Ancestral sequence reconstruction (ASR) offers a revolutionary approach to resurrect functional proteins, yet its potential in transporter engineering remains underexplored. Here, we pioneered the application of ASR to reconstructing ancestral xylose transporters, addressing the persistent challenge of glucose-mediated inhibition of xylose uptake in Saccharomyces cerevisiae during xylose co-fermentation. Through rigorous ASR analysis, we reconstructed ancestral xylose transporters (Xt) and selected two candidates—Xt3 (approximately 140 million years old) and Xt7 (approximately 40 million years old)—based on their phylogenetic positioning, degree of sequence divergence from extant homologs, and predicted structural integrity. Functional characterization demonstrated that both Xt3 and Xt7 significantly enhance xylose uptake efficiency and mitigate glucose-induced repression. In fermentation experiments with mixed sugars (40 g/L xylose and 40 g/L glucose) within 72 h, recombinant S. cerevisiae expressing Xt3 achieved 22.75 g/L xylose consumption, surpassing the benchmark N326F^Xltr1p (16.22 g/L) by 40.27% and outperforming Xt7 (21.36 g/L) by 6.51%, highlighting Xt3 as the most efficient transporter. Molecular docking suggested a potentially more favorable binding mode for xylose in the ancestral transporters (binding affinity: −3.68 kcal/mol for Xt3 vs. −3.15 kcal/mol for N326F^Xltr1p). Molecular dynamics simulations further demonstrated that the ancestral transporters formed complexes with xylose that exhibited faster convergence to a stable state and maintained significantly greater conformational stability throughout the simulation compared to the N326F^Xltr1p complex. These computational insights provide a plausible structural basis for their enhanced performance. This work contributes to the advancement of lignocellulosic biorefinery technology and provides a practical reference for resurrecting other valuable proteins using ASR’.

Natural exogenous additives (EA) suitable for the tobacco fermentation need to be developed to enhance the fermentation quality and economic value of low-grade cigar tobacco leaves (CTLs). This study analyzed the impacts of three compound Chinese herbal medicine (CHM) on metabolites and microorganisms during CTLs fermentation. The results manifested that EA facilitated the degradation of total sugar, starch and protein, while enhancing the accumulation of reducing sugar in CTLs. Furthermore, EA raised contents of free amino acids (FAAs), while Asp, Glu, Ser and His were found to be key differential FAAs of CTLs. During fermentation, the total contents of volatile flavor components (VFCs) initially increased and then declined. Furthermore, EA contributed to more harmonious compositions of VFCs by promoting the formation of neophytadiene, ketones, esters and aldehydes, as well as facilitating nicotine degradation. According to variable importance in the projection (VIP) > 1 and odor activity value (OAV) > 1, 7 key differential VFCs were identified. EA enhanced positive microbial interactions and led to a more stable and coordinated symbiotic network. Linear discriminant analysis effect size (LEfSe) identified 9 genera as differentially dominant microorganisms in CTLs, which were closely associated with chemical compositions and key differential flavor metabolites. In addition, EA promoted cigar tobacco characteristics (CTCs) by altering bacterial alpha diversity and influencing the assembly of dominant microbial communities. Overall, this study offered theoretical insights into the innovative applications of CHM in CTLs fermentation, and presented new perspectives for enhancing CTLs quality and customizing flavor profiles.

Escherichia coli, a bacterium indicating improper hygiene practices during food production, is commonly found in the intestines of humans and animals, while Salmonella spp. are dangerous bacteria that cause typhoid fever and severe diarrhea. These pathogens have been found in fresh vegetables. This study investigated how the vegetable surface characteristics influenced bacterial adhesion. The reduction of bacteria during the washing process was assessed using different concentrations and types of chemicals. The relationships between variables obtained from image analysis techniques and bacterial adhesion on vegetable surfaces were also evaluated. The most effective way to inhibit bacteria was by washing with 2.0% lactic acid, with bacterial reduction from an initial concentration of 8.74 to 2.92 log CFU/m². Pearson’s correlation with the highest r value was surface area (A) with values ranging from 0.764 to 0.993, followed by surface roughness (R) with values between 0.019 and 0.986, and Fractal dimension (FD) with values between − 0.510 and − 0.992. The correlation between A and the number of bacteria (E. coli and Salmonella) was the highest, with surface area influencing bacterial adhesion to the vegetable surface. Greater surface roughness was associated with a higher initial bacterial load, making the A value a good predictor of changes in bacteria during washing with organic acids at various concentrations.

Synthetic chemical seed treatments, while effective, often raise significant environmental and health concerns. These concerns stem from the use of hazardous chemicals such as fungicides and insecticides that, besides posing risks to workers, have broader environmental impacts. These hazardous chemicals can leach into the soil and water systems, disrupting ecosystems, harming beneficial organisms, and entering the food chain. Agro-industrial byproducts/wastes (AIBWs) represent an abundant, environmentally friendly resource with potential for seed treatments. We focused on AIBWs that are produced in enormous amounts and do not pose potential hazards since they are commonly used to feed animals as well as food additives for humans, including wheat bran (WB), wine pomace (WP), and brewer’s spent grain (BSG). We investigated the effects of imbibing wheat seeds in water-soluble extracts of AIBWs or coating seeds with a biopolymer supplemented with AIBW substances on wheat growth and reproduction. As controls, we used water-soaked (WS) and non-soaked (NS) seeds, as well as chemically Celest Top-coated seeds. Petri dish assays showed that seeds imbibed in AIBW extracts exhibited enhanced post-germination growth as compared to NS seeds. Thus, while 81% of NS seedlings produced up to 3 seminal roots (SRs), 84% of WB and 64% of Celest Top seedlings produced 4 and 5 SRs. Net-house experiments revealed that Celest Top and AIBW extracts had a positive effect on reproduction as compared to NS, displaying 17.4%, 14.5%, 30.3%, and 34.3% increases in grain weight per spike in Celest Top, WB, GP, and WP, respectively. Metabolic analysis of seeds derived from treated plants revealed variation in metabolite profiles with a notable increase in the amino acid tryptophan. We utilized the nature-sourced polysaccharide carboxymethylcellulose (CMC) to coat seeds with AIBW substances derived from GP, referred to as CMC-GP. The results indicated that CMC-GP and Celest Top enhanced root growth, displaying 2- and 1.5-fold increases in fresh and dry weight, respectively, as compared to NS and CMC-coated seeds. Thus, AIBWs appear to provide cost-effective, eco-friendly alternatives to the hazardous chemical seed coatings, whether applied via imbibition or coating, while aiding in waste valorization within the circular economy.

Baiying Juhua Decoction (BYJHD) is a well-established traditional Chinese herbal formula primarily composed of Solanum lyratum and chrysanthemum, which necessitates a thorough investigation to clarify its mechanisms in combating non-small cell lung cancer (NSCLC). This study employed a combination of network pharmacology predictions, serum pharmacochemistry analysis, and various machine learning algorithms (including LASSO, SVM-RFE, and RF) to identify 38 bioactive compounds that target 653 proteins associated with NSCLC. A cross-analysis of 2161 differentially expressed genes (DEGs) and 3124 functional modules led to the identification of 54 critical therapeutic targets. Following this, protein-protein interaction (PPI) and machine learning analysis pinpointed five key signaling regulators. Molecular docking studies demonstrated strong binding affinities between four representative compounds from BYJHD and these targets. Both in vitro and in vivo experiments confirmed that BYJHD inhibits the progression of NSCLC by exerting anti-angiogenic effects, specifically through the inhibition of the ACVRL-1/Smad/ID-1 signaling pathway and the downregulation of CD34. These findings effectively connect traditional clinical applications with contemporary mechanistic insights, positioning BYJHD as a promising multi-target therapeutic candidate for NSCLC.

Conventional soybean processing relies on hexane extraction and high-temperature treatments, which cause protein denaturation and hinder the separate recovery of oil, protein, and carbohydrate. To address this limitation, this study aimed to establish a sustainable enzymatic soybean processing (ESP) strategy for separate collection of all three major components: intact oil bodies, undenatured protein, and monomerized carbohydrate. This is the first demonstration that ESP efficiency can be significantly enhanced by integrating pulsed sonication. Multi-enzyme systems were produced via solid-state fermentation (SSF) of soyhull by Aspergillus niger and applied to cracked soybean particles. Screening of 15 SSF enzyme extracts revealed that pectinase, polygalacturonase, and invertase were the limiting carbohydrase activities for cell wall degradation. Effects of processing variables including protease activity, reaction media, and reaction time were evaluated to minimize protein loss. Using water instead of citrate buffer as reaction medium and limiting processing time to≤48 h reduced protein dissolution to below 20%. ESP was further enhanced through pulsed probe-sonication (12 W/mL, 1 s on/23 s off), which reduced processing time to 24 h while increasing carbohydrate solubilization to up to approximately 90% depending on enzyme loading. Simple centrifugation enabled efficient fractionation into intact oil bodies (100%), native proteins (≈70%), and hydrolysates containing soluble proteins (≈30%) and monomerized carbohydrate (≈90%). These findings demonstrate an integrated enzymatic-sonication approach that enables hexane-free, low-temperature soybean processing with minimally denatured, high-value products and offers a pathway for sustainable soybean biorefinery.

