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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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sgRNA 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. Josefanny Tham; Alfred Patisenah; Tommy Octavianus Soetrisno Tjia; Santiago Signorelli; Intan Taufik; Karlia Meitha
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.86778

Abstract

Chili (Capsicum annuum 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 eIF4E1 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 eIF4E1 gene. The production of Cas9 protein was assessed with varying IPTG concentrations in Escherichia coli 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 in vitro endonuclease activity assays. The next step involved transfecting chili protoplasts with these RNP complexes to edit the chili eIF4E1 gene.
A comprehensive study of potential Arthrospira platensis cultivated in various manure‐based media for biodiesel feedstock Rachmawati Rusydi; Eva Ayuzar; Muliani Muliani; Saifuddin Saifuddin
Indonesian Journal of Biotechnology Vol 29, No 1 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.81862

Abstract

Arthrospira platensis has emerged as a promising biodiesel feedstock due to its rapid growth and substantial biomass. In efforts to reduce production costs, researchers have explored alternative media derived from livestock waste to modify conventional mediums for Arthrospira platensis cultivation. The experimental design of this research employed a Completely Randomized Design, with treatments comprising inorganic fertilizer (A), chicken manure (B), cow manure (C), and goat manure (D). The livestock manures were macerated for seven days before being utilized as A. platensis medium. The results revealed significant (p < 0.05) impacts of different media on peak growth values and biomass production, reaching 2.03 ± 0.06 g/L and 1.76 ± 0.05 g/ L, respectively for chicken manure. The highest peak lipid content was observed in A. platensis cultured in goat manure medium. This study recommends goat manure as the preferred medium for mass cultivation of A. platensis. Mass cultivation in goat manure medium yielded 1.53 kg of dried biomass, with a lipid content of 1.91% and a biodiesel yield of 1.65%. The predominant fatty acid in this biodiesel was heneicosane, constituting 26.4% of the total area.
Effect of medium supplementations and extraction conditions on cellulase production through solid state fermentation of oil palm empty fruit bunches Vita Wonoputri; Jansen Wijaya; Joevin Saudalimka; Ronny Purwadi
Indonesian Journal of Biotechnology Vol 29, No 1 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.82363

Abstract

In this study, cellulase enzyme was produced through solid state fermentation (SSF), employing oil palm empty fruit bunches (EFB) as the primary substrate. Two key aspects were explored to enhance crude enzyme yield, which are medium supplementation effects during SSF and cellulase recovery. During medium supplementation, glucose and/or Tween 80 were added alongside EFB substrate and other nutrients. Enzyme yield was determined using a filter paper assay and expressed as enzyme activity. The initial addition of glucose during fermentation led to increased crude enzyme activity, as measured by the filter paper assay. The peak crude enzyme activity was observed with the addition of 3 mg of glucose, with higher amounts showing no further increase in activity. Conversely, the addition of Tween 80 did not yield any significant increase in crude enzyme activity across all concentrations tested. The extraction conditions were varied to study cellulase recovery, specifically by adjusting the solid‐to‐solvent ratio and the number of extraction stages. Higher enzyme activity was achieved with lower solid‐to‐liquid ratios, as the increased solvent volume facilitated greater enzyme extraction. However, increasing the number of extraction steps did not significantly affect the resulting cellulase activity. Overall, this research underscores the need for further process optimization for cellulase production via SSF, utilizing the widely available EFB in Indonesia.
Easy extraction of Ganoderma boninense liquid sample using portable on‐chip device Adella Josephin; Yudan Whulanza; Siti Fauziyah Rahman; Kenny Lischer; Muhammad Imam Surya; Irfan Martiansyah; Wiguna Rahman; Uda Hashim
Indonesian Journal of Biotechnology Vol 29, No 1 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.83645

