Indonesian Journal of Biotechnology
https://journal.ugm.ac.id/ijbiotech
<p>The <em>Indonesian Journal of Biotechnology</em> (<em>IJBiotech</em>) 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. <em>IJBiotech</em> is published four times a year (<span>March, June, September, and</span><span> December)</span> 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.</p><p>We invite authors to submit articles in the fields of food and agricultural biotechnology, health and medical biotechnology, biomaterials, environmental biotechnology, industrial biotechnology, bioinformatics, genomics, transcriptomics, proteomics, and metabolomics.</p><p><em>IJBiotech</em> is published by the <a href="http://biotech.ugm.ac.id">the Research Center for Biotechnology</a> in collaboration with the <a href="http://www.pasca.ugm.ac.id">Graduate School of Universitas Gadjah Mada</a>, and is nationally accredited by the Directorate General of Research and Development of the Ministry of Research, Technology, and Higher Education, Republic of Indonesia, Decree No. 230/E/KPT/2022 valid until 2024.</p><h4>Submitting to the journal</h4><p><em>IJBiotech</em> uses an online submission and peer review platform, which allows authors to track the progress of their manuscript and enables shorter processing times. Only submissions made through this platform are accepted, with submitting authors required to <a href="/ijbiotech/user/register">create an <em>IJBiotech</em> account</a>. Manuscripts submitted by any other means are automatically discarded.</p><p>For more information on our submission system, please refer to the <a href="https://drive.google.com/file/d/1YQ_XKVPYOXdb0-96mb0bdMpYSoHq4B_J/view">Submission Guidelines</a>. Authors can also download the <a href="https://drive.google.com/drive/folders/1z5rQfcJNTjKelSrQfVhUrGEOv_OvKQlD"><em>IJBiotech</em> author pack</a> containing an article template, CSE citation guide, and author guidelines.</p>Universitas Gadjah Madaen-USIndonesian Journal of Biotechnology0853-8654<p id="docs-internal-guid-b23ef14b-a106-d67c-3e82-5f81c6ec326d" style="font-size: 9pt; font-family: 'EB garamond'; color: #222222; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; text-decoration: none; vertical-align: baseline;"><a href="http://creativecommons.org/licenses/by-sa/4.0/" rel="license"><img style="border-width: 0;" src="https://i.creativecommons.org/l/by-sa/4.0/88x31.png" alt="Creative Commons License" /></a></p><ul><li>Articles published in IJBiotech are licensed under a <a title="CC BY SA" href="https://creativecommons.org/licenses/by-sa/4.0/">Creative Commons Attribution-ShareAlike 4.0 International</a> license. You are free to copy, transform, or redistribute articles for any lawful purpose in any medium, provided you give appropriate credit to the original author(s) and IJBiotech, link to the license, indicate if changes were made, and redistribute any derivative work under the same license.</li></ul><ul><li>Copyright on articles is retained by the respective author(s), without restrictions. A non-exclusive license is granted to IJBiotech to publish the article and identify itself as its original publisher, along with the commercial right to include the article in a hardcopy issue for sale to libraries and individuals.</li></ul><ul><li>By publishing in IJBiotech, authors grant any third party the right to use their article to the extent provided by the <a title="CC BY SA" href="https://creativecommons.org/licenses/by-sa/4.0/">Creative Commons Attribution-ShareAlike 4.0 International</a> license.</li></ul>Chitosan Xylotrupes gideon encapsulated lemongrass leaf ethanol extract reduce H2O2‐induced oxidative stress in human dermal fibroblast
https://journal.ugm.ac.id/ijbiotech/article/view/81544
<p><span class="fontstyle0">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 </span><span class="fontstyle2">X. gideon </span><span class="fontstyle0">(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 (</span><span class="fontstyle2">p </span><span class="fontstyle0">> 0.05) among the groups. However, the wound closure at 4 and 6 h showed a significant difference (</span><span class="fontstyle2">p </span><span class="fontstyle0">< 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.</span></p>Komariah KomariahPretty TrisfilhaRahman WahyudiNada EricaDidi NugrohoYessy AriesantiSarat Kumar Swain
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2023-12-302023-12-3028419119910.22146/ijbiotech.81544Cloning and characterization of bgl6111 gene encoding β‐glucosidase from bagasse metagenome
https://journal.ugm.ac.id/ijbiotech/article/view/81536