To explore the bioaugmentation mechanism of biogas-production promotion and risk reduction of antibiotic-resistance genes (ARGs) in the anerobic co-digestion of cattle manure and rice straw with biochar addition, the performances of digestion and productivity with different amounts of biochar additions (0, 1.25, 3.75 and 5 g·L⁻¹ slurry) were studied. The results indicated that, biochar addition could effectively promote biogas production, and the cumulative methane (CH₄) yields from the treatments with 3.75 g·L⁻¹ slurry and 5 g·L⁻¹ slurry biochar additions were18.7 times and 14.8 times of CK (0 g·L⁻¹ slurry), respectively. Combined with Fourier transform infrared spectroscopy (FTIR) analysis and high-throughput sequencing-based microbial community quantification, the methanogenesis was enhanced through three possible pathways: (1) the porous structure and aromatization characteristics of biochar could promote destruction of cellulose bundle structure, thereby promoting the hydrolysis of lignocellulosic substrates; (2) Biochar regulated volatile fatty acid (VFA) concentrations within an optimal range, enhancing the buffering capacity of the anaerobic digestion system; (3) The low-dose biochar (1.25 g·L⁻¹ slurry) achieving the optimal ARG risk mitigation by suppressing the primary ARG host Bacteroidota.

Daqu is a critical saccharifying and fermenting agent in the traditional solid-state production of strong-aroma Baijiu, with its physicochemical properties and microbial communities playing a vital role in both starter quality and final aroma. This study analyzed twelve Daqu samples from four key production regions in Sichuan Province—Luzhou (L), Suining (S), Yibin (Y), and Zigong (Z)—assessing physicochemical parameters such as moisture content, acidity, saccharification, liquefaction, and esterification activities. Microbial communities were characterized using Illumina high-throughput sequencing. Regional variations in physicochemical properties were observed, with Y showing the highest acidity, saccharification, and esterification activities. While no significant regional differences in alpha-diversity were found, β-diversity analysis (PCoA) revealed distinct microbial structures. Bacteria were predominantly represented by Bacillus, Lactobacillus, and Weissella, while Aspergillus, Saccharomycopsis, and Rhizopus dominated fungi. LEfSe analysis (LDA≥4.0) identified region-specific microbial shifts. PICRUSt2 and FUNGuild predictions indicated significant potential for amino acid and carbohydrate metabolism, with saprotrophic fungi being dominant. Correlation analysis highlighted Thermoactinomyces, Weissella, Bacillus, and Rhizopus as key microbes influencing saccharification, starch degradation, and esterification. These findings provide insights into microbial and biochemical factors driving regional differences in Daqu, offering a foundation for standardized production methods and quality control.

Heparin, mainly used as an anticoagulant, has also shown potential in the treatment of diseases such as inflammation and cancer. Currently, heparin is mainly extracted from the intestinal mucosa of pigs. However, due to concerns about disease transmission and contamination associated with animal-derived products, biomanufacturing techniques have been explored as alternative production methods. Through enzyme engineering, metabolic engineering, and synthetic biology approaches, the heparin biosynthetic pathways have been systematically optimized. The main biomanufacturing techniques include in vivo/in vitro combination strategy (microbial heparosan fermentation followed by chemoenzymatic modification) and de novo biosynthesis. This article comprehensively discusses the latest advancements, challenges, and future perspectives of these heparin biomanufacturing techniques.

Gardeniae Fructus (GF), the dried fruit of Gardenia jasminoides J. Ellis, has been used in East Asian medicine for centuries. Its carbonized form, Gardeniae Fructus Carbonisatus (GFC), is produced through processing, yet the effects of this transformation on active constituents and neuroprotective mechanisms remain unclear. This study aims to elucidate the key compositional changes induced by processing and explore their relevance to neuroprotective activity.

After obtaining GF and GFC extracts via CO₂ supercritical fluid extraction (SFE), UPLC-Q-TOF-MS/MS was employed for qualitative analysis of differential compounds. A pathology-specific network pharmacology screening approach, combined with UPLC-UV-DAD, was applied to quantify major bioactive differential components. Finally, in vitro models and molecular pharmacology techniques were utilized to validate the neuroprotective effects of key compounds.

We identified 23 differential compounds and quantified 10 key bioactive constituents. Integrated network pharmacology and quantitative analysis implicated neuroinflammation and ferroptosis in GF’s neuroprotection, with geniposide and crocetin as pivotal compounds. Mechanistic studies confirmed roles for TLR4/NF-κB and Nrf2 pathways.

Geniposide and Crocetin were identified as key compounds responsible for the neuroprotective effects of GF and GFC, primarily through the inhibition of neuroinflammation and ferroptosis. Crocetin is highlighted as a potential marker for GFC.

Processing transforms Gardeniae Fructus into GFC, enhancing glycoside–aglycone conversion and markedly increasing crocetin. Integrated network pharmacology and quantitative analysis reveal geniposide and crocetin as core neuroprotective agents. In vitro analysis, these compounds inhibit neuroinflammation and ferroptosis via TLR4/NF-κB suppression and Nrf2 activation, supporting crocetin as a characteristic marker of GFC.

This study aimed to extract chitosan (CS) from cuttlefish (Sepia pharaonis) bones (CB) and then chemically modify it to produce carboxymethyl chitosan (CMC). Marine cuttlefish skin collagen peptide (MCP) was then cross-linked with CMC to form a novel CMC-MCP complex. The physicochemical properties and biological effects of CS, CMC, MCP, and CMC-MCP were evaluated using human keratinocyte (HaCaT) cell lines. All materials showed cytotoxicity at high concentrations (100–1600 µg/mL), negatively affecting cell viability. At a lower concentration of 50 µg/mL, the materials were used to assess cell migration. Among them, the CMC-MCP complex significantly promoted cell migration. Additionally, CMC-MCP treatment led to increased expression levels of matrix metalloproteinases (MMP-2 and 9) and tissue inhibitors of metalloproteinases (TIMP-1 and 2), which are key regulators in the wound healing process. These findings suggest that the CMC-MCP complex has potential as an economical, safe, and effective biological dressing for promoting wound healing. Further studies are recommended to explore its interaction with other healing-related factors, such as nutrients and growth factors, to better understand its influence on various stages of tissue repair.

Microorganisms, particularly filamentous fungi, have become the dominant platforms for industrial enzyme production due to their rapid growth, low cost, and adaptability. However, current production technologies face limitations in yield and cost-efficiency, prompting the need for innovative enhancement strategies. Non-thermal atmospheric-pressure plasma has emerged as a promising tool for stimulating microbial enzyme production. In this study, we have employed micro-surface dielectric barrier discharge (MS-DBD) plasma, which operates in a completely different manner from jet plasma, and evaluated its potential for enhancing the production of cellulolytic enzymes in Neurospora crassa. The extracellular activity of cellulases increased (maximum 10.41±3.44% increase) after MS-DBD plasma treatment. The transcription levels of the four cellulase genes were significantly elevated (highest in the 120 s treatment). The fungal hyphal membrane was depolarized and chemically altered after plasma treatment. The levels of intracellular Ca²⁺ and nitric oxide (NO) were elevated, and a high-affinity Ca²⁺ influx system was activated after plasma treatment. Ca²⁺ channel inhibitors reduced fungal cellulase production by downregulating intracellular NO levels. Plasma-mediated enhancement of enzyme production seemed to occur at plasma energies below 500–600 J. However, the combination of the plasma source type and treatment time can affect the efficiency of enzyme production. We also observed the promotion of fungal cellulase production when jet plasma was applied to larger volume of fungal hyphae. Our results suggest that plasma may be a genetically and environmentally safe tool for fungal enzyme production on an industrial scale and can be applied to bioreactors.