Abstract

Detecting Ganoderma boninense in Indonesia is crucial for effectively controlling and mitigating the spread of basal stem disease in oil palm fields. While there is ongoing development of tolerant plants, no such plant has been successfully created yet. Consequently, researchers are actively studying detection methods for Ganoderma boninense. One established and highly accurate approach is the use of polymerase chain reaction (PCR) techniques for molecular detection. However, this method requires time‐consuming sample preparation, which can pose challenges in plantation settings. To address this problem, a portable lab‐on‐chip device has been introduced. This technology enables easy and automatic DNA retrieval from liquid samples by absorbing lysed DNA using magnetic beads. An efficient mechanism for manipulating the magnetic bead within the semiconductor has been successfully implemented. The extraction process typically takes around 15 minutes using a modified methodology on the chip device approach. The chip facilitates the retrieval of two samples with a capacity of 120 µL for each sample. The PCR method was utilized to validate the equivalence of the lab‐on‐chip device extraction to the standard extraction method. This represents a promising alternative for expedited and simplified detection of Ganoderma boninense in field conditions.
Genetic polymorphism and frequency study at 15 short tandem repeat loci in the North and East Indian populations for use in personal identification and applications in India Prabakaran Mathiyazhagan; Thangaraju Palanimuthu; Agasthi Padmanathan
Indonesian Journal of Biotechnology Vol 29, No 1 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.84333

Abstract

Allele frequency is a crucial factor in estimating the weight of evidence (WoE) for an individual’s involvement in a DNA sample. To determine the allele and genotype frequencies within the populations of the northern and eastern states of India, 15 short tandem repeats (STRs) were used, including Penta E, CSF1PO, D18S51, D7S820, D21S11, TH01, D3S1358, Vwa, FGA, TPOX, D8S1179, D16S539, D13S317, Penta D, and D5S818. The study involved 509 randomly selected individuals, analyzed using the PowerPlex 16 System Kit. Various statistical parameters of forensic significance were calculated using Forensic Statistic Analysis Toolbox (FORSTAT) software, including the typical paternity index (TPI), power of exclusion (PE), matching probability (MP), power of discrimination (PD), polymorphism information content (PIC), and observed (Hobs) and expected heterozygosities (Hexp). The analysis revealed a maximum allele frequency of 0.4282 at TPOX, with a minimum frequency of 0.0009 observed at different loci. FGA was found to be the most polymorphic loci among the 15 loci analyzed in the North and East Indian populations. Furthermore, no divergence from the Hardy‐Weinberg equilibrium (HWE) was observed. The results serve as a valuable source of information for establishing a DNA database for North and East Indian populations, providing essential information for population genetics studies and forensic casework in India.
Detection and quantification of splicing variants of Hd3a gene in oil palm Aqwin Polosoro; Wening Enggarini; Kusumawaty Kusumanegara; Toto Hadiarto; Miftahudin Miftahudin; Ence Darmo Jaya Supena
Indonesian Journal of Biotechnology Vol 29, No 1 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.88327

Abstract

Alternative splicing is a complex process that contributes to the generation of diverse mRNA and protein isoforms, including in oil palm (Elaeis guineensis). Despite their importance, many functions of alternative splicing genes remain poorly characterized. This study aims to investigate splicing variants of gene encoding Heading date 3a in E. guineensis (EgHd3a) using the GenBank database and ClustalW algorithm. To ensure the data accuracy and reliability of design isoform‐ specific primers, special emphasis is given to primer design techniques and validation using polymerase chain reaction (PCR) and quantitative real‐time (qRT)‐PCR analysis. The designed primers demonstrated high specificity and discrimination between mRNA specimens. Nucleotide variations at the 3’‐end influenced the specificity of primers with the addition of GC composition. Furthermore, qRT‐PCR analysis revealed a strong correlation between Ct values and gene concentration for the isoforms which indicates a reliable amplification of EgHd3a. Although two isoforms, Hd3a‐X2 and Hd3a‐X3, showed slightly higher than acceptable PCR efficiency values, caution is advised to prevent non‐specific amplification. Despite the challenge posed by the limitation of primer positioning due to alternative splicing, the chosen primer proved optimal for analysis. This study highlights the importance of considering alternative splicing in gene quantification experiments and provides insights into the critical steps, methods, and quality control measures necessary for accurately detecting alternative splicing events, contributing to understanding this complex biological process.
Protective effects of Zingiber cassumunar Roxb. extract against UVB‐induced oxidative stress in Wistar albino rats (Rattus novergicus Berkenhout, 1769) Dian Ayuning Tyas; Nastiti Wijayanti; Tri Rini Nuringtyas; Subagus Wahyuono
Indonesian Journal of Biotechnology Vol 29, No 1 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.90224

