3 Biotech最新文献

The present study investigated the cumulative effect of pretreatment of rice straw with two enzymes-Silicase (first report) and Laccase as initial stages. The optimal conditions for silicase pretreatment were determined to be a dosage of 100 U/10 g of rice straw, pH 7.0, temperature 40 ºC, and a treatment duration of 30 h. For laccase pretreatment, the ideal parameters were enzyme dose of 40 U/10 g of rice straw, pH 5.0, temperature 50 ºC, and a treatment time of 30 h. At optimized conditions, the silica reduction of ~ 20% was achieved by Silicase pretreatment, whereas the reduction in lignin was upgraded by ~ 29.8% after two stage pretreatment. A reduction of 28.6% in ash content of rice straw and 29.4% in silica was obtained during two stage enzymatic pretreatment. The FTIR studies of the pretreated and untreated straw also depicted the delignification, ash and silica removal of agro-waste. A peak observed at 1542 cm^-1 and 1643 cm^-1 suggests cyclic stretching in phenolic lignin, while the absorption band at 1419 cm^-1 corresponds to the bending (scissoring) of - OCH₃ in the syringyl and guaiacyl units of the phenolic composition. A notable decrease in these vibrations was observed in the silicase + laccase-treated sample, likely resulting from the removal of syringols and guaiacols during the enzymatic pretreatment. Using present outcomes, the study presented that the cumulative impact of Silicase and Laccase was proficient in preparing rice straw for industrial applications and reducing environmental barriers during its conversion.

This study aimed to investigate the toxic effects of ellipticine on liver cancer cells and predict its anti-liver cancer mechanism through network pharmacology, especially by targeting FGFR3 to regulate the RAS/MAPK-P38 signaling pathway, thereby inducing apoptosis of liver cancer cells. The inhibitory effect of ellipticine on the proliferation of HepG2, Huh-7, SMMC7721, BEL-7402, SK-HEP-1, LX-2, and MHCC97H cells was detected by CCK-8 assay, and the IC₅₀ value was calculated. The potential targets of ellipticine were predicted by the database, and the intersection analysis with liver cancer-related targets was performed to construct a protein interaction network (PPI), (KEGG) pathway enrichment analysis, and molecular docking verification. FGFR3 in HepG2 cells was knocked down by siRNA, and the effects on cell proliferation, apoptosis, and ROS levels were observed. The expression changes of FGFR3, RAS, P38, and their phosphorylated forms after ellipticine treatment, as well as the effects of RAS agonist ML-908 and P38 inhibitor PD169316 on cell proliferation, apoptosis, and migration, were detected by Western blotting. Ellipticine has an inhibitory effect on all tested liver cancer cell lines, among which HepG2 has the strongest inhibitory effect, with an IC50 of 5.15 ± 0.25 μM. Ellipticine is predicted to have 32 potential targets, and 5 common targets among the 225 targets related to liver cancer, including PDGFRA, KIT, FGFR3, ERBB2, and STAT3. KEGG analysis showed that these targets are mainly involved in cancer pathways. Molecular docking showed that Ellipticine can bind strongly to FGFR3. FGFR3 expression is highest in HepG2 cells. After knocking down FGFR3, the proliferation ability of HepG2 cells is further weakened, and the addition of apoptosis inhibitor ZVAD can partially restore the proliferation ability. ROS levels increase after Ellipticine treatment, and ROS levels further increase after knocking down FGFR3, and ZVAD treatment can reduce ROS levels. After Ellipticine treatment, the expression levels of FGFR3, RAS, and p-P38 decrease. Ellipticine-induced cell proliferation inhibition and apoptosis were reversed by RAS agonist ML-908, whereas P38 inhibitor PD169316 exacerbated cell apoptosis and migration inhibition. Ellipticine induces apoptosis of liver cancer cells by targeting FGFR3 and inhibiting the RAS/MAPK-P38 signaling pathway. This discovery provides new mechanistic insights into Ellipticine as a liver cancer treatment and may lay the foundation for the development of targeted therapeutic strategies.