L-(+)-Tartaric acid is a valuable organic acid with broad applications in the food, pharmaceutical, and chemical industries. Its eco-friendly synthesis typically relies on the enzymatic hydrolysis of cis-epoxysuccinate (CES) catalyzed by cis-epoxysuccinate hydrolases (CESHs), but conventional single-batch processes suffer from low space–time yields and poor continuity. To address these challenges, we devised two complementary fed-batch strategies to simplify the enzyme–product separation by exploiting differences in their solubilities. Strategy A employs carrier-free cross-linking immobilization of whole cells using 0.02% glutaraldehyde and 0.1% polyethylenimine. In this system, both the substrate sodium cis-epoxysuccinate (CESNa) and the product sodium L-(+)-tartrate remain soluble, while the enzyme is retained in the insoluble cell matrix. Under fed-batch operation, this configuration achieves a space–time yield of 150 g L⁻¹ h⁻¹. Strategy B uses cell-free extract of CESH to hydrolyze calcium cis-epoxysuccinate (CESCa) with inherently low solubility. Here, the enzyme is fully soluble but the L-(+)-tartrate formed precipitates as an insoluble calcium salt, allowing easy separation of the product from the reaction mixture. This approach overcomes potential substrate inhibition and minimizes sodium-ion discharge, delivering a space–time yield of 136 g L⁻¹ h⁻¹ and a specific productivity of 484 g_product/g_catalyst. Both the soluble-product/insoluble-enzyme system (A) and the insoluble-product/soluble-enzyme system (B) represent effective strategies to streamline downstream processing and markedly enhance productivity. Together, they offer a viable route to scalable and cost-effective industrial production of L-(+)-tartaric acid.

D-Pantothenic acid (DPA), also known as vitamin B₅, is a water-soluble organic acid, widely applied in foods, feeds, cosmetics, and medicines. Although numerous and rapidly developing cell factories have been established for DPA biosynthesis, there has been no report of any attempts to engineer Yarrowia lipolytica to synthesize DPA. To explore further possibilities in DPA biosynthesis, we tried to employ systematic metabolic engineering strategies to identify and break the potential bottlenecks in DPA biosynthesis by Y. lipolytica. By improving the rate-limiting steps of the DPA biosynthesis pathway, weakening the strongly competitive pathways, and enhancing the multiple cofactor supplies, a robust Y. lipolytica cell factory for DPA biosynthesis was successfully constructed. Consequently, the resulting strain DPA34 produced 2.18 g/L DPA in a 5-L bioreactor, representing the first report of DPA production to date in Y. lipolytica. This work is believed to facilitate the development of Y. lipolytica for sustainable manufacturing of vitamin B₅ and its derivatives.

This work investigates the green synthesis of silver nanoparticles (AgNPs) using mixed aqueous extracts of Azadirachta indica leaves and roots as natural reducing and stabilizing agents. The synthesis was optimized by varying extract concentration, pH, and temperature, and nanoparticle formation was confirmed by UV–Vis spectroscopy showing a characteristic surface plasmon resonance between 350 and 450 nm. Structural and morphological analyses {X-ray diffraction (XRD), scanning electron microscope (SEM), Fourier-Transform Infrared (FT-IR), particle size analysis} revealed predominantly crystalline, spherical AgNPs capped by phytochemicals like flavonoids, phenols, amide- and carbonyl-containing compounds. The phytochemical profile of the extract was further validated by Gas Chromatography-Mass Spectrometry (GC–MS) analysis. The biosynthesized AgNPs exhibited strong colorimetric sensing capability for heavy metals, showing noticeable spectral and visible color changes particularly in the presence of Hg²⁺, Pb²⁺, and Cd²⁺ ions. Antibacterial evaluation indicated significant inhibitory activity against Staphylococcus aureus (33±0.13 mm) and Escherichia coli (45±0.21 mm), outperforming standard gentamycin controls. These findings highlight neem-derived AgNPs as low-cost, eco-friendly nanomaterials with dual applications in environmental monitoring of heavy metals and antimicrobial therapy.

The employment of plant extracts for green production of bimetallic nanoparticles (BNPs) has gotten significant consideration because of its cheap, ecological, single–step, and easily scalable procedures. This methodology enables the manufacture of biocompatible nanoparticles (NPs) with improved activity. In this study, an environmentally friendly approach was utilized to biosynthesize manganese oxide–silver BNPs (MnO–Ag BNPs) using Cucumis melo (C. melo) peel extract (CPE), which served as the source of the required reducing and stabilizing materials. Several spectroscopic analytical methods, including ultraviolet–visible (UV–vis) spectroscopy, Fourier transform infrared (FTIR) spectroscopy, energy–dispersive X–ray (EDX) spectroscopy, X–ray diffraction (XRD), scanning electron microscopy (SEM), and transmission electron microscopy (TEM), were applied for careful confirmation and characterization of successful MnO–Ag BNPs assembly. This work introduces a novel green route employing CPE for MnO–Ag BNPs synthesis, providing distinct phytochemical efficiency and multifunctional bioactivity compared with previously reported plant–based systems. The biosynthesized MnO–Ag BNPs bacterial inhibitory capability as well as free radical scavenging effect were evaluated. Also, human kidney normal epithelial–derived cells (Vero cell line CCL–81) was employed for assessment of the cytotoxic outcome of MnO–Ag BNPs at various concentrations. Regarding the elemental composition, the manganese (Mn) and Ag contents were detected by the UV–vis, XRD, and EDX studies with consequent validation of MnO–Ag BNPs biosynthesis. The range of the assessed BNPs size was 2 to 10 nm with average diameter of 5.8 ± 1.7 nm and an average area of 22.7 nm². Analysis based on EDX technique revealed the presence of Mn and Ag metals with 23.7–46.6% of the atomic percentages and 32.2–28.0% of the weight percentages, respectively. The biosynthesized NPs showed strong free radical scavenging, achieving 85–90% inhibition at higher concentrations. The cytotoxic activity findings indicated no significant harmful effects, at concentration range of 31.25–250 µg/mL, on Vero cell line. Additionally, the viability of the tested cell line infected with herpes simplex virus type–1 (HSV–1) significantly increased from 43% (untreated) to 78–99% when treated with 125 µg/mL MnO–Ag BNPs and acyclovir, respectively. Moreover, the inhibition rates achieved against the tested virus were 73% for MnO–Ag BNPs and 99% for acyclovir. These outcomes highlight the potential of MnO–Ag BNPs as promising candidates for biomedical and antiviral applications.

Nemadectin, a milbemycin-class macrocyclic lactone antibiotic produced by Streptomyces cyaneogriseus, is a potent broad-spectrum insecticide with excellent environmental compatibility. Its derivative moxidectin, featuring a C-23 methoxime modification, demonstrates enhanced insecticidal activity and has become a commercially successful agrochemical. This study reveals ammonium regulation effectively boosts nemadectin biosynthesis in S. cyaneogriseus, with mechanistic insights gained through integrated multi-omics analysis. Transcriptomic profiling showed ammonium sulfate supplementation significantly upregulates the nemadectin biosynthetic gene cluster, including polyketide synthase (PKS) genes, backbone modification genes, and pathway-specific transcription factors, while also enhancing the expression of Avenolide-like signaling molecules and global transcription factor Afskne. Metabolomic dynamics revealed reinforced precursor biosynthesis through coordinated metabolic reprogramming: enhanced acetyl-CoA production, reinforced Embden–Meyerhof–Parnas pathway and amino acid/acyl-CoA metabolism, coupled with reduced tricarboxylic acid cycle activity. Systematic integration of physiological phenotyping, metabolite profiling, and transcriptional regulation data comprehensively elucidated the ammonium-driven overproduction mechanism, providing critical insights for developing advanced fermentation strategies and genetic engineering approaches in industrial antibiotic production.

Driven by waste resource utilization and carbon neutrality imperatives, this study synthesized cyanobacterial growth elicitor (CGE) and cyanobacterial-bamboo growth elicitor (CBGE) via acid-hydrothermal hydrolysis. The coupling potential of cyanobacterial biochar (CB) for improving rhizosphere soil and crop quality was investigated through four pot trial treatments: (1) CK (control), (2) BR (rhizospheric CB), (3) LBR (rhizospheric CB with CGE), (4) LZBR (rhizospheric CB with CBGE). Integration of phenotypic analyses, microbiome profiling, functional gene predictions, and risk assessment elucidated biostimulant mechanisms. Compared to CK, all treatments elevated soil nutrient levels. BR exhibited superior nitrogen enrichment (15±3 g/kg), while LBR and LZBR—particularly LZBR—enhanced phosphorus/potassium bioavailability and maximized soil organic carbon (SOC). LZBR treatment markedly increased Chryseobacterium abundance (an organic matter-decomposing genus). Functional verification confirmed enhanced C-N-P cycling activity, minimized environmental nutrient leakage, and improved plant nutrient assimilation. Specifically, LZBR increased soybean grain protein content by 37.0 g/kg and plant nitrogen accumulation by 5.4 g/kg compared to CK, and risk assessments indicated no detectable ecotoxicological effects. Consequently, the coupled application of CGE and CBGE derived from cyanobacteria and bamboo powder simultaneously improves soil quality and crop performance. This approach establishes a novel waste valorization pathway, suitable for partial replacement of chemical fertilizers and carbon emission reduction.