Abstract

Protecting the skin from the effects of UVB radiation using natural products is crucial in the cosmeceutical industry. This study aims to investigate the protective effects of Bangle (Zingiber cassumunar Roxb.) against UVB‐induced skin damage in Wistar albino rats. The rhizomes were macerated using 70% ethanol v/v, followed by n‐hexane to obtain n‐hexane soluble and n‐hexane insoluble fraction. The antioxidant properties of the ethanol extracts and n‐hexane soluble fraction were evaluated using a 2,2‐diphenyl‐1‐picrylhydrazyl (DPPH) assay. The study also examined the antiphotoaging properties through reactive oxygen species (ROS) scavenging assay, matrix metalloproteinase‐1 (MMP‐1) expression, and tyrosinase expression against UVB radiation in Wistar albino rats. The results demonstrated that the Z. cassumunar extract and fraction effectively converted DPPH radicals into a more stable compound. Analysis revealed the presence of Benzene, 4‐(1Z)‐1,3‐butadien‐1‐yl‐1,2‐dimethoxy‐ and (E)‐4‐(3,4‐Dimethoxyphenyl) but‐3‐en‐1‐ol as the primary compounds in both the extract and fraction, suggesting their contribution to the observed activity. Furthermore, Z. cassumunar compounds could reduce UVB‐induced ROS production and may protect against skin photoaging by changing the expression of MMP‐1 and tyrosinase levels in Wistar albino rats. These findings suggest that Z. cassumunar holds promise for preventing skin aging.
Performance of salt‐bridge microbial fuel cell (SB‐MFC) with various microorganism cultures on the generation of electricity from tofu wastewater Dani Permana; Herlian Eriska Putra; Oman Rohman; Mahyar Ependi; Djaenudin Djaenudin
Indonesian Journal of Biotechnology Vol 29, No 2 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.80928

Abstract

A suitable wastewater treatment system is required due to the high organic compound content in tofu wastewater, which can harm the environment. Biological treatment methods are effective for treating tofu wastewater due to its characteristics. Microbial fuel cells (MFCs) represent one such biological treatment option, effectively removing organic contaminants while generating low‐power electricity through bioenergetic reactions. In MFCs, microorganisms are used as biocatalysts to degrade the organic compounds present in wastewater. This study aimed to assess the efficacy of Salt‐bridge microbial fuel cells (SB‐MFC) using various acclimatized microbe cultures for reducing organic compounds and generating energy from tofu wastewater. Tofu wastewater was sterilized prior to introduction into the reactor. Additional microbes, including the native microbe consortium from tofu wastewater, Escherichia coli, Saccharomycopsis fibuligera, and a mixed culture of E. coli and S. fibuligera, were then introduced as biocatalysts. Carbon electrodes were utilized as both the anode and cathode. The results indicate that the mixed culture of E. coli and S. fibuligera significantly reduced COD and BOD5 levels, with removal rates of 82.74% and 76.53%, respectively, after 48 h. Furthermore, the culture generated a voltage of 676 mV, a current of 2.53 mA, a power density of 428 mWatt/m2, and 4.789×10‐2 kWh of energy. This study contributes to the advancement of SB‐MFC by utilizing wastewater and a combination of bacteria and yeast as biocatalysts.
The effect of non‐contact electro capacitive cancer therapy on DMBA‐induced rat breast tumor angiogenesis Endah Sri Palupi; Bambang Retnoaji; Pudji Astuti; Firman Alamsyah; Warsito Purwo Taruno; Rarastoeti Pratiwi
Indonesian Journal of Biotechnology Vol 29, No 2 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.87396