Amyloid plaque buildup, tau protein tangles, oxidative stress, and neuronal death are the hallmarks of Alzheimer's disease (AD). Using network pharmacology, molecular docking, and in vivo experiments, this study investigated the neuroprotective potential of Bergenia ligulata (BL) and Nelumbo nucifera (NN) against aluminum chloride (AlCl₃)-induced AD. Network pharmacology focused on important biomarker proteins like acetylcholinesterase (AChE), BCL2, and caspase-3 to identify 74 bioactive targets linked to AD. The evaluation of ligand-protein interactions was done using molecular docking. Male Wistar rats were exposed to AlCl₃ to cause AD-like pathology in vivo, and a combination treatment of BL and NN at varying doses was provided. Apoptosis markers (BCL2, caspase-3), biochemical investigations (AChE activity, oxidative stress markers-GSH, SOD, catalase, and lipid peroxidation), behavioral evaluations (elevated plus maze, conditioned avoidance test), and histopathological analyses were investigated. The combination of BL and NN demonstrated substantial neuroprotection in a dose-dependent manner. Reduced AChE levels point out improved cholinergic activity. Oxidative stress indicators showed improvement, with lower levels of malondialdehyde and higher anti-oxidant levels of GSH, SOD, and catalase. Apoptotic markers showed an increase in BCL2 expression and a decrease in caspase-3, suggesting anti-apoptotic effects. Reduced neuronal degeneration in the cortex and hippocampal regions was confirmed by histopathology of the brain. The synergistic potential of BL and NN demonstrated potent neuroprotective effects by modulating AChE activity, reducing oxidative stress, increasing anti-oxidant levels, and inhibiting apoptosis. These findings highlighted the potential of BL and NN as a new therapeutic approach for the AD.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04274-w.

Diabetes mellitus (DM) is a serious worldwide health issue in the twenty-first century. Additionally, DM, a metabolic endocrine illness that affects the digestion of proteins, carbohydrates, and lipids, has a death rate of 4.9 million individuals globally. This study aims to find anti-diabetic inhibitor for type 2 diabetes (T2D) that inhibits the dipeptidyl peptidase IV (DPP-IV) enzyme using in silico methods. From a range of published literature sources, thirty (30) isoxazole derivatives of UA (IDUA) were selected for this study. To ascertain the possible inhibitory effects of IDUA, ADMET, molecular docking, density functional theory analyses, molecular dynamic simulation and MM/PBSA were conducted. Eleven compounds (1, 2, 3, 4, 7, 13, 18, 21, 22, 24, and 27) were selected from the ADMET study, which were subjected to perform molecular docking against the DPP-IV enzyme of T2D, and findings indicated two compounds (compound 2 and compound 3) showed comparable binding affinity with the reference compound "Linagliptin". In contrast to the reference molecule, which had a binding affinity of - 8.6 kcal/mol against DPP-IV, compound 2 and compound 3 have binding affinities of - 8.1 and - 8.0 kcal/mol, respectively. Furthermore, based on Lipinski's Rule of Five, E_LUMO, E_HOMO, band energy gap, drug-likeness and DFT-based studies demonstrated druggability and high reactivity for these compounds. In addition, the molecular dynamic (MD) techniques to confirm that docked complexes remained stable and that the binding orientation obtained during docking tests were accurate. These compounds may be investigated in vitro and in vivo for the development of potential DPP-IV of T2D inhibitors.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04287-5.

The COVID-19 pandemic highlighted the potential of peptide-based therapies as an alternative to traditional pharmaceutical treatments for SARS-CoV-2 and its variants. Our review explores the role of therapeutic peptides in modulating immune responses, inhibiting viral entry, and disrupting replication. Despite challenges such as stability, bioavailability, and the rapid mutation of the virus, ongoing research and clinical trials show that peptide-based treatments are increasingly becoming integral to future viral outbreak responses. Advancements in computational modelling methods in combination with artificial intelligence will enable mass screening of therapeutic peptides and thereby, comprehending a peptide repurposing strategy similar to the small molecule repurposing. These findings suggest that peptide-based therapies play a critical and promising role in future pandemic preparedness and outbreak management.