The dual crises of antimicrobial resistance and cancer demand innovative therapeutic platforms that overcome conventional treatment limitations. This study uniquely combines systematic Box-Behnken optimization of green-synthesized copper oxide nanoparticles from Thymus vulgaris with comprehensive evaluation of their synergistic antimicrobial and anticancer activities. HPLC profiling identified quercetin (55.92%), chlorogenic acid (15.33%), and gallic acid (12.28%) as principal phytochemical reducing and capping agents. Statistical optimization (R²=0.9886) established copper acetate concentration (F=670.48, p<0.0001) and incubation time (F=124.11, p<0.0001) as critical synthesis determinants, yielding monodisperse spherical nanoparticles (19–25 nm TEM; Z-average 119.2 nm, PDI 0.22; ζ-potential−45.8 mV). XRD confirmed a crystalline monoclinic CuO phase, while FTIR validated phytochemical surface functionalization. TE-CuONPs exhibited concentration-dependent bactericidal activity (MIC 250–950 μg/mL; MBC/MIC≤0.58) against Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, and Enterococcus faecalis as well as inhibition of biofilm formation in S. aureus and P. aeruginosa, with BIC₅₀ of 299 and 315 μg/mL, respectively. Critically, checkerboard assays revealed strong synergy with gentamicin (FICI 0.13–0.28), achieving eightfold dose reduction for both agents against S. aureus and P. aeruginosa. Time-kill kinetics demonstrated accelerated bacterial eradication, with combination therapy achieving≥3-log₁₀ reduction 8–12 h faster than monotherapies, a clinically significant advantage for acute infections. Furthermore, TE-CuONPs showed moderate antiproliferative activity (IC₅₀=117.26 μg/mL) against MCF-7 breast cancer cells, with limited selectivity over normal fibroblasts (SI=1.85), representing a sixfold enhancement over the crude extract. Additionally, Flow cytometric analysis revealed profound apoptotic induction, with 77.25% of cancer cells undergoing cell death (29.73% early apoptosis, 47.52% late apoptosis/necrosis). DPPH radical scavenging (IC₅₀=55 μg/mL) demonstrated a threefold superior antioxidant capacity versus plant extract alone. These findings advance the reproducible botanical nanoparticle synthesis and translational potential of plant-mediated nanomedicine for infectious disease management.

Oil palm trunks (OPT) represent an underutilized agricultural byproduct that poses significant environmental challenges. The effectiveness of OPT as feedstock for biochar production will be depends on carbonization conditions, yet the relationship between process parameters and biochar properties remains insufficiently explored. This study investigates the potential of converting OPT into micropores bioadsorbent through controlled carbonization. Biochar was produced at temperatures of 300, 400, and 500 °C, with residence times of 2, 3, and 4 h, and subsequently characterized for its physicochemical properties and adsorption capacity. The results indicate that biochar produced at 300 °C for 2 h exhibited the highest surface area (10.24 m²/g), while the carbon content peaked at 79.9% in biochar synthesized at 500 °C for 4 h. Notably, although the maximum surface area was observed at 300 °C for 2 h, superior MB removal (52.5%) at longer residence time (4 h) indicates that adsorption performance was governed primarily by surface functional chemistry and pore accessibility rather than surface area alone. The enhanced adsorption at mild carbonization was attributed to the preservation of oxygen-containing surface functional groups rather than surface area alone. Langmuir isotherm analysis provided the best fit (R²>0.9), yielding a maximum monolayer adsorption capacity of 3.57 mg g⁻¹ and a favourable separation factor (R_L<1). These results demonstrate that adsorption performance of OPT-derived biochar is governed by surface chemistry controlled through carbonization severity, positioning OPT as a promising low-cost precursor for sustainable dye adsorption applications.

Enzymatic synthesis is currently the primary method for preparing 1,3-medium chain- 2-long-chain triacylglycerols (MLM-TAGs), which serve as both a dietary component and clinical nutrient for specific populations. The application of MLM-TAGs is obviously constrained by the high cost of catalysts. Hence, a novel approach was proposed for MLM-TAGs production by engineered yeast. Overexpressing the mutated fas1^R1834K increased the production of medium-chain fatty acids (C8–C12) and resulted in an MLM content of 0.41 mol% of the total TAGs. The introduction of RnACSM4 enabled the recombinant to produce MLM-TAGs at a level of 4.2 mol% when supplemented with 0.2 mM sodium laurate. Further deletion of GAT2 and LRO1 increased the content of MLM-TAGs to 6.7 mol%. Iterative optimization involving sodium laurate dosage, culture temperature, and amino acid addition elevated the MLM-TAGs content to 34.4 mol%. Under the optimized conditions, the maximum yield of MLM-TAGs reached 18.5 mg/g DCW, representing a 135-fold improvement over the original strain. This research presents a promising and sustainable alternative for MLM-TAGs production and demonstrates the feasibility of tailoring the acyl composition of intracellular TAGs.

(+)-Bicyclogermacrene and its derivatives, with promising antimicrobial, anticancer, and insecticidal properties, hold significant potential for applications in pharmaceuticals, agriculture, and industry. However, traditional extraction methods from plant essential oils are unsustainable. In this study, we achieved the de novo biosynthesis of (+)-bicyclogermacrene using a metabolically engineered Escherichia coli strain. The biosynthetic pathway of (+)-bicyclogermacrene was partitioned into upstream and downstream modules to enable precise regulation. This was accomplished through the genome-integrated overexpression of the endogenous methylerythritol phosphate pathway to ensure an adequate supply of terpenoid precursors, which pulled the titer from the initial 11.3 mg/L to 50.1 mg/L. Production was further enhanced to 96.9 mg/L by fusion of downstream key genes to facilitate precursor channeling, along with expression level optimization to improve pathway efficiency. Additionally, NADPH supply was fine-tuned through overexpressing dehydrogenases to improve the overall metabolic balance and this approach achieved a titer of 119 mg/L. Following site-directed of (+)-bicyclogermacrene synthase, the engineered E. coli strain M6-36 produced 565 mg/L of (+)-bicyclogermacrene in a 5-L bioreactor, an approximately 50-fold increase from the initial. To the best of our knowledge, the obtained titer in this study represents the highest level ever reported for the production of (+)-bicyclogermacrene. This study demonstrates an effective approach for the heterologous biosynthesis of sesquiterpenoids in E. coli and provides a scalable platform for the sustainable production of terpenoid-derived valuable chemicals.

This study aims at improving the undissociated lactic acid production by Lactobacillus helveticus using a whey-based fermentation. It first describes the effect of pH on the ability of this bacterium to produce lactic acid, by considering final lactic acid concentration, production rate, volumetric productivity and sugar consumption. As a low performance was achieved at pH 4.3, an adaptive evolution of Lb. helveticus LH-B01 to acidic conditions was performed during continuous cultures of sweet hydrolysed whey. Two mutants have been isolated, which exhibited different characteristics. The mutant Lb. helveticus LH-B01-B4 displayed the higher maximal total lactic acid concentration (37.9 g/L), sugar consumption (82%) and volumetric productivity (0.39 g/L/h), when compared to the parental strain and the mutant Lb. helveticus LH-B01-A4. This performance was explained by the higher critical undissociated lactic acid concentration (10.1 g/L) of Lb. helveticus LH-B01-B4, compared with those of the parental strain (8.7 g/L) and the mutant Lb. helveticus LH-B01-A4 (7.5 g/L). From these results, the mutant strain Lb. helveticus LH-B01-B4 was the most promising option to produce undissociated lactic acid during low pH fermentation, thus making it suitable for industrial use as a descaling agent and biocide in detergents.

Based on the self-assembling properties of the SpyCatcher/SpyTag system and the structural advantages of Dps protein, this study successfully constructed a three-dimensional nano-enzyme cascade reactor (3DNECR) through the covalent self-assembly of SpyTag-ADH and SpyCatcher-Dps-ATA117 fusion proteins. The 3DNECR exhibited significantly enhanced catalytic efficiency compared to the two-dimensional control, attributed to optimized spatial organization promoting substrate channeling. The reactor exhibited remarkable storage, pH, and thermal stability. It maintained over 80% activity after 9 days of storage, showed superior pH tolerance across pH 8–10, and remained stable in the temperature range of 4–40 ℃. Molecular docking confirmed strong interfacial binding (− 17.3 kcal/mol) between assembly components and favorable substrate binding (− 7.4 kcal/mol) within the active site. Furthermore, the 3DNECR was applied to the asymmetric synthesis of (R)-1-[3,5-bis(trifluoromethyl)phenyl]ethanamine (R-BPA) in an oil-water biphasic system. Under optimized conditions, the 3DNECR consistently achieved high yields (99.9%) and excellent enantioselectivity (99.9%). The 3DNECR maintained a relative enzyme activity as high as 92% even after six cycles of reuse. This integrated platform showcases substantial potential for efficient and sustainable biocatalytic applications.