Abstract

Alternating Current‐Electric Field (AC‐EF) generated by non‐contact Electro Capacitive Cancer Therapy (ECCT) can inhibit breast tumor growth. However, its effect on breast tumor angiogenesis remains unclear. Since angiogenesis is involved in normal physiology and tumors, it is crucial to investigate the effect of ECCT on normal and breast tumor angiogenesis. Samples consisting of rat breast normal tissue and breast tumors were obtained from the biobank, with tumors induced by 7,12‐dimethylbenz (α) anthracene (DMBA) at 20 mg/kg BW 10 times over five weeks. Meanwhile, ECCT exposure of 150 kHz and 18 Vpp was conducted for 21 days at 10 hours/day. The qPCR method was used for gene expression analysis, while immunohistochemistry used antibody anti‐Vegfr2 that was used to detect Vegfr2 protein expression. Data were analyzed using one‐way ANOVA and t‐tests performed with GraphPad Prism ver.9.5.1 software. The results revealed no impact of ECCT exposure on normal breast tissue angiogenesis. Interestingly, there was a significant increase in the number of blood vessels following the upregulation of Vascular Endothelial Growth Factor Receptor‐2 (Vegfr2) as opposed to its primary signal, Vascular Endothelial Growth Factor‐A (Vegfa). Furthermore, gene expression of Hypoxia Inducible Factor‐1α (Hif1α) and Specificity Protein‐1 (Sp1) was similar to that of the control group, suggesting that Vegfr2‐dependent angiogenesis regulates ECCT‐treated breast tumor angiogenesis.
Elimination of ineffective inorganic salt component in medium for indole‐3‐acetic acid synthesis by Serratia plymuthica UBCF_13 and its effect on the growth of chili seedlings Liza Aulia Yusfi; Djong Hon Tjong; Irawati Chaniago; Muhamad Irsyad; Jamsari Jamsari
Indonesian Journal of Biotechnology Vol 29, No 2 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.88774

Abstract

Indole‐3‐acetic acid (IAA) is an essential phytohormone that controls a variety of plant growth mechanisms. Bacteria can produce IAA to stimulate plant growth, with its production influenced by the culture conditions. Serratia plymuthica UBCF_13 is recognized as an IAA‐producing bacterium, exhibiting maximum IAA production in a yeast medium comprising yeast extract, sucrose, K2HPO4, MgSO4, NaCl, and CaCO3. However, prior studies optimizing individual inorganic salt components indicated minimal impact on IAA synthesis within this medium. This study aimed to eliminate the unnecessary inorganic salt components and the medium was then applied to investigate the IAA biosynthesis pathway and the plant growth‐promoting assay. The elimination assay consisted of yeast sucrose medium devoid of K2HPO4, MgSO4, NaCl, or CaCO3, and yeast sucrose medium containing only MgSO4 and CaCO3. Various indole compounds were then added to the revised medium composition to investigate the IAA biosynthesis pathway of UBCF_13 using high‐performance liquid chromatography (HPLC). Furthermore, the effect of UBCF_13 culture supernatant, cultivated in the new medium, on chili plant growth was evaluated. The highest IAA production (138.8 µg/mL) was observed in the yeast sucrose with CaCO3 and MgSO4 (elimination of K2HPO4 and NaCl). The presence of indole‐3‐acetamide (IAM) compound from the medium extracts, supplemented with multiple indole compounds, revealed that UBCF_13 may use the IAM pathway. The application of UBCF_13 supernatant enhanced the shoot, root length, fresh weight, and germination time of chili seeds by 37.7%, 49.3%, 204.3%, and 38.6%, respectively. This study demonstrated that eliminating K2HPO4 and NaCl provided a new culture medium composition conducive to IAA production by UBCF_13. Moreover, the UBCF_13 extract has the potential to promote plant growth.

Page 48 of 52 | Total Record : 518

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