Biotechnology and applied biochemistry最新文献

α-l-Rhamnosidases are ubiquitous enzymes responsible for derhamnosylation of α-l-rhamnose moiety from a variety of glycoconjugates and numerous natural glycosides. An α-l-rhamnosidase-secreting fungal strain was isolated from soil sample. Further, it was identified as Aspergillus flavus through internal transcribed spacer (ITS) gene sequencing. The enzyme was purified to homogeneity using ion-exchange and gel filtration chromatography and exhibited molecular weight of 71 ± 1 kDa. The maximum catalytic efficiency for the α-l-rhamnosidase was established to be pH 10.0 and at a temperature of 50°C. The purified enzyme exhibits a K_m 0.41 ± 0.06 mM and a V_max 2.43 ± 0.17 µmol/min/mg for naringin hydrolysis. In this study, we modeled the 3D structure of A. flavus α-l-rhamnosidase using SWISS Model and validated it via PDBsum and PROCHECK. Molecular docking of A. flavus α-l-rhamnosidase with naringin and p-nitrophenyl-α-l-rhamnopyranoside (pNPR) identified key binding interactions. Electrostatic surface analysis highlighted ligand-binding sites, revealing crucial residues for substrate recognition and enzyme stability. Active site residues of A. flavus α-l-rhamnosidase forming hydrogen bonds and hydrophobic interactions with naringin and pNPR were identified, providing insights into substrate specificity and its potential applications in glycoside hydrolysis.

This study investigates the inhibitory potential of 2-aminothiazole derivatives on α-glucosidase (α-Glu) activity and their antioxidant properties using a combination of in vitro and in silico methods. Diabetes mellitus, characterized by chronic hyperglycemia, necessitates effective enzyme inhibitors to manage postprandial glucose levels. Among the studied compounds, structural variations significantly influenced α-Glu inhibition, with 2-amino-4-(4-bromophenyl) thiazole showing the highest potency (K_i: 56.61 ± 1.31 µM). Molecular docking analyses revealed critical interactions within the enzyme's active site, emphasizing the importance of electron-withdrawing groups for enhancing inhibitory activity. Antioxidant properties were assessed using Fe³⁺, Cu²⁺, and ABTS radical scavenging assays, where specific derivatives, particularly compound 5 demonstrated strong radical scavenging activity (ABTS IC₅₀ = 8.5-9 µg/mL) and the highest TPTZ-Fe³⁺ reducing capacity among the derivatives (λ₅₉₃ = 0.637 ± 0.005). Density functional theory (DFT) analysis further elucidated the electronic properties of these derivatives, identifying low HOMO-LUMO energy gaps as a determinant of reactivity. These findings underscore the therapeutic potential of 2-aminothiazoles as α-Glu inhibitors and antioxidants, paving the way for developing novel treatments for diabetes and oxidative stress-related disorders. This research contributes to the rational design of bioactive molecules with enhanced efficacy and reduced side effects.

Background: Differentially expressed genes (DEGs) have been known to provide important information on disease mechanisms and potential therapeutic targets. The traditional Chinese medicine (TCM) offers a large reservoir of bioactive compounds that could modulate at these targets. This study is an attempt to investigate the biomarkers in Sepsis and COVID-19 using gene expression analysis and molecular modeling validation of TCM-derived candidate compounds targeting key DEGs associated with sepsis.

Methods: Gene expression data were obtained from NCBI, and limma package in R Studio was used to identify DEGs. Functional annotation was followed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. Protein-protein interaction (PPI) networks were created using STRING, and key hub proteins identified utilizing Cytoscape. Molecular docking was conducted using 216 bioactive compounds obtained from TCM databases against target proteins. To study binding stability, molecular dynamics (MD) simulations of 100 ns were performed using GROMACS on top ranked protein-ligand complexes.

Results: A total of 432 key DEGs were functionally enriched in disease related pathways. Bioinformatics analysis identified the RRM2, AURKB, and CDK1 as hub proteins that could serve as promising therapeutic agents. Salvianolic Acid C, Hesperidin, and Gallocatechin Gallate were lead TCM compounds which showed strong binding affinity to these targets on the basis of molecular docking. Selected protein-ligand complexes were stable according to MD simulations.

Conclusion: The current study indicates the possibility of TCM compounds to target DEGs crucial in sepsis pathology. The integrated bioinformatics approach establishes an approach to identify novel drug candidates, which need further experimental validation.

