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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
 1 
Search results for , issue "Vol 28, No 1 (2023)" : 7 Documents clear
Revealing disease‐specific endogenous target mimic of microRNA from long non‐coding RNA identification and characterization in Musa spp. Audie Masola Putra; Husna Nugrahapraja; Fenny Martha Dwivany
Indonesian Journal of Biotechnology Vol 28, No 1 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.49368

Abstract

Banana (Musa spp.) is one of the most widely consumed fruits in the world. Unfortunately, the plants are at risk from many disease problems, which mainly derive from microorganism. It is a little known about the relationship between disease‐inducing microorganisms and plants, particularly at the molecular level. This research aimed to characterize long non‐coding RNA (lncRNA) from bananas that may have roles in regulating gene expression related to the disease response mechanism in banana derived from transcriptomic libraries. Furthermore, the detected transcripts were analyzed to identify the endogenous target mimics (eTMs) interaction between lncRNA and microRNA (miRNA) using computational approaches. Data from Cavendish banana (AAA group), Berangan (AAA group), Yunnan Banana (Itinerans), Dajiao (ABB group), and Klutuk (BB group) were used in this research. We found that lncRNA tends to be unsustainable, and most sizes are below 1000 bp (≥ 75%). Based on this result, we investigated the eTMs to determine lncRNA transcripts and miRNA, such as miR397 in Cavendish and miR444 in Klutuk. This transcript would be regulated following exposure to extreme temperatures and disease, indicating the possibility of disease‐specific interaction between bananas and their environment at the molecular level.
Evaluation of the patchouli essential oil (Pogostemon cablin Benth.) aromatic characteristic by near‐infrared spectroscopy Diego Mauricio Cano-Reinoso; Yohanes Aris Purwanto; I Wayan Budiastra; Shinichiro Kuroki; Sutrisno Sutrisno; Slamet Widodo
Indonesian Journal of Biotechnology Vol 28, No 1 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.69073

Abstract

This study aimed to evaluate the aromatic characteristic of patchouli essential oil (Pogostemon cablin Benth.) by near‐infrared spectroscopy combined with chemometric treatments. The study used 84 oil samples collected from around Indonesia, namely in Konawe, Kolaka, Bogor, Garut, Aceh, Jambi, and Masamba. Several pretreatments were used to process the spectral data, together with the application of partial least squares. The spectrum wavelength applied was between 1000 and 2500 nm. The spectra data were separated to develop two models based on their physical and chemical properties (Bogor, Garut, Konawe, and Kolaka in the first model; Aceh, Jambi, and Masamba in the second one). Liquid chromatography‐mass spectrometry (LC‐MS) was used as a reference method. Patchouli alcohol was established as the main chemical compound of this aromatic oil. The best calibration for the first model was that with mean center normalization as a data pretreatment, while for the second model, it was the one using the second derivative. Both models had a correlation coefficient higher than 0.90 and a coefficient of variation lower than 2.98%. In conclusion, near‐infrared spectroscopy can be employed as an accurate tool to determine the characteristic of patchouli oil.
Inhibition of protease activity and anti‐quorum sensing of the potential fraction of ethanolic extract from Sansevieria trifasciata Prain leaves against Pseudomonas aeruginosa Whika Febria Dewatisari; Laurentius Hartanto Nugroho; Endah Retnaningrum; Yekti Asih Purwestri
Indonesian Journal of Biotechnology Vol 28, No 1 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.73649

Abstract

Sansevieria trifasciata is a plant that is commonly utilized in traditional medicine. The leaves of S. trifasciata show antibacterial properties against Pseudomonas aeruginosa. This bacterium is an opportunistic pathogen that can cause serious illness in humans and produce a variety of virulence factors responsible for bacterial pathogenesis with quorum sensing (QS) systems that mediate intracellular communication. Bacteria produce protease through a QS mechanism in which they express signaling molecules to become pathogens. Proteases are extracellular enzymes required for successful infection that mediate biofilm spread through QS and regulate a variety of cellular and physiological functions. This research aimed to evaluate the protease, and anti‐QS activities of the ethanolic extract from S. trifasciata leaves against P. aeruginosa and the expression of QS genes. An azocasein test was used to determine the protease activity in qualitative and quantitative methods. Using real‐time quantitative polymerase chain reaction, a study was conducted to investigate the effect of ethanolic extract from S. trifasciata leaves on selected QS‐regulatory genes at the transcriptional level. The results showed that the potential ethanolic extract from S. trifasciata leaves inhibited the protease enzyme activity by as much as 77.1%. The potential ethanolic extract from S. trifasciata leaves decreased the expressions of lasA, lasB, lasI, lasR, rhlI, and rhlR with 2‐ΔΔCt values of 0.81, 0.93, 0.76, 0.97, 0.90, and 0.55 respectively.
Whole genome sequence analyses of Indonesian isolates SARS‐CoV‐2 variants and their clinical manifestations Elnora Listianto Lie; Tedi Dwi Fauzi Hermawan; Kholis Abdurachim Audah
Indonesian Journal of Biotechnology Vol 28, No 1 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.73783

