Indonesian Journal of Biotechnology
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Genetic variation and genomic constitution in orchid Dendrobium hybrid section Spatulata derived from interspecific hybridization based on sequence related amplified polymorphism marker
No full textDendrobium hybrid section Spatulata is widely cultivated in Indonesia due to its ease of cultivation, high economic value and adaptability, also extended flower shelf life. Various attempts to meet the rising market demand for Dendrobium hybrid section Spatulata, including the development of new varieties with unique flower traits such as flower color, a longer and bigger horn, and disease resistance. In this study, we conducted a breeding program aimed at developing a new cultivar of Dendrobium hybrid section Spatulata (antelope orchids) through interspecific hybridization. The study aimed to investigate the genetic variation and genomic constitution of the eight hybrids and their corresponding parental lines that resulted from interspecific hybridization using sequence‐related amplified polymorphism (SRAP) marker. Six species of Dendrobium section Spatulata i.e., Dendrobium Sri Mulyani, D. Cochliodes, D. strepsiceros, D. stratiotes, D. Alice Noda, D. helix, and several hybrids of antelope orchids derived from three hybridizations including D. Sri Mulyani × D. cochliodes, D. stratiotes × D. strepsiceros, and D. Alice Noda × D. helix, respectively, were subjected into SRAP markers for genotyping analysis. Dendrobium hybrid section Spatulata hybrids produced by interspecific hybridization were genuine hybrids with substantial genetic variability based on flower morphology, including labellum shapes and color intensities, as well as curly horn shapes and color intensities. The SRAP marker, which was used to genotype the hybrid and parental lines, exhibited a significant degree of polymorphism, and might be used to distinguish each accession. It produced a unique DNA amplicon that ranged from 180 to 530 bp and inherited a certain progeny line. The unweighted pair group mean average (UPGMA) dendrogram and Principal Coordinate Analysis (PCoA) biplot showed that all the hybrids were grouped into three major clusters according to their corresponding parental lines based on their genetic background and ge‐ nomic constitution. These findings are critical for the genetic improvement of the Antelope orchid to develop novel varieties
In silico analysis of antibiotic resistance genes in Lactiplantibacillus plan‐ tarum subsp. plantarum Kita‐3
No full textThe absence of transferable antibiotic resistance genes is required for the safety of commercial probiotics. Previous studies have found that antibiotic resistance genes on plasmids in Lactobacilli make them unsafe for food purposes due to the genes’ ability to transfer to pathogenic microorganisms. In contrast, bacteria from the Lactobacillaceae family are widely used as a probiotic. This study assessed the antibiotic susceptibility of Lactiplantibacillus plantarum subsp. plantarum Kita‐3 (previously known as Lactobacillus plantarum K‐3) isolated from Halloumi cheese using eight antibiotics. Genome sequencing was performed using the Illumina NovaSeq 6000 sequencing platform to detect the presence of antibiotic resistance genes on chromosomes and plasmids. L. plantarum subsp. plantarum Kita‐3 was resistant to clindamycin, streptomycin, and chloramphenicol but susceptible to tetracycline, ampicillin, kanamycin, erythromycin, and ciprofloxacin. Genome sequencing of L. plantarum subsp. plantarum Kita‐3 verified the presence of tetracycline, fluoroquinolones, β‐lactamase resistance genes, and multidrug resistance efflux. Kita‐3 had no transposable elements, gene transfer agents, plasmid‐related functions, or intact prophages. Overall, this study produced the antibiotic resistance profile of L. plantarum subsp. plantarum Kita‐3 to assess the risk of transferring antibiotic resistance genes to other bacteria. The study provides essential data on the safe use of L. plantarum subsp. plantarum Kita‐3 as probiotics
Foldon fusion of RBD and S1 fragments of SARS‐CoV‐2 to stabilize the structure of subunit protein as a vaccine candidate
No full textThe 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
Computational approaches to identify novel inhibitors for the drug‐resistant Mycobacterium tuberculosis DprE1 enzyme
No full textMycobacterium 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
Cloning and characterization of bgl6111 gene encoding β‐glucosidase from bagasse metagenome
No full textβ‐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
The development of papain‐like protease from SARS‐CoV‐2, a potential drug target for antiviral screening: A review
No full textThe 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
Evaluation of the patchouli essential oil (Pogostemon cablin Benth.) aromatic characteristic by near‐infrared spectroscopy
No full textThis 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
Electrochemical performance of plant trace element incorporated silver nanoparticles synthesis from Datura metel L.
No full textIn our report, silver nanoparticles (AgNPs) were prepared from the leaf extract of Datura metel L. via the green synthesis method. Datura metel L. is a herbal medicinal plant from the Solanaceae family. The as‐prepared AgNPs were characterized using UV‐Vis spectrometer, X‐ray Diffraction (XRD), Fourier Transform Infrared (FTIR) spectroscopy and Scanning Electron Microscopy (SEM) with Energy Dispersive X‐ray (EDAX) analysis. The peak appearance of a Surface Plasmon Resonance (SPR) at 415 nm suggested the creation of AgNPs in the UV‐Vis spectrum. The XRD pattern showed the face‐centered cubic crystal structure of AgNPs with organometallic complex phase. Based on the FTIR spectrum, the peaks revealed the existence of biomolecules. SEM images showed the shape of the clastic rocks and the EDAX profile authenticated the presence of Ag and plant trace element. The cyclic voltammetry, Chronopotentiometry, and electrochemical impedance spectroscopy analysis were performed on an as‐prepared Ag electrode. A specific capacitance of 267.59 F/g at 0.5 A/g and a cyclic retention of 83.7% after 5000 charge‐discharge cycles were obtained. Hence, this material could be utilized in supercapacitor energy storage devices
Kinetic modeling, optimization of biomass and astaxanthin production in Spirogyra sp. under nitrogen and phosphorus deficiency
No full textThis 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
Manufacturing and characterization of an effective and eco‐friendly nano insecticide with the aid of green alga Chlorella vulgaris in contrast to traditional insecticide
No full textThere is a growing demand for the manufacture of eco‐friendly insecticide. This study aimed to establish an aqueous extract of Chlorella vulgaris as a green factory to manufacture nano‐insecticide of titanium nanoparticles to control house flies (Musca domestica) by describing the basic properties of TiO2 solution before and after manufacturing. The absorbance was raised to 0.58, while transmission decreased to 38 under UV‐Visible spectra. Regarding to XRD analysis, seven sharp diffraction peaks appeared for a bulk solution while only three sharp peaks were noticed after phyco‐based synthesis. The crystal size of the prepared titanium nanoparticles was determined to be 27.39 nm. Furthermore, the observed size for bulk particles ranged from 92.33 to 249.6 nm through SEM, while for nanocrystalline the size ranged from 9.395 to 206 nm. Various phytochemicals were detected within the algal extract, including phenols, tannins, alkaloids, flavonoids, resins, and saponins. All of these active compounds participated in nano‐synthesis by acting as reducing and stabilizing agents. Finally, titanium nanoparticles were used as a controlling agent against house flies Musca domestica. In this study, this nanoparticles application also has been compared with traditional insecticide Imidacloprid. The high mortality percentages reached 100% against the first larval stage, 70% against the third larval stage, and 93.3% in adult flies. These mortalities were higher after using Imidacloprid for all tested stages. Many phenotypic distortions were also observed in house flies treated with TiO2 NPs prepared by Chlorella, including failure in pupal emergence and maturity, incomplete development in the head, legs, and wings, and disappearance of the genital organs. The study demonstrated that C. vulgaris is a good candidate for nanomanufacturing and a rich naturally derived nanopesticide