Ribonucleases (RNases) represent a distinct category of nucleases that facilitate RNA degradation into smaller components. These enzymes are particularly adept at dismantling RNA strands and other materials. A promising strategy for the targeted treatment of cancer cells involves the administration of antibody-based toxic agents designed to eliminate tumor cells specifically. These poisonous agents may include synthetic small-molecule drugs or cytotoxic proteins known as immunotoxins (ITs). ITs are defined by their dual structure, comprising a receptor-targeting element and a cytotoxic component, which may be derived from RNase sourced from plants, bacteria, fungi, or humans. When RNases are used as IT, they can trigger cell cycle arrest or interfere with vital cellular pathways, ultimately leading to apoptosis or the specific destruction of cancer cells. Consequently, this review highlights the application of various RNases in cancer treatment, underscoring their cytotoxic properties, which are crucial for advancing research on health and therapeutic interventions.

Butyl acetate, a valuable flavor ester, is conventionally synthesized through acid-catalyzed reactions, which suffer from environmental concerns and inefficiencies. This study explores a greener alternative using liquid lipase Novozym 400238 for its enzymatic synthesis. The central composite design (CCD) within response surface methodology (RSM) was employed to assess the reaction parameters, including temperature, substrate molar ratio, enzyme concentration, and hexane content, along with their effects on the conversion rate. Following model optimization, the optimal reaction conditions were identified as follows: a temperature of 45°C, a molar ratio of n-butanol to acetate ion of 4:1, an enzyme concentration of 8.3%, and a hexane content of 60%. Under these conditions, the esterification reaction lasted for 5 h and achieved a yield exceeding 90%. Furthermore, the liquid lipase exhibited high reusability, maintaining over 80% yield for 11 cycles under optimal conditions. These findings showcase the potential of liquid lipase as a cost-effective and sustainable catalyst for butyl acetate synthesis, offering a promising avenue for green and eco-friendly production processes.

Natural seepage, anthropogenic activities and accidents affect the ecosystem by increasing hydrocarbon footprints in the environment and cause a disruption in the biogeochemical balance. In addition, these imbalances result in human diseases and a decrease in the diversity of animals and microorganisms. Microbial bioremediation is the only sustainable option for the cleanup of hydrocarbon-impacted wastes, and the genus Alcanivorax is famous for its extraordinary ability to degrade hydrocarbons. The remarkable capacity of the Gram-negative bacterial genus Alcanivorax to break down a variety of hydrocarbons, including long-chain n-alkanes, has attracted a lot of attention in the field of environmental biotechnology. Because they can effectively use petroleum hydrocarbons as their only carbon and energy source, these bacteria are very well-suited for bioremediation and contribute significantly to the natural mitigation of oil spills and other hydrocarbon contaminants. To the best of our knowledge, this is the first comprehensive review specifically addressing the taxonomy, genomic features, and hydrocarbon degradation mechanisms of the genus Alcanivorax.

This study involved the isolation of ten psychrophilic bacterial strains from cold water in Söğütlü village, Erzurum. Following isolation, the strains were characterized using molecular and conventional methods. On the basis of the results of Petri dish assays, Aeromonas salmonicida subsp. salmonicida EDT1 (GenBank accession no: PP068881) exhibited the highest protease activity. The cold-active protease obtained from A. salmonicida subsp. salmonicida EDT1 was partially purified using a one-step, three-phase partitioning (TPP) method under the following conditions: pH 9.0; a ratio of crude extract to t-butanol of 1.0:1.5; and 80% saturated ammonium sulfate. This resulted in a yield of 244% and a purification fold of 42. The molecular weight of the enzyme was found to be approximately 39.44 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis. The optimal pH and temperature for the protease were 9.0 and 5°C, respectively. Although enzymatic activity increased after 60 min at 5°C, it gradually declined thereafter. Protease activity increased in the presence of Mg²⁺ (1 mM), Na⁺ (5 mM), and Mn²⁺ (10 mM) by 253%, 213%, and 169%, respectively. Phenylmethylsulfonyl fluoride (PMSF) significantly inhibited the enzyme, reducing its activity to 15%. After 1 h of incubation, activity increased in the presence of 50% acetone and 50% isopropanol to 393% and 256%, respectively. SDS increased protease activity by 336%. The enzyme exhibited a K_m of 0.751 mg/mL and a V_max of 43.29 µmol/mL/min for casein. The enzyme retained substantial activity after exposure to various commercial detergents. Purified EDT1 protease effectively removed wet and dried blood, as well as grass stains. The enzyme-detergent combination was most effective after 1 h of incubation.