Abstract

The SARS‐CoV‐2 virus has been the cause of the global pandemic since the end of 2019. Since then, the virus has mutated to create different types of variants with numerous effects on those infected. This has complicated human intervention for prevention. Indonesia was heavily affected by the pandemic, specifically from May to August 2021, and as a country has recorded many distinct isolates. Thus, characterization of the virus strains from Indonesia is important. GISAID, NCBI BLAST, and MAFFT version 7 were used. There were 9,488 isolates in Indonesia as of November 2021, with the majority including the Delta variant. While most of the isolates have mutations common to those from other countries, there are some atypical ones, such as mutation V1264L in the Delta variant that was suspected to play a role in worsening the pandemic. The Delta variant had the most mutations in the spike protein when compared to the Alpha and Beta variants, giving it important roles in infectivity and vigorous entry into cells, with some general clinical manifestations like fever and sore throat; however, the severity of the Delta variant is attributable to its rapid growth. This is why, from May to November 2021 in Indonesia, cases of the Delta variant rocketed, unlike the other variants.
The efficacy of a chicken antibody for the development of immunoassay‐based rapid detection in sugarcane mosaic virus disease Nurmalasari Darsono; Widhi Dyah Sawitri; Retnosari Apriasti; Agus Heri Setyo Wahyudi; Putri Andreyna Saragi; Victorin Mega Putri; Sugiharto Sugiharto; Win Darmanto
Indonesian Journal of Biotechnology Vol 28, No 1 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.74104

Abstract

Sugarcane Mosaic Virus (SCMV) infection is one of the most serious problems that can result in severe yield loss of sugarcane. Since the symptoms of SCMV infection are similar to other biotic and abiotic stress symptoms, the development of a rapid diagnostic with high precision is required. The use of laboratory animals such as rabbits is required for antibody production in immunoassay‐based detection. However, due to its many advantages, specific chicken egg yolk immunoglobulin (IgY) has received considerable attention as an alternative antibody production in immunodiagnostics for infectious diseases. In this study, IgY antibody against SCMV recombinant coat protein (CP) was successfully obtained from chicken blood serum and tested to compare its efficacy against antibody from rabbit (IgG) using immunocapture reverse transcription‐polymerase chain reaction (IC‐RT‐PCR). The result showed that IgY and IgG could detect 0.1 g SCMV infected leaves using 1000‐times‐diluted antibodies. The IgY antibody was also confirmed to be reproducible and potentially applicable in plant disease diagnostics using an antibody‐based detection.
Biophysical characterization of folded state type II luciferase‐like monooxygenase Adinda Fitri Salsabila; Abidah Tauchid; Muhammad Saifur Rohman; Donny Widianto; Sebastian Margino
Indonesian Journal of Biotechnology Vol 28, No 1 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.75783

Abstract

We noticed that the Priestia megaterium genome contains five Luciferase‐like monooxygenase (LLM) encoding genes, however, their functions are unknown. The objective of this work was to characterize the biophysical properties of the recombinant LLM2 from Priestia megaterium PSA10 through in vitro and in silico approaches. We successfully cloned into the pET vector system and expressed the recombinant LLM2 in Escherichia coli BL21(DE3). The recombinant LLM2 was overproduced and purified in the form of an inclusion body with a molecular weight of ±39.5 kDa when it was analyzed in 15% SDS‐PAGE. The inclusion body of recombinant LLM2 was then refolded and characterized for its biophysical properties by measuring the UV spectrum of 200 to 250 nm wavelength and determining the change of enthalpy (ΔH) and entropy (ΔS) at the melting temperature. The refolded recombinant LLM2 exhibited a strong spectrum at 205 nm, while the unfolded recombinant LLM2 did not. The Tm, ΔHTm, and ΔSTm values of the refolded recombinant LLM2 were determined to be 318.31±4.4 K, 11.76±1.3 kJ.mol‐1, and (3.74±0.48)x10‐2 kJ.mol‐1.K‐1, respectively. The predicted 3D structure of LLM2 showed that the protein contains the TIM‐barrel, resembling the common global fold of bacterial luciferases. Determination of the cofactor preference suggested that the LLM2 preferred FAD for its cofactor.
Production, purification and characterization of chitinase from Micromonospora sp. AR17 Yohanes Harvinda; Ustadi Ustadi; Masagus Muhammad Prima Putra
Indonesian Journal of Biotechnology Vol 28, No 1 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.77137

Abstract

N‐acetylglucosamine (NAG) is the monomer product of chitin, which has been widely used as a bioactive com‐ pound in applications such as anti‐tumor, anti‐microbial, and antioxidant activities. In production, biological processes using enzymes are preferable to chemicals due to environmental issues. This study aims to determine the activity, purity level, and molecular weight of purified chitinase from Micromonospora sp. AR17 determines the concentration of NAG produced by purified chitinase that has been characterized. Chitinase was produced by fermentation in colloidal chitin broth at 40 °C, pH 7, for 7 days, while chitinase activity was checked every 24 h. The optimal fermentation time was used to produce chitinase for a further purification step. Enzyme purification was carried out by ultrafiltration, ammonium sulfate precipitation, ion exchange chromatography (Q Sepharose Fast Flow), and gel filtration (Sephacryl S‐300). The purified enzyme was then char‐ acterized for optimum time, pH, and temperature to produce NAG. The results suggested that the fourth day was the optimal time for chitinase production, with chitinase activity of 0.0040 U/mL and a NAG concentration of 7.62 µg/mL. The purifica‐ tion step successfully increased the purity by 6.82 times with chitinase‐specific activity at 1.4648 U/mg. Production of NAG with purified chitinase produced a NAG concentration of 32.472 µg/mL with an incubation time of 30 min at 40 °C and pH 7.

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