<p align="justify">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 <span class="fontstyle2">bgl6111 </span><span class="fontstyle0">gene (accession number MW221260) in </span><span class="fontstyle2">Pichia pastoris </span><span class="fontstyle0">KM71, and the biochemical characterization of the recombinant enzyme. We successfully identified the </span><span class="fontstyle2">bgl6111 </span><span class="fontstyle0">sequence of 2,520 bp and 839 amino acids with a molecular size of 89.4 kDa. The amino acid sequence of the </span><span class="fontstyle2">bgl6111 </span><span class="fontstyle0">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 </span><span class="fontstyle2">bgl6111 </span><span class="fontstyle0">obtained from bagasse metagenome could be an alternative candidate for industrial applications in the future.</span></p>Fitra Adi PrayogoBenjarat BunterngsookPattanop KanokratanaHermin Pancasakti KusumaningrumDyah WulandariAnto Budiharjo
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2023-12-302023-12-3028420020810.22146/ijbiotech.81536A response surface methodology for the use of MIL‐101 as a catalyst for the one‐step synthesis of lactide
https://journal.ugm.ac.id/ijbiotech/article/view/82387
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.<br /><em></em>Clara NoviaCatia Angli CurieMisri Gozan
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2023-12-302023-12-3028420921510.22146/ijbiotech.82387Fermentation medium optimization of Streptomyces sp. as an antifungal agent against the Ganoderma boninensis pathogen in oil palm
https://journal.ugm.ac.id/ijbiotech/article/view/82396
<span class="fontstyle0">Ganoderma boninensis </span><span class="fontstyle2">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 </span><span class="fontstyle0">Streptomyces </span><span class="fontstyle2">sp. The optimization of the </span><span class="fontstyle0">Streptomyces </span><span class="fontstyle2">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 </span><span class="fontstyle0">Streptomyces </span><span class="fontstyle2">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.</span>Syamsika TahirWidya Dwi Rukmi PutriAgustin Krisna WardaniRofiq Sunaryanto
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2023-12-302023-12-3028421622410.22146/ijbiotech.82396Kinetic modeling, optimization of biomass and astaxanthin production in Spirogyra sp. under nitrogen and phosphorus deficiency
https://journal.ugm.ac.id/ijbiotech/article/view/82751
<span class="fontstyle0">This study studied the optimum nitrogen (N) and phosphorus (P) concentrations for biomass and astaxanthin production in </span><span class="fontstyle2">Spirogyra </span><span class="fontstyle0">sp. </span><span class="fontstyle2">Spirogyra </span><span class="fontstyle0">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 mg</span><span class="fontstyle0">dryweight </span><span class="fontstyle0">and a growth rate of 0.22 d</span><span class="fontstyle0">‐1</span><span class="fontstyle0">. Astaxanthin accumulation was also found to increase, with the highest at N/P 1.1/0.01 mM, i.e. 0.269 mg/g</span><span class="fontstyle0">dryweight</span><span class="fontstyle0">, on the 12</span><span class="fontstyle0">th </span><span class="fontstyle0">day of cultivation. Based on biomass and astaxanthin accumulation, the highest astaxanthin productivity was 0.07 μg/cm</span><span class="fontstyle0">2</span><span class="fontstyle0">/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</span><span class="fontstyle0">‐1</span><span class="fontstyle0">, k</span><span class="fontstyle0">N </span><span class="fontstyle0">68.2 ± 24.2 mg/L, k</span><span class="fontstyle0">i </span><span class="fontstyle0">301.8 ± 78.5 mg/L, Y</span><span class="fontstyle0">N </span><span class="fontstyle0">0.93 ± 0.68 g</span><span class="fontstyle0">biomass/nitrate</span><span class="fontstyle0">, α 0.36 ± 0.69, β ‐0.01 ± 0.02, and k</span><span class="fontstyle0">A </span><span class="fontstyle0">0.04 ± 0.03, thus indicating that a lower N concentration is suitable for the cultivation of </span><span class="fontstyle2">Spirogyra </span><span class="fontstyle0">sp. In conclusion, </span><span class="fontstyle2">Spirogyra </span><span class="fontstyle0">sp. should be cultivated under nitrogen deficiency for continuous astaxanthin production.</span>Nadia Delfi ZafiraMalvin Yulius Christian PakpahanI Putu Ikrar SatyadharmaKhairul Hadi BurhanErly Marwani
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2023-12-302023-12-3028422523710.22146/ijbiotech.82751sgRNA design and in vitro nucleolytic analysis of the Cas9‐RNP complex for transgene‐free genome editing of the eIF4E1 gene from Capsicum an‐ nuum L.