Filamentous algae, characterized by high cellulose content and absence of lignin, present a promising sustainable alternative to conventional plant and synthetic fibers. The present study systematically evaluated the suitability of freshwater filamentous algae as a new resource for textile fibers, targeting applications in moisture-absorbent textiles. Among twelve strains screened, the isolate Rhizoclonium sp. emerged as the most promising candidate due to its high biomass yield (1.04 g dry weight L^− 1) after 21 days of cultivation. In addition, it showed superior visible fiber flexibility following air-drying, an essential prerequisite for textile processing. Cultivation conditions were optimized (using WHM medium, pH 8, and thiamin supplementation) to maximize fiber quality, resulting in 8.6% increase in biomass productivity. Biochemical profiling of the optimized biomass revealed a significant enhancement of total carbohydrates (+ 18.0%), alongside reductions in protein (-18.4%) and ash content (-14.9%), supporting improved fiber durability and flexibility. Comparative FTIR analysis showed a strong cellulose signature and marked similarity to cotton, while also revealing high native starch content, further supporting their applicability as bio-based binders in nonwoven products. Functional characterization demonstrated that optimized Rhizoclonium sp. fibers exhibited exceptional moisture regain (~ 12%), surpassing conventional fibers such as cotton and lyocell. Overall, this study establishes native Rhizoclonium sp. as a highly versatile and renewable bioresource for innovative aquatic fibers, underpinning the development of an environmentally responsible algae-derived textile value chain.

As the terminal management for evaluating the engineering effectiveness of antibiotics production and utilization, the toxic effects of moxifloxacin (MOX) and trace concentration of Cu²⁺ (MOX-Cu) on Caenorhabditis elegans (C. elegans) were investigated at physiological, biochemical, and molecular level. Although the stimulate effects were observed after prolonged exposure (72 h) to MOX (0.2-2.0 mg/L), the expressions of HSPs, ace genes, and daf-16 were inhibited, indicating its adverse impact on cellular health, locomotion behaviors, and antioxidant defense of C. elegans. Similarly, the down-regulation of oxidative stress (sod-1 and daf-16) and cell damage (HSPs) related genes and the up-regulation of apoptosis-related genes (cep-1 and ape-1) indicated the oxidative stress and genotoxicity after prolonged exposure to MOX-Cu. For the chronic exposure (10 days) to MOX, the level of ROS was reduced due to the increased expressions of daf-16, sod-3, and hsp-16, accompanied with and the down-regulation of cep-1. Meanwhile, at the exposure to MOX-Cu, the levels of ROS and lipofuscin were decreased due to the up-regulation of sod-1 and daf-16, and the antioxidant defense was promoted and confirmed by the increase of amino acids and their related metabolic pathways. These results can provide a theoretical basis for the toxicity evaluation of typical antibiotics (MOX) that co-existing with trace heavy metals in natural environment media and bioresources processes.

Via efficient, scalable, and climate resilient processes, seaweed biorefineries can advance cleaner production, delivering nutrient-rich ingredients with relatively lower land and freshwater requirements. Here, a land-based Ulva ohnoi platform that integrates optimized outdoor tank cultivation, pH-shift protein extraction with dual-product valorization, scale-aware techno-economic analysis (TEA), and a climate-scenario emulator was developed and evaluated. Year-round cultivation yielded a pooled feedstock with carbohydrate and protein contents at 46.6% and 26.8%, respectively, and under optimal conditions, protein yield was 10.30% DW. Further, the protein content of cultivated Ulva protein (CUP) was 47.64%, with bound amino acids showing predominance (96%), implying food-grade utility. pH-shift extraction also improved in-vitro pepsin digestibility to 68.08%. The total dietary fiber content of CUP residue (CUPR) was 40.59%, with insoluble dietary fiber (31.59%) showing predominance, supporting the applicability of CUPR in improving gastrointestinal tract function. TEA revealed strong economies of scale for the platform. The 10,000-kg production model outperformed the 100- and 1,000-kg production models, with gross margin, Return On Investment (ROI), and Internal Rate of Return (IRR) at 78.56%, 110%, and 66.02%, respectively, and a payback time of only 0.91 years. Based on site-specific regression analysis (R² = 0.884), protein yield increased with temperature but decreased with rainfall, and further warming increased mean protein yield, while higher-emission pathways introduced rainfall-driven volatility, necessitating strategies for sustaining performance under climate variability. Overall, the use of the Ulva platform showed a broad growth temperature window as well as rapid acclimation for U. ohnoi, implying resilience even under global warming conditions and increasing weather variability.

Gut microbiota regulation is a key strategy for treating metabolic dysfunction-associated fatty liver disease (MAFLD). Arbutin (ARB) is a natural hydroquinone active agent with anti-inflammatory and antioxidant effects, as well as regulatory effects on the gut microbiota. However, its therapeutic effect on MAFLD and the responsible mechanisms remain unclear.

This study explored the therapeutic effect and mechanisms of ARB in MAFLD treatment.

High-fat diet (HFD)-fed mice served as the in vivo MAFLD model, and ARB treatment was given simultaneously. The extent of liver injury was assessed through histopathological staining. AML12 cells treated with free fatty acids served as the in vitro model. The effects of ARB were evaluated via oil red O staining and biochemical assays. Subsequently, we utilized bioinformatics techniques to predict the potential mechanisms and targets of ARB. The expression of liver apoptosis-related genes was detected using molecular biology techniques. Alterations in the gut microbiota were analyzed by 16S rRNA sequencing. Ultrahigh-performance liquid chromatography–high-resolution mass spectrometry was used to analyze the changes in fecal metabolite levels.

ARB treatment effectively improved liver injury in mice with MAFLD. Its mechanism was associated with anti-apoptotic effects mediated by signal transducer and activator of transcription 3. Meanwhile, ARB effectively reversed gut microbiota imbalance in mice with MAFLD and altered the composition of gut microbes and fecal metabolites.

ARB displayed potential effects in alleviating the pathology of MAFLD, exerting anti-apoptotic actions, and restoring the gut microbiota balance.

The enzymatic esterification of 5-hydroxymethylfurfural (HMF) with long-chain fatty acids offers a sustainable route for producing biolubricants and other high-value chemicals. This work evaluates the synthesis of 5-hidroxymethylfurfural stearate catalyzed by immobilized lipases in both batch and continuous packed-bed bioreactors, combining molecular dynamics (MD) simulations with experimental validation to identify suitable green solvents. Four solvents were tested: 2-methyl-3-buten-2-ol (2-MB), tert-butanol (TB), 2-methyltetrahydrofuran (2-MeTHF), and cyclopentyl methyl ether (CPME). MD simulations revealed that CPME increased hydrophobic surface exposure and flexibility near the catalytic site, favoring substrate accessibility. In preliminary experimental tests, CPME provided the highest conversion (50%). In batch bioreactor at 40 °C, 30 mM HMF and 250 mM stearic acid achieved 67% conversion with Candida antarctica lipase B (CALB), maintaining full activity (100%) over four reuse cycles. In continuous operation, using a single packed-bed bioreactor at 0.02 mL min⁻¹ yielded conversions above 50% (residence time ≈ 55 min), while connecting two packed-bed bioreactors in series increased conversion to over 90% and productivity to 0.094 h⁻¹, compared with 0.076 h⁻¹ for one column and 0.003 h⁻¹ in batch mode. Deviations from ideal plug flow were observed over time, attributed to substrate or product deposition and in-situ water formation shifting the reaction equilibrium. Overall, CPME proved to be an efficient and sustainable solvent for the enzymatic synthesis of 5-hydroxymethylfurfural stearate, demonstrating the feasibility of continuous operation and highlighting pathways for further optimization through improved immobilization or reactor design.

Agricultural residues like sugarcane bagasse and rice straw are rich in cellulose and xylan. Their efficient conversion into (oligo)saccharides and value-added products requires microbial cellulases and xylanases, but low enzyme yields and high production costs hinder industrial application. This study isolated Penicillium oxalicum UNN1, a high-xylanase-producing strain with an initial activity of 51.63 U/mL. Submerged fermentation conditions were optimized using different carbon/nitrogen sources to enhance enzyme production. The optimized xylanase activity reached 191.22 U/mL (sugarcane bagasse xylan as sole carbon source) and 142.32 U/mL (combined with Avicel), with filter paper cellulase activity of 0.76 U/mL. The crude enzymes exhibited optimal activity at pH 5.0 and 50 °C. Cellulase retained over 75% activity after 7 h at pH 4.0–6.0 (4 °C) or 40 °C (pH 5.0), while xylanase activity remained nearly unchanged, even after over 21 days of storage at 4 °C (pH 5.0). However, the half-life of xylanase was less than 1 h at 50 °C, though it exceeded 72 h at 40 °C (pH 5.5). 3–5 mM Ca²⁺ and Cu²⁺ strongly inhibited both enzymes. Crude enzyme addition (about 7 U cellulase and 1,400 U xylanase) effectively enhanced reducing sugar production from agricultural residues. Single-factor and response surface optimization yielded optimal hydrolysis conditions: 480 U/g sugarcane bagasse xylan of xylanase, hydrolysate pH of 5.5, hydrolysis temperature of 40 °C, achieving a maximum reducing sugar yield of 0.355 g/g dry biomass. This work demonstrates the potential of P. oxalicum UNN1 enzymes for efficient and stable saccharification of agricultural residues, offering a viable approach for their valorization and environmental management.

