi Burhan; Erly Marwani
Indonesian Journal of Biotechnology Vol 28, No 4 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.82751

Abstract

This study studied the optimum nitrogen (N) and phosphorus (P) concentrations for biomass and astaxanthin production in Spirogyra sp. Spirogyra sp. was cultivated in Blue Green (BG) medium with N/P concentrations adjusted to 1.1/0.01; 1.1/0.03; 1.1/06; 1.1/0.09; 2.2/0.01; 2.2/0.03; 2.2/0.06; 2.2/0.09; 4.4/0.01; 4.4/0.03; 4.4/0.06; 4.4/0.09, 6.6/0.01; 6.6/0.03; 6.6/0.06 and 6.6/0.09 mM. The results showed an increase in biomass accumulation for lower concen‐ trations of N and N:P ratio with the highest accumulation at N/P 1.1/0.03 mM, i.e. 485 mgdryweight and a growth rate of 0.22 d‐1. Astaxanthin accumulation was also found to increase, with the highest at N/P 1.1/0.01 mM, i.e. 0.269 mg/gdryweight, on the 12th day of cultivation. Based on biomass and astaxanthin accumulation, the highest astaxanthin productivity was 0.07 μg/cm2/d at N/P concentration 1.1/0.09 mM. Kinetic models were developed using the Haldane and Luedeking–Piret equations. The growth and astaxanthin production parameters obtained were μmax 0.18±0.02 d‐1, kN 68.2 ± 24.2 mg/L, ki 301.8 ± 78.5 mg/L, YN 0.93 ± 0.68 gbiomass/nitrate, α 0.36 ± 0.69, β ‐0.01 ± 0.02, and kA 0.04 ± 0.03, thus indicating that a lower N concentration is suitable for the cultivation of Spirogyra sp. In conclusion, Spirogyra sp. should be cultivated under nitrogen deficiency for continuous astaxanthin production.

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