https://journal.ugm.ac.id/ijbiotech/article/view/86778
<p class="Abstract"><span class="fontstyle0">Chili (</span><span class="fontstyle2">Capsicum annuum </span><span class="fontstyle0">L.) is a highly valued vegetable, renowned for its unique taste and aroma. However, chili production faces challenges in meeting the high demand due to infections caused by pathogens such as ChiVMV (potyvirus). Previous studies have suggested that chili </span><span class="fontstyle2">eIF4E1 </span><span class="fontstyle0">plays a crucial role in potyvirus gene transcription. Therefore, this study explores the potential of CRISPR‐Cas9‐based genome editing to enhance chili resistance by introducing premature stop codons or truncated proteins. Two sgRNAs were designed, targeting the first and second intron of the </span><span class="fontstyle2">eIF4E1 </span><span class="fontstyle0">gene. The production of Cas9 protein was assessed with varying IPTG concentrations in </span><span class="fontstyle2">Escherichia coli </span><span class="fontstyle0">BL21(DE3), carrying 4xNLS‐pMJ915v2‐sfGFP plasmid with a TEV protease cut‐site at the N terminal. The findings indicate that the optimal IPTG concentration is 500 µM. Purification using an IMAC column confirmed the presence of Cas9 in the initial 2 mL of the eluted fractions, as indicated by numerous background proteins. Nevertheless, successful formation of Cas9‐RNP complexes was achieved for both sgRNAs. The nucleolytic activity of Tag‐Cas9 (carrying the MBP‐tag) and Cas9 was confirmed through </span><span class="fontstyle2">in vitro </span><span class="fontstyle0">endonuclease activity assays. The next step involved transfecting chili protoplasts with these RNP complexes to edit the chili </span><span class="fontstyle2">eIF4E1 </span><span class="fontstyle0">gene.</span></p>Josefanny ThamAlfred PatisenahTommy Octavianus Soetrisno TjiaSantiago SignorelliIntan TaufikKarlia Meitha
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2023-12-302023-12-3028423824710.22146/ijbiotech.86778Thrombolytic protease characterization from leaves and fruit flesh of the jernang rattan plant (Daemonorops draco)
https://journal.ugm.ac.id/ijbiotech/article/view/82390
<span class="fontstyle0">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. </span><span class="fontstyle2">Jernang </span><span class="fontstyle0">rattan (</span><span class="fontstyle2">Daemonorops draco</span><span class="fontstyle0">) is a plant of the Arecaceae family and is known to produce resin. </span><span class="fontstyle2">Jernang </span><span class="fontstyle0">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 </span><span class="fontstyle2">jernang </span><span class="fontstyle0">plant (</span><span class="fontstyle2">D. draco</span><span class="fontstyle0">) 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.</span>Urbanus Yustus LebuanRoga Florida KembarenMerry Meryam MartgritaCut Rizlani Kholibrina
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2023-12-302023-12-3028424825310.22146/ijbiotech.82390