The yeast Komagataella phaffii is an emerging microbial host for the production of functional recombinant proteins. However, proteolytic degradation during fermentation often compromises product yield and stability, posing a major hurdle for industrial-scale applications. This study presents a strategy to enhance the production of recombinant humanized type I collagen (rhColI) by engineering a host strain with reduced protease activity. An initial production strain, CL1, was engineered using post-transformational vector amplification (PTVA), achieving a titer of 558.86 ± 20.05 mg/L in flask culture. Subsequent scale-up fermentation, however, revealed significant rhColI degradation. To address this, we systematically deleted 11 candidate endogenous protease genes. The knockout of a serine protease gene, KpSub2, resulted in the most pronounced improvement, elevating the rhColI titer to 1039.06 ± 34.08 mg/L, a 23.47% increase over the parent strain CL1. Furthermore, the purified KpSub2 protein, obtained from inclusion bodies in Escherichia coli, demonstrated broad proteolytic activity against various types of recombinant humanized collagens. This broad substrate specificity was consistent with the observation that KpSub2 deletion also mitigated the degradation of recombinant humanized type III collagen (rhColIII). Our findings establish KpSub2 as a key mediator of collagen degradation in K. phaffii and provide an effective engineering strategy for optimizing the production of collagen and other degradation-susceptible functional proteins in this host.

The aqueous phase (AP) generated during biomass pyrolysis is often considered a waste product due to its dilute and toxic nature, making it difficult to upgrade. This study explores the potential of using AP as a laccase inducer for the white-rot fungus, Pleorotus ostreatus, and as a mediator in laccase-catalyzed reactions. As an inducer, AP increased laccase production from P. ostreatus to 570 U/g, outperforming copper, a common inducer, by almost 180%. A maximum laccase yield of 955 U/g was achieved when P. ostreatus was co-induced by both AP and copper. Characterization of the AP-induced laccase revealed greater pH tolerance relative of this enzyme compared to copper-induced laccase. The AP-induced laccase was further evaluated for various applications. Laccase alone was effective in decolorizing coomassie blue dye, increasing saccharification yield from prairie biomass, and detoxifying tetracycline. When laccase was mediated with AP, the enzyme was also capable of decolorizing crystal violet dye, demonstrating additional benefit of AP to mediate laccase-based oxidation reactions with certain substrates. Overall, these findings suggest that using AP to induce laccase production, and potentially mediate the laccase-based reactions, could be a promising method to valorize this byproduct from biomass pyrolysis.

Climate change and environmental pollution are among the most pressing global challenges today, with water pollution standing out as a particularly critical issue. Industrial wastewater discharge, especially from distilleries, significantly contributes to the degradation of aquatic and terrestrial ecosystems. Molasses-based distilleries are major perpetrators, producing vast quantities of dark brown effluent known as spent wash. This colouration is largely due to the presence of melanoidin, a recalcitrant compound formed via the Maillard reaction. Although many distilleries now utilize anaerobic digestion to convert this organic-rich waste into biogas, the resultant biomethanated spent wash remains highly coloured and environmentally hazardous. Direct discharge of untreated or partially treated spent wash into rivers, lakes, or soil severely disrupts ecological balance and poses risks to biodiversity. Existing disposal practices, such as lagoon storage or composting with press mud, offer limited solutions to the colour problem. Fungi, particularly those producing laccase and other oxidative enzymes, have demonstrated promising potential for decolourizing spent wash in laboratory studies. However, the enzymatic pathways involved in melanoidin degradation are still not fully understood. To address the persistant colour challenge, integrated treatment strategies combining fungal systems with complementary physical or chemical processes (eg, adsorption or advanced oxidation) may be required to achieve effective decolourisation. Such advancements are vital for creating effective, eco-friendly solutions to mitigate the environmental impact of the distillery industry and promote a circular bioeconomy.

Allergic rhinitis (AR) is a prevalent inflammatory disorder of the upper respiratory tract, affecting 20–40% of the global population and severely impairing quality of life. Given the limitations and adverse effects associated with conventional pharmacotherapy, naturally derived bioactives with low toxicity are gaining prominence as alternative interventions. In this study, we developed a bioresource-based nanoemulsion (NE) by integrating Sargassum polysaccharides (SP) into algal oil (AO) to enhance intranasal delivery and therapeutic efficacy against AR. Structural analysis confirmed that SP comprised sulfated polysaccharides enriched in fucose, glucose, and galactose. The optimized SP–AO NE, formulated with Tween 80 and prepared via ultrasonic emulsification, exhibited uniform spherical droplets (53.4 ± 1.8 nm), a low polydispersity index (0.3 ± 0.1), and a negative zeta potential (− 29.1 ± 2.8 mV), indicating high colloidal stability and effective oxidative protection of AO during refrigerated storage. In an ovalbumin-induced AR mouse model, intranasal administration of SP–AO NE significantly alleviated nasal rubbing, epithelial hypertrophy, goblet cell hyperplasia, mast cell infiltration, and pulmonary inflammation. Intranasal SP–AO NE treatment decreased IgE levels in serum, nasal lavage, and bronchoalveolar lavage fluids, while enhancing mucosal IgA. In addition, SP–AO NE downregulated IL-4 and TNF-α expression and upregulated TGF-β1, demonstrating a robust immunomodulatory effect. Overall, this work presents a stable, biocompatible, and functional NE that improves intranasal delivery of algal bioactives, offering a promising natural therapeutic strategy for the management of AR.

Natural products are rich therapeutic sources, yet their translation into effective medicines remains challenging. Bee venom (BV) contains a diverse repertoire of bioactive molecules, but gentle, scalable methods to enhance its functionality are limited. This study, therefore, investigates a novel, solvent-free, post-extraction infrared (IR) conditioning step to fine-tune BV's composition and bioactivity. BV was irradiated (230 V, 50 Hz, 150 W) and compared to native extract using GC–MS and bioactivity assays. GC–MS revealed selective compositional tuning, with significant enrichment (p ≤ 0.05) of 4H-1-benzopyran-4-one, 2-(3,4-dimethoxyphenyl)-3,5-dihydroxy-7-methoxy. IR-treated BV exhibited enhanced antimicrobial activity, with increased zones of inhibition for Staphylococcus aureus (15 ± 0.1 vs. 11 ± 0.4 mm), Bacillus subtilis (24 ± 0.2 vs. 22 ± 0.6 mm), Candida albicans (26 ± 0.1 vs. 22 ± 0.5 mm), Klebsiella pneumoniae (24 ± 0.4 vs. 15 ± 0.3 mm), and Salmonella typhi (27 ± 0.8 vs. 20 ± 0.7 mm). MICs decreased for S. aureus, B. subtilis, and K. pneumoniae. The treated BV also showed stronger antibiofilm activity at 25% MBC concentrations for K. pneumoniae and S. typhi (p ≤ 0.05) and significantly reduced hemolysis at 25% MIC for S. aureus and B. subtilis (p ≤ 0.05). Antioxidant capacity increased (DPPH IC₅₀: 16.47 ± 1.1 vs. 27.65 ± 0.8 µg/mL), as did anti-inflammatory activity (COX-2 IC₅₀: 48.84 ± 0.2 vs. 50.99 ± 0.9 µg/mL; COX-1 IC₅₀: 24.7 ± 0.2 vs. 41.74 ± 0.2 µg/mL). Cytotoxicity against PC-3 and SKOV-3 cells was maintained (IC₅₀: 19.73 ± 0.9 and 19.76 ± 0.11 µg/mL, respectively, vs. native BV's 11.48 ± 0.3 and 17.46 ± 0.27 µg/mL). These findings establish brief IR irradiation as a practical, scalable post-processing strategy to selectively enhance the therapeutic potential of BV for biomedical applications.

