Indonesian Journal of Biotechnology
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Extracellular alpha‐amylase from halophilic bacteria Marinobacter sp. LES TG5: Isolation, optimization, and characterization
No full textThe growing demand for stable and effective enzymes requires the discovery of novel microbial producers. Alpha‐amylase is an enzyme in high demand by various industries; however, the discovery of novel and stable alpha‐amylase producers remains limited. This study aims to isolate, optimize, and characterize extracellular alpha‐amylase from halophilic bacteria Marinobacter sp. LES TG5. Bacteria were isolated from saltwater and soil samples collected from traditional salt ponds in Les Village, Bali, Indonesia. Initial screening on starch agar yielded several amylase‐producing colonies, and subsequent spectrophotometric assays identified one promising isolate (LES TG5), which demonstrated an initial activity of 0.63 U/mL. The production of amylase was significantly enhanced by a multi‐stage optimization process. This involved first identifying optimal carbon and nitrogen sources, followed by a one‐variable‐at‐a‐time approach to determine the ideal nutrient levels, salt concentration, and incubation time. This optimization led to an 11‐fold increase in activity, from 0.63 U/mL to 6.99 U/mL, achieved with a medium containing 2.4% (w/v) nutrient broth, 0.4% (w/v) maltose, and 3% (w/v) NaCl with an incubation time of 22 hours. Enzyme characterization revealed optimal amylase activity at pH 7, 55 °C, and 3% (w/v) NaCl. While Ca2+ and Mg2+ had no effect on amylase activity, Pb2+, Fe2+, Sn2+, and Al3+ significantly reduced it. Importantly, the amylase demonstrated outstanding stability in organic solvents such as methanol, ethanol, and n‐hexane, suggesting its potential as a biocatalyst for chemical synthesis in non‐aqueous systems. Furthermore, its notable stability against surfactants and detergents highlights its promise as an additive in cleaning product formulations
Black seed oil inhibits the migration of triple‐negative breast cancer cells and regulates MMP‐9 expression
No full textBlack seed (Nigella sativa L.) is well known for its pharmacological properties, particularly its anticancer activity, with previous studies demonstrating its cytotoxic effects on several cell lines, such as A‐549, DLD‐1, MDA‐MB231, or HCT. This study aims to investigate the effects of black seed oil (BSO) on the migratory activity of 4T1 triple‐negative breast cancer (TNBC) cells, focusing on its bioactive properties. BSO was extracted via hydro‐distillation and analyzed for its phytochemical composition using gas chromatography–mass spectrometry (GC‐MS). The cytotoxicity of BSO and doxorubicin (Dox) was assessed using the MTT assay. The effects of BSO and Dox on cell migration and matrix metalloproteinase‐9 (MMP‐9) expression were evaluated using a scratch wound‐healing assay and gelatin zymography method respectively. Additionally, intracellular reactive oxygen species (ROS) levels were measured using 2’,7’‐dichlorofluorescin diacetate (DCFDA) staining. GC‐MS analysis identified p‐cymene as a major component of BSO, along with various other bioactive compounds. BSO exhibited low toxicity toward 4T1 cells, while its combination with Dox reduced cell viability in a dose‐dependent manner. Furthermore, BSO in combination with Dox inhibited cell migration and suppressed MMP‐9 expressions in 4T1 cells. BSO treatment also led to an increase in ROS levels. In conclusion, BSO exhibits potential anticancer properties by inhibiting cell migration and downregulating MMP‐9 expression, highlighting its possible therapeutic role in TNBC treatment
Enzyme and hormone activities related to phosphorus uptake limitation in oil palm (Elaeis guineensis Jacq.)