This study was conducted to elucidate the mechanism of action of the Traditional Chinese Medicine XinShuaiNing (XSN) formula in CHF based on network pharmacology. A total of 489 compounds in the XSN formula were screened. These compounds predicted 778 targets. A search of CHF yielded 789 corresponding targets, and 151 intersections between the potential targets of the XSN formula and CHF, involving AKT1, AGT, eNOS, and VEGF. Abdominal aortic coarctation (AAC) was used to establish a CHF rat model, and isoproterenol-induced H9c2 cells to establish a myocardial injury cell model. The results showed that the XSN formula downregulated ET-1, BNP, and Hcy and upregulated the ALB levels and also relieved cardiac histopathological damage. The XSN formula reduced the content of pro-inflammatory factors and inhibited the apoptosis of cardiomyocytes. In addition, the expression of fibronectin, α-SMA, collagen 1, and collagen 3 was downregulated by XSN formula treatment, and the fibrotic areas of myocardial tissue were reduced. The XSN formula promoted phosphorylation of AKT1-induced VEGF and eNOS signaling and inhibited AGT signaling. Besides, the XSN formula can affect the apoptosis of H9c2 cells by affecting AKT1, AGT, eNOS, and VEGF. The XSN formula regulates inflammatory factors by inducing phosphorylation of AKT1, upregulating eNOS and VEGF, and downregulating AGT to protect cardiomyocytes from apoptosis and myocardial fibrosis to alleviate CHF. In conclusion, this study identified the target of XSN prescription through network pharmacology screening and experimental validation and confirmed its anti-inflammatory, antiapoptotic, and antifibrotic effects.

To decipher the molecular mechanism behind submergence tolerance in a typical rice genotype (var. Kumrogarh), leaf transcriptome analysis was performed on submerged plant tissue with 7 and 14 days of induced submergence, followed by cataloguing the differentially expressed transcripts. Subsequent bioinformatics analysis identified 5,267 differentially expressed genes (DEGs), of which 2,657 were upregulated and 2,610 were downregulated in four comparative combinations: T7-C7, T14-T7, T14-T7, and C14-C7. A group of 41 co-expressed genes was found across all sets, while 1427, 558 and 83 transcripts were uniquely expressed in the T7-C7, T14-T7, and C14-C7 combinations, respectively. Constructed Ven diagram showed that 1428, 65, and 44 transcripts were commonly expressed in the paired combinations "T7-C7" and "T14-T7", "C14-C7" and "T7-C7", and "C14-C7" and "T14-T7". Gene ontology study functionally categorized the DEGs into molecular functions, biological processes, and cellular components. Additionally, nine transcription factor families were identified, including MYB, WRKY, bZIP, bHLH, SET domain, NAC domain, C2H2 zinc finger, E2F, and HSF, along with a set of differentially regulated signalling genes. Twelve genes related to submergence adaptation were selected for final validation through quantitative real-time PCR-based expression analysis, which demonstrated a strong association with a coefficient (R ² = 0.716) after aligning with the RNA-Seq data. Derived results showed upregulation of gibberellin receptor GID1L2 (LOC_Os02g35940.1), ethylene-responsive element-binding protein (LOC_Os06g08360.1), glyceraldehyde-3-phosphate dehydrogenase (LOC_Os04g38600.1), decarboxylase (LOC_Os08g04540.1), sucrose synthase (LOC_Os03g22120.1), aldehyde dehydrogenase (LOC_Os12g07810.1), endonuclease/exonuclease/phosphatase family domain-containing protein (LOC_Os01g08780.1), polygalacturonase inhibitor 1 precursor (LOC_Os07g38130.1), transmembrane amino acid transporter protein (LOC_Os01g41420.1), and SAM-dependent carboxyl methyltransferase (LOC_Os02g48770.1). This study provides a comprehensive profile of leaf transcriptomics in a traditionally tall-type rice landrace containing both submergence-tolerant Sub1 and SK alleles, highlighting an area of research that remains largely unexplored. These remarkable findings have driven this investigation to decipher the interplay among these key genetic factors by hypothesizing a model leading to the development of a genetic network associated with improved survival under prolonged deep submergence of such a unique rice genotype.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04277-7.