Created in BioRender. Qanash, H. (2026) https://BioRender.com/6war4d0

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Acacia seyal is a medicinal plant rich in bioactive compounds known for their antimicrobial, antioxidant, and anticancer properties. Conventional plant extracts often suffer from poor stability and limited bioavailability, reducing their therapeutic effectiveness. The utilization of chitosan nanoparticles (CS-NPs) offers a promising strategy to enhance biological activity of plant extracts. Encapsulation of A. seyal seeds extract (ASSE) in CS-NPs (ASSE@CS-NPs) was the aim of the present investigation to compete Helicobacter pylori and HCT116 cancer cells. The phytochemical profile of ASSE revealed diverse phenolic acids and flavonoids via HPLC analysis. Methyl gallate was dominated (20.98 mg/g), followed by gallic acid, and catechin. FTIR analysis confirmed characteristic functional groups in ASSE and CS-NPs. Peak shifts and intensity variations in ASSE@CS-NPs indicated successful encapsulation through hydrogen bonding and electrostatic interactions. ASSE@CS-NPs showed the strongest anti-H. pylori effect with inhibition zone (23.7 mm) and lowest MIC/MBC (15.62 µg/mL). Compared to CS-NPs (20.7 mm, 31.25 µg/mL) and ASSE (19.7 mm, 31.25 µg/mL). ASSE@CS-NPs showed notable antioxidant activity, achieving 96% scavenging at 1000 µg/mL with IC₅₀ of 3µg/mL compared to ASSE (5 µg/mL) and CS-NPs (74 µg/mL). ASSE@CS-NPs exhibited potent cytotoxicity against HCT116 cells with IC₅₀ of 23 µg/mL, outperforming ASSE (588 µg/mL) and CS-NPs (120 µg/mL). The formulation achieved > 80% inhibition at 62.5 µg/mL. Molecular docking was performed to evaluate the binding affinity and interaction patterns of methyl gallate (a main constituent of ASSE) and chitosan against H. pylori urease (PDB ID: 6ZJA). Docking results revealed favorable binding scores for both ligands, with chitosan showing higher affinity (S score: − 6.42 kcal/mol) compared to methyl gallate (S score: − 5.45 kcal/mol). Key hydrogen bond interactions were observed with active site residues ASP362 and ALA169 for methyl gallate, and ASP223 and HIS323 for chitosan. These results suggest that ASSE@CS-NPs possess inhibitory potential against H. pylori and HCT116 cells.

Membrane fouling during ultrafiltration/diafiltration (UF/DF) remains a major challenge for extending membrane lifetime in biologics manufacturing. Developing cleaning strategies that combine high efficiency with scalability is essential for robust downstream processing. In this study, different UF/DF membrane cleaning methods were assessed under bench-scale conditions with consideration for large-scale implementation. Permeate-closed cleaning (PCC), which temporarily closes the permeate port to enhance shear, effectively mitigated normalized water permeability (NWP) decline. Furthermore, forward and reverse PCC at elevated feed flux achieved comparable fouling control with fewer steps by leveraging hydrodynamic shear and localized backwashing. To simplify large-scale adoption, high-flux PCC was developed and demonstrated the ability to restore NWP and maintain stability over extended cycles. Quantitatively, high‑flux PCC reduced early NWP decay by ~ 18% over the first three cycles and recovered > 15% NWP in previously fouled membranes, stabilizing permeability over extended reuse. Backwashing under controlled negative transmembrane pressure (TMP) further improved pore-level cleaning and extended membrane usability. Additionally, combining sodium hypochlorite (NaClO) with sodium hydroxide (NaOH) provided strong oxidative and alkaline action; within the evaluated range (25–150 ppm NaClO), 50 ppm was identified as a practical lower limit for effective recovery, while 150 ppm restored NWP from ~ 70 to ~ 100% with residual NaClO < 0.02 ppm after final rinsing. Collectively, these findings present a portfolio of cleaning strategies—hydrodynamic, chemical, and combined approaches—that enhance cleaning efficiency, reduce chemical exposure, and support sustainable UF/DF operations in biologics manufacturing.

This study investigates the optimisation of poly(3-hydroxybutyrate) (PHB) production by Mycolicibacterium smegmatis using sugarcane bagasse (SCB) hydrolysate as a low-cost, renewable carbon source. Key fermentation parameters including temperature, pH, agitation, inoculum size and nitrogen supplementation were optimised to enhance biomass growth and PHB accumulation. Under optimised conditions (37 °C, pH 7, 100 rpm, 3% inoculum), M. smegmatis achieved a maximum PHB content of 64% of DCW from SCB hydrolysate, corresponding to a PHB titre of ~ 1.0 g L⁻¹ and a volumetric productivity of 0.014 g L⁻¹ h⁻¹ after 72 h of cultivation, with yeast extract identified as the most effective nitrogen source. Thin-layer chromatography (TLC) analysis demonstrated that M. smegmatis could not only co-utilise glucose and xylose simultaneously but preferentially consumed xylose, which is a major advantage when processing lignocellulosic biomasses, where xylose is abundant and typically underutilised by many microorganisms. Whole-genome sequencing with Oxford Nanopore Technologies (ONT) confirmed the presence of PHB production genes (phbA, phbB, phbC) and a xylose-utilisation pathway, supporting its metabolic capability. These findings establish M. smegmatis as a promising candidate for converting agricultural waste into biodegradable bioplastics, contributing to circular bioeconomy strategies.

The valorization of anaerobic digestates through slow pyrolysis offers a sustainable pathway for agricultural systems. This study assessed the effects of digestate type (swine, cattle, and dairy) and pyrolysis temperature (400, 500, and 600 °C) on biochar properties and evaluated their impact on maize (Zea mays) fodder grown under hydroponic-like soilless conditions. Thirty-six treatments were evaluated in a factorial design combining digestate source, temperature, and application rate (0–6.25 g per container). Biochar from dairy digestate (BDST) pyrolyzed at 500 °C exhibited the most favorable characteristics, with high carbon content (60.4%), low electrical conductivity (≈ 916 µS cm⁻¹), and improved water and nutrient retention. At an application rate of 6.25 g per container, BDST–500 also achieved the highest SPAD and dry mass values. In contrast, swine- and cattle-derived biochars presented higher ash and salinity, reducing their agronomic performance. Multivariate analysis indicated that digestate type was the main determinant of plant physiological performance, beyond the individual effects of pyrolysis temperature and application rate. Overall, dairy-derived biochar demonstrates strong potential as a functional amendment for hydroponic fodder systems and as a tool to advance circular bioeconomy practices.

Bioprocesses grant us with broad opportunities to build a circular carbon economy. Using microbes allows us to replace non-renewable resources and change waste management strategies, including recycling and upcycling. However, research still lags on strategies to enable economic viability of these types of bioprocesses relative to the traditional production methods. Tuning the composition of the microbial growth medium is one way to address these issues. This allows us to gain insight into the interactions of nutrients and the focal organisms in order to formulate appropriate media recipes to support the metabolic needs. This step, which is often overlooked in proof-of-concept research, can substantially improve process metrics. After carbon, nitrogen is the most important and costly nutrient and should be given thorough consideration. In this study, we utilized nitrogen sourcing to tackle the biological upcycling of thermally oxo-degraded plastic waste using a previously described non-conventional yeast with the ability to utilize hydrophobic substrates, Candida maltosa. We compare the use of algae extract and casamino acids as organic, amino acid-based nitrogen sources to inorganic ammonium sulfate with the goal of increasing growth metric and biomass production. Our findings show that the use of algae extract and casamino acids promotes 2X–25X higher growth in model compounds and up to 2X on TOD products. Significant changes were observed in elemental composition of the cells in response to the change in nitrogen and carbon source. These changes align with the ~ 3X increase in internal protein content in the case of cells grown on casamino acids and TOD. Membrane properties and fatty acid content of the cells are also largely impacted, with a significant decrease in saturated and unsaturated fatty acid content, resulting in a reduced average lipid length in the case of casamino acid and TOD grown cells. Three proteins, namely the nonspecific lipid transfer protein POX18, the glycine zipper 2 transmembrane domain-containing protein, and the histidine triad nucleotide binding protein HNT1 were expressed in cells grown on TOD. The results from this study highlight the importance of nutrient management in non-model organisms and the biological challenges associated with the utilization of these compounds which can be insightful in future genetic engineering efforts for improved performance.

Hypocrellin A (HA), a photoactive perylenequinone from the bambusicolous Shiraia fungi, possesses potent photodynamic anticancer and antimicrobial properties. However, the signaling mechanisms governing its biosynthesis remain poorly understood. In this study, we identify spermidine (Spd), a ubiquitous polyamine, as a novel elicitor that significantly enhances HA production in Shiraia sp. S9. Spd activated both nitric oxide synthase (NOS) and nitrate reductase (NR) for nitric oxide (NO) generation, leading to the stimulation of the soluble guanylate cyclase (sGC)–cyclic guanosine monophosphate (cGMP) signaling cascade. Inhibition of NO generation or sGC activity suppressed both cGMP accumulation and HA biosynthesis. Transcriptomic analysis revealed that Spd-induced NO signaling upregulated genes in central carbon metabolism and the hypocrellin biosynthetic gene cluster. The dual elicitation strategy by the combined addition of Spd and the NO donor sodium nitroprusside (SNP) exhibited a strong enhancing effect, increasing HA yield by 4.6-fold compared with control cultures. These results demonstrate that Spd regulates HA biosynthesis through a NO–cGMP–mediated signaling pathway, unveiling polyamines as new metabolic elicitors and providing an efficient dual-elicitation strategy for large-scale hypocrellin production.