No full textPhosphorus (P) is an essential element for oil palm growth and development. Acid phosphatase (Apase) and Pti‐interacting serine/threonine kinase are two enzymes which enzymes confirmed to be related to P‐uptake in oil palm, therefore their activities in oil palm treated with P‐limitation need to be quantified. Acid phosphatase is believed to be induced by P‐deprivation. Conversely, the Pto‐interaction (Pti) serine/threonine kinase activity is associated with abiotic stress. The aim of this study was to quantify of activities of two selected enzymes and phytohormone content in oil palm‐clones in the P‐limitation condition. Two oil palms genotypes were treated with three P dosages i.e. 0% (v/v), 4.67% (v/v), and 14.02% (v/v) represented as starvation, deficiency, and optimum condition, respectively. The activity of these two enzymes was quantified in mitochondria and cytoplasm using spectrophotometry and modified dot‐blot methods, while abscisic acid, indole acetic acid and gibberellic acid content was quantified using ultra performance liquid chromatography (UPLC). The result showed that the Apase activity in P‐optimum was higher than starvation and deficiency in leaf and root tissues in both genotypes, whereas Pti serine/threonine kinase activity was higher in prolific than non‐prolific genotypes in P‐deficient dosage. Furthermore, abscisic acid content was higher in prolific than non‐prolific genotypes in starvation and deficient, whereas other hormone contents were similar. Association study showed that prolific was separated with non‐prolific ones at different doses of P. Finally, the prolific genotype is more adaptable with P deficiency
Orchid‐associated endophytic Bacillus mediates Fusarium suppression and promotes in vitro regeneration of banana plantlets via culture supernatant
No full textThe application of Fusarium‐antagonistic endophytic bacteria with plant growth‐promoting traits offers an effective method to enhance the success of banana plantlet tissue culture while combating Fusarium wilt disease caused by Fusarium oxysporum f.sp. cubense Tropical Race 4 (FocTR4) (VCG 01213). This study evaluates the endophytic bacterium AP3311, isolated from healthy banana roots in direct association with orchid roots. AP3311 exhibited strong antagonism toward FocTR4, hyphal colonization ability, and multiple growth‐promoting activities, including phosphate solubilization, nitrogen fixation and auxin production. 16S rRNA gene sequencing identified that AP3311 belongs to the genus Bacillus, while metabarcoding analysis revealed that Bacillus species dominate the root microbiomes of both bananas and orchids. The bacterial supernatants stimulated root development and leaf growth in vitro. Metabolomic profiling indicated that antimicrobial compounds, together with plant growth regulators, promoted both root and shoot growth. Overall, the research demonstrates that Bacillus sp. AP3311 and its supernatants are valuable components in banana tissue culture, providing the dual benefits of plant growth promotion and effective disease control
Characterization and antibacterial activity of biosynthesized silver nanoparticles using Stachytarpheta jamaicensis leaf extract as bioreduction
No full textTheir nanometer size, broad spectrum, and antibacterial mechanism give silver nanoparticles (NPAg) the potential to be used to inhibit the growth and spread of methicillin‐resistant Staphylococcus aureus (MSRA) in medical devices. Synthesis of AgNPs from Stachytarpheta jamaicensis leaf extract is considered more environmentally friendly and has low production costs. The objective of this study was to investigate the properties and antibacterial potential of AgNPs by utilizing S. jamaicensis leaf extract at concentrations of 0.5%, 1.0%, and 1.5% in a 1 mM AgNO3 precursor. Nanoparticle characterization was performed on the AgNP supernatant obtained by centrifuging the synthesis solution at 100 rpm for 5 min. Characterization of the NPAg size was confirmed by surface plasmon resonance (SPR) analysis in UV‐Vis spectrophotometer, while the size distribution was measured by a particle size analyzer. Surface morphology was performed using scanning electron microscopy (SEM), and antibacterial activity was evaluated by the disc diffusion method. The results showed that AgNPs had the best nanoparticle characteristics in an extract concentration of 0.5%, the synthesis indicated by SPR at a wavelength of 434 nm and an average size of 80.67 nm. SEM analysis showed the formation of clusters at variations of 1.0% and 1.5%. The antibacterial activity of AgNPs against MRSA was the highest at 0.5%, with an inhibition zone diameter of 0.77 mm. The higher concentration of S. jamaicencis leaf extract increases the risk of cluster formation, which enlarges the AgNPs, while antibacterial activity was reduced
Anti‐inflammatory properties of conditioned medium from human Wharton’s jelly mesenchymal stem cells
No full textAcute respiratory distress syndrome (ARDS) is a critical respiratory dysfunction triggered by intense in‐ flammation, microvascular damage, and increased epithelial and pulmonary vascular permeability. Human Wharton’s jelly mesenchymal stem cells (hWJMSCs) possess regenerative and anti‐inflammatory activities through the cytokines, chemokines, and growth factor secretion. The development of anti‐inflammatory agents derived from hWJMSCs has become one of the therapeutic solutions. Instead of direct cell use of hWJMSCs, their conditioned medium (CM) provides a cell‐free approach that delivers bioactive factors while minimizing the risks associated with stem cell transplantation. This study aims to measure the levels of vascular endothelial growth factor‐α (VEGF‐α), epidermal growth factor‐β (EGF‐β), interleukin‐10 (IL‐10), and hepatocyte growth factor (HGF) in CM‐hWJMSCs under non‐starvation and starvation conditions (24, 48 and 72 hours) using ELISA. The anti‐inflammatory potential of these factors was then analyzed through molecular docking with pro‐inflammatory cytokines. VEGF‐α, EGF‐β, IL‐10 and HGF levels were measured across all conditions. VEGF‐α ranged from 2590.37 to 3613.92 ng/mg protein; EGF‐β 347.01–504.43 ng/mg; IL‐10 302.59–729.28 pg/mg; and HGF 1747.20–2903.52 ng/mg. The molecular docking revealed strong binding between VEGF‐α, EGF‐β, IL‐10 and HGF with pro‐inflammatory cytokines, namely IL‐1β, IL‐6 and TNF‐α. VEGF‐α had the strongest bond with TNF‐α (–1162.3 kJ/mol), while EGF‐β formed the most hydrophobic and hydrogen interactions. The findings suggest that CM‐hWJMSCs, enriched with anti‐inflammatory and regenerative cytokines, may serve as a promising candidate for modulating the inflammatory pathways involved in ARDS pathogenesis. Longer starvation increased the secretion of VEGF‐α, EGF‐β, IL‐10 and HGF. These factors are known to promote angiogenesis, regulate immune responses, and protect against epithelial injury, thereby supporting the anti‐inflammatory and regenerative potential of hWJMSCs‐CM for ARDS therapy