A common problem among preterm newborns is extrauterine growth restriction, or EUGR. The Evidence-based Practice for Improving Quality (EPIQ) strategy aims to reduce EUGR and enhance growth outcomes in neonatal intensive care units (NICUs). The objective of this study is to assess whether implementing EPIQ-based quality improvement interventions is associated with reduced EUGR among preterm infants (< 34 weeks gestation) in a before-after observational study. This study used a before-after design, analyzing retrospective baseline data and prospective postintervention data. A total of 817 preterm infants were included: 231 in the control group (admitted between January 1, 2022, and June 30, 2022; data collected retrospectively) and 586 in the experimental group (admitted between July 1, 2022, and December 31, 2023; data collected prospectively) at Shanxi Children's Hospital. The impact of the interventions was assessed using chi-square and t-tests. There was no significant difference in maternal conditions across groups (p > 0.05). The overall incidence of EUGR was significantly lower in the experimental group (37.54%) than in the control group (57.14%) (p < 0.01). Breast milk usage increased from 25.97% to 41.12% (p < 0.05) and human milk fortifier use increased from 9.09% to 28.84% (p < 0.01), indicating significant improvements in average length and weight growth in the experimental group (p < 0.05). Implementation of EPIQ-based interventions was associated with a significant reduction in EUGR incidence and improved growth outcomes in preterm infants under 34 weeks, supporting its role in enhancing neonatal care.

The exact mechanism by which berberine alleviates depression remains unclear. In this study, we explored the relationship between the antidepressant effect of berberine and the microbiota-brain-gut axis. The levels of IL-1β, TNF-α, IL-6, corticosterone, serotonin, and brain-derived neurotrophic factor (BDNF) were quantified using enzyme-linked immunosorbent assays (ELISA) and Western blotting. Variations in the composition of the gut microbiota were examined using 16S rRNA gene sequencing. Berberine significantly mitigated depressive behaviors in mice with CRS, as manifested by increased total distance traveled and central zone duration in the open-field examination, increased time and number of entries into the outstretched arms during the elevated and maze tests, and an increase in the exercise time during the tail suspension and forced swimming tests. Histopathological analysis indicated that berberine ameliorated CRS-induced hippocampal and colonic damage in mice. Additionally, berberine substantially restrained the generation of proinflammatory cytokines and corticosterone in mice with CRS, while increasing the levels of BDNF and serotonin. Importantly, berberine significantly ameliorated CRS-induced depression-like behaviors (p < 0.01) and restored gut microbial diversity and short-chain fatty acid (SCFA) levels (fold-change: acetate 1.8-fold, butyrate 2.2-fold; p < 0.05). Furthermore, berberine restored the CRS-induced alterations in SCFA production. Our results indicate that berberine may exert antidepressant effects via a pleiotropic mechanism that modulates the microbiome-brain-gut axis.

The use of whole cells represents a modern approach to enzymatic bioconversion for the production of various compounds, particularly pharmaceuticals. In recent decades, the use of wild strains as whole-cell biocatalysts has faced limitations due to challenges such as the lack of control over enzyme production and activity, as well as inefficiencies in enzyme production. As a result, recombinant cells are often employed. Among these, Escherichia coli is the most widely preferred bacterial host for producing recombinant proteins, thanks to its rapid growth, well-developed molecular manipulation tools, the ability to achieve high cell density using cost-effective culture components, and desirable genetic stability. The surface expression of enzymes is one of the most appropriate ways to increase the biotransformation efficiency by recombinant E. coli and reduce overall production costs due to the elimination of the need to purify enzymes and perform the enzyme conversion process in the presence of the pure substrate dissolved in the buffer. This article provides a thorough review of the various factors that influence the production of recombinant surface proteins. It examines aspects that affect biomass growth and methods to enhance protein expression. Additionally, recent research achievements in increasing the production of surface proteins are highlighted, along with promising insights that could pave the way for more sustainable and efficient approaches to producing surface-expressed proteins.