The study used 80 BnTCP genes (Brassica napus TCP genes) in rapeseed, which were identified and designated with nomenclature based on their chromosomal locations. A systematic analysis encompassed the evolutionary relationships, classifications, gene structures, motif compositions, chromosome localization, and gene replication events within these BnTCP genes. These 80 BnTCP proteins were categorized into three subfamilies, with the PCF subfamily showing significant expansion during evolution. Segmental duplications were identified as a major driver of TCP family amplification. To comprehensively assess the evolutionary relationships of the TCP family across diverse plant species, nine comparative genomic maps were constructed, elucidating homologous genes between B. napus and representative monocotyledonous and dicotyledonous plants. In the final phase of the study, the gene expression response characteristics of 15 selected BnTCP genes across various biological processes and stress responses were examined. Noteworthy candidates, including BnTCP28, BnTCP30, and BnTCP76, were identified as potentially crucial in tissue development and environmental stress responses.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04273-x.

This study aimed to develop novel composite films made of Ag, bacterial cellulose (BC), and Clitoria ternatea flower extract for food packaging applications. The films were synthesized using varying concentrations of Ag ion (10^-3-10^-1 M) and flower extract (0-2x10⁴ µg/ml), followed by characterization using scanning electron microscopy-energy dispersive X-ray (SEM-EDX), X-ray diffraction (XRD), and Fourier-transform infrared (FTIR) spectroscopy. The antibacterial activity of the films was assessed against five bacteria, including Escherichia coli, Salmonella Typhimurium, Pseudomonas aeruginosa, Bacillus subtilis, and Staphylococcus aureus. The composite films appeared opaque and slightly dark. A porous network of microfibrils was observed under SEM, and higher Ag concentrations resulted in a rougher film surface. Higher Ag⁺ and extract concentrations resulted in higher percentages of Ag deposited on the surface, as confirmed by EDX (up to 34.7% at 2x10⁴ µg/ml extract and 10^-1 M Ag⁺). Ag/BC/C. ternatea extract combinations generally exhibit higher antibacterial activity than pure BC film. The highest inhibition of S. Typhimurium, P. aeruginosa, and B. subtilis was achieved by a composite film made with 10^-1 M Ag⁺ and 2x10⁴ µg/ml extract with inhibition values of 7.78 mm, 8.12 mm, and 8.25 mm, respectively. All tested composite films also had lower water vapor sorption capacity (2.31-6.71%, depending on the compositions) than BC (6.93%), enabling better protection of the preserved food from surrounding moisture. The Ag/BC/C. ternatea extract composite films are promising, sustainable packaging materials for preserving food quality.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04284-8.

Developing countries have been able to control and minimise the mortality rates caused by pathogenic infections by ensuring affordable access to antibiotics. However, a large number of bacterial ailments are treated with wrong antibiotic prescription due to improper disease diagnosis. Apart from healthcare, antibiotics are also imprudently utilised in crop processing and animal husbandry. This unsupervised usage of antibiotics has propelled the generation of multidrug-resistant species of bacteria. Presently, several traditional antimicrobial susceptibility/resistance tests (AST/ART) are available; however, the accuracy and reproducibility of these tests are often debatable. Rigorous efforts are essential to develop techniques and methods which substantially decrease turnaround time for resistance screening. The present review has comprehensively incorporated the improvements in instrumentation and molecular methods for antimicrobial resistance studies. We have enlisted some innovative takes on conventional techniques such as isothermal calorimetry, Raman spectroscopy, mass spectrometry and microscopy. The contributions of modern molecular tools such as CRISPR-Cas, aptamers and Oxford-MinION sequencers have also been discussed. Persistent evolution has been observed towards adding innovation in diagnostic platforms for drug resistome screening, with the major attraction being the involvement of non-conventional analytical methods and technological improvements in existing setups. This review highlights these updates and provides a detailed account of principal developments in molecular methods for the testing of drug resistance in bacteria.