Network pharmacology‐based exploration of gut microbiota‐derived metabolites for type‐2 diabetes
No full textProbiotics confer health benefits and have been investigated for their potential therapeutic properties in type‐2 diabetes (T2D) treatment. This study employs a network pharmacology approach to explore gut microbiota‐derived metabolites that potentially alleviate T2D. Several strains and species of gut microbiota were identified that may produce metabolites with therapeutic potential for T2D. Interestingly, quercetin produced by Bacteroides uniformis and daidzein produced by Bifidobacterium adolescentis and Bifidobacterium breve have been studied for their antidiabetic effects. Using a network pharmacology approach, it was found that quercetin may target AKT1 and EGFR, critical proteins involved in insulin signaling pathways related to T2D. Additionally, 10‐oxo‐11‐octadecenoic acid produced by Lactobacillus plantarum and 10‐keto‐12Z‐octadecenoic acid produced by Lactobacillus paracasei were found to target PPARG, a gene regulating insulin signaling. These findings were further validated by the molecular docking analysis, which showed suitable to satisfactory binding strengths
Antibacterial activity of mycelial extract from a local fungus, Sclerotium rolfsii
No full textMycelium‐to‐sclerotium differentiation in fungi involves not only morphological but also biochemical changes throughout the process, which may contribute to their persistence and be a possible source of bioactive compounds. This study aims to evaluate the antibacterial activity and identify the bioactive compound in the local isolate Sclerotium rolfsii. Fungal culture was grown in media containing potato extract (20 g/L), dextrose (20 g/L), and peptone (5 g/L) for 27 days under static conditions at room temperature. Mycelium, sclerotium and filtrate were collected every three days and extracted with methanol, followed by evaporation and antibacterial screening. Significant activity was observed in day three of mycelial extract, which showed morphology of initial sclerotium formation (MIC 0.39 mg/mL) against B. subtilis and E. coli. An improved extraction method (sequential extraction) was employed for mycelial sample on the third day. N‐hexane and ethyl acetate extracts exhibited stronger activities (0.20 mg/mL). Ergosterol was identified after TLC‐bioautography, radial chromatography, and NMR elucidation analysis. S. rolfsii mycelium (third day‐sclerotial initiation) was found to contain ergosterol, demonstrating strong defense against bacteria, and possibly related to sclerotium‐differentiation metabolites. These findings may pave the way for more extensive studies of sclerotium differentiation as an interesting phenomenon of fungal development and bioactive compound origins
In vitro evaluation, molecular docking, and molecular dynamics studies of resorcinol derivatives against yeast α‐glucosidase
No full textNine resorcinol derivatives were evaluated for their ability to inhibit yeast α‐glucosidase using the in vitro method. Three molecular docking programs (Autodock Vina, Autodock4 and DockThor) were employed to determine the binding energies. The results showed that two resorcinol derivatives possessing butanoyl (1) and butyl (9) groups demonstrated good inhibitory activity against α‐glucosidase, with IC50 values of 75.9 and 33.3 µM respectively, compared with other derivatives (2–8) and acarbose (IC50 = 832.8 µM). Furthermore, molecular docking indicated that compounds 1 and 9 had better binding affinities than acarbose and the native ligand. Both compounds showed similar interactions with Asp349 and Glu408, which were associated with acarbose and the native ligand. Moreover, molecular dynamics analysis indicated that compound 9 exhibited greater stability than compound 1 when complexed with α‐glucosidase. Therefore, compound 9 has the potential for further studies, both in vitro and in vivo, to evaluate its toxicity, side effects and efficacy
Morphological and molecular identification of an unknown fungal isolate from Al‐Dujail District: A new record of Tulostoma winterhoffii in Iraq
No full textThe Tulostoma genus, known as stalkballs or stalked puffballs, belongs to the Agaricaceae family. This study was designed to identify an unknown fungal species collected from the Al‐Dujail district in Iraq based on morphological examination and molecular analysis of the internal transcribed spacer (ITS) region. Between April and July 2019, samples were collected from garden soil in the Al‐Dujail district, Salah Al‐Din Governorate, Iraq. Morphological characteristics were documented using light microscopy. Genomic DNA was extracted and purified, and the ITS region was amplified using conventional PCR with specific primers. The amplified products were sequenced, and phylogenetic analysis was conducted using MEGA11 software. Morphological analysis revealed smooth, yellow to brown, nearly circular basidiospores. The ITS region amplification yielded a 588 bp fragment. Basic Local Alignment Search Tool (BLAST) analysis showed 91% similarity between the sample (S1‐ITS‐Iraq) and Tulostoma winterhoffii (accession number KU518975.1). The isolate was assigned in GenBank under accession number PV249065, with phylogenetic analysis positioning S1‐ITS‐Iraq in a cluster with the Tulostoma species, with a bootstrap value of 97%, indicating a close relationship. The fungal sample from Iraq was identified as a new record within the genus Tulostoma, marking the first report of T. winterhoffii in the region