Tobacco aging is a critical for developing desirable flavor profiles, driven primarily by microbial and enzymatic activities. This study systematically evaluated the effects of Bacillus clausii inoculation (FJ) and B. clausii-cellulase co-treatment (JM) on the surface microbial communities and aroma compounds of Yunyan 87 tobacco leaves during 9 months of aging, with natural aging as the control (CK). High-throughput 16S rRNA sequencing revealed that the JM treatment significantly increased microbial diversity and enhanced the structural similarity of microbial communities across different aging stages compared with the CK and FJ treatments, while also promoting the proliferation of beneficial taxa (e.g., Bacteroidota, Cyanobacteria). PICRUSt functional prediction revealed that JM enriched metabolic pathways related to carbohydrate metabolism (18.2–20.6%), amino acid metabolism (15.1–16.7%), and metabolism of cofactors and vitamins (16.5–17.7%)–key pathways for flavor precursor conversion. A total of 29 key aroma compounds (odor activity value > 1) were significantly influenced the quality of tobacco leaves, with JM significantly increasing total volatile content (317.1–388.8 μg/g vs. 124.7–143.0 μg/g in CK and 283.2–300.8 μg/g in FJ). Notably, JM promoted the accumulation of esters (ethyl palmitate, ethyl linoleate) and ketones (4,7,9-megastigmatrien-3-one, damascenone), contributing desirable fruity, floral, and sweet notes. Correlation analysis linked Pseudomonas, Bacillus, and Acinetobacter to the formation of key volatiles. These findings demonstrate that microbial-enzyme co-fermentation enriched desirable aromas, and stabilized microbial communities, providing a practical and efficient strategy for industrial production of high-quality aged tobacco.

Chinese hamster ovary (CHO) cells constitute the industry-standard platform for the production of complex therapeutic proteins, yet genomic heterogeneity arising from random integration leads to clonal variability and unstable expression, necessitating a robust cell line development process to efficiently isolate stable, high-expressing clones. By employing an optimized integration strategy, recombinant cell line performance can be enhanced through improved genomic stability and increased productivity. In this study, GFP reporter analysis demonstrated that the PiggyBac system significantly boosts the yield of both stable and high-expression clones. Subsequently, transposase modified with a nuclear localization signal (NLS) exhibited superior stability in recombinant cell lines and polyclonal pools. The nucleoplasmin NLS resulted in transgene integration into genomic loci that promote enhanced and more stable expression, thereby improving clonal distribution. Furthermore, this strategy also increased recombinant mAb expression by 97% in pools while enhancing average and specific productivity in derived cell lines. Additionally, recombinant suspension cells generated with the optimized system exhibited comparable performance, with over 50% of minipools showing robust growth. Overall, these findings highlight the promising utility of the NLS-optimized PiggyBac system for improving transgene stability and expression while streamlining the cell line screening process.

Biochar yield prediction plays a critical role in optimizing pyrolysis processes and advancing sustainable biomass utilization. This study introduces a hybrid machine learning framework that integrates Decision Tree models with four optimization strategies including Tabu Search, Ant Colony Optimization, Evolutionary Strategies, and Batch Bayesian Optimization (DT-BBO). A curated dataset of 211 samples was preprocessed using Leverage outlier detection and normalization to ensure model robustness. Among all tested models, the DT-BBO approach achieved the highest accuracy, with an R² of 0.98, an MSE of 1.9, and an AARE% of 2.2%, outperforming the other optimization techniques. SHAP analysis revealed that pyrolysis temperature, residence time, and ash content were the most influential parameters governing biochar yield. Comparative benchmarking against previously published models confirmed the superior predictive capability and stability of the proposed framework. The results demonstrate that the DT-BBO model offers a scalable, interpretable, and high-performing solution for biochar yield prediction, contributing to methodological innovation and sustainable biomass valorization.

Vascular endothelial growth factor (VEGF) is widely used in regenerative medicine and therapeutic research. However, the purification of recombinant VEGF largely relies on affinity chromatography, which requires expensive chromatographic columns, specialized equipment, and multistep processing. These column-based workflows increase operational complexity and cost, particularly for large-scale production. Therefore, the development of an alternative purification strategy to conventional chromatography-based purification for VEGF is needed.

In this study, we developed a chromatography-free VEGF purification strategy using an anti-VEGF-scFv–calsequestrin (CSQ) fusion protein that enables calcium-dependent affinity precipitation. The fusion protein retained strong binding affinity for VEGF (K_d = 1.1 nM) while exhibiting rapid and reversible Ca²⁺-dependent polymerization. Upon CaCl₂ addition, the anti-VEGF-scFv-CSQ–VEGF complex rapidly formed aggregates, enabling efficient separation of VEGF from impurities. Using this strategy, VEGF was purified within 30 min with a purity of 94% and a yield of 93%. SEC-HPLC analysis confirmed a purity of 94.3%, and host cell protein contamination was reduced from 1.44 × 10⁴ ppm to 774 ppm. The fusion protein also maintained stable purification performance over five repeated cycles, with VEGF recovery consistently maintained above 85%.

These findings demonstrate that the scFv-CSQ fusion protein enables rapid separation of VEGF through calcium-dependent polymerization. This column-free mechanism reduces operational cost and technical complexity, highlighting its potential as an alternative to conventional chromatography-based purification.

Antimicrobial food pads play a key role in the food packaging industry by improving food safety and quality. To control the growth of bacterial pathogens in fish fillets, this study aims to develop a bioactive system using absorbent food pads composed of bacterial cellulose (BC) infused with tangerine essential oil (TEO) as an antibacterial agent. The effects of active BC-pads, gamma irradiation, and their combination on artificially inoculated bacteria (previously isolated) were studied for 6 days at 4 °C using fish fillet samples as a model food system. The results revealed that the initial population counts of Klebsiella oxytoca, Serratia ficaria, Enterobacter cloacae, and Kocuria rosea, were 5.47, 5.63, 5.14, and 5.25 log CFU/g, respectively. These counts increased during the storage period, reaching 8.80 log CFU/g as a mean for all tested strains. After six days of storage, BC, BC/TEO, BC + 1.0 kGy, and BC/TEO + 1.0 kGy pads reduced the initial load of the four bacteria in the fish fillet samples by [1.59, 1.68, 1.92, 2.35], [3.21, 3.12, 3.36, 3.72], [3.53, 3.26, 3.26, 3.37] and [4.97, 5.02, 4.95, 4.83] log CFU/g, respectively. The combination of BC and TEO with low-dose gamma radiation (1.0 kGy) enhances the decontamination effectiveness of fish fillets through synergistic effects. FTIR analysis revealed a slight shift in the absorbance peaks of some functional group interactions and the formation of new bonds between BC and TEO in the presence of gamma irradiation. The study has successfully developed sustainable, eco-friendly, functional bioactive food pads that reduce microbial growth and prevent spoilage of fish fillets during storage.

Inadequate sludge treatment poses a significant risk of environmental pollution. To reduce pollution, utilizing waste sludge as an energy source offers a sustainable solution to mitigate pollution. Since sludges contain abundant organics, they are expected to produce more valuable organics, such as volatile fatty acids (VFAs). Although sludge fermentation has been widely studied, direct yields of VFA production from different sludge types are still limited, particularly for sludge materials originating from Finnish wastewater treatment plants. In this study, laboratory-scale bioreactors were built to examine VFA production from digester feed sludge, digested sludge, and ammonia removal sludge, which were collected from local wastewater treatment plants. Among the tested substrates, digested feed sludge resulted in the highest VFA yield, reaching 171.6 ± 6.3 mg/g volatile solids after 11 days of incubation, which indicated its superior potential for VFA generation. In contrast, bioreactors fed with digested sludge or ammonia removal sludge showed no clear increasing trend in VFA production. The addition of sawdust led to lower overall VFA yields, approximately half of those obtained with digested feed sludge alone, and increasing the sludge proportion did not result in further yield enhancement. Acetic acid was the dominant VFA in all bioreactors, accounting for 61.2–97.9% of total VFAs. Microbial community analysis indicated the prevalence of phyla Bacillota and Pseudomonadota, with Lactobacillus being relatively abundant in bioreactors exhibiting higher VFA production. These findings suggest that sludge type plays an important role in determining VFA production performance and may support more informed selection of sludge substrates for VFA-oriented sludge valorisation.

p-Coumaric acid (p-CA) is a key aromatic precursor for the biosynthesis of flavonoids, stilbenoids, and other high-value phenylpropanoids. While microbial production of p-CA typically relies on sugar-based substrates, methanol offers a sustainable and cost-effective alternative, though its use for aromatic biosynthesis remains unexplored. Here, we report the first de novo production of p-CA from methanol using engineered methylotrophic yeast Pichia pastoris. Through heterologous expression of a tyrosine ammonia-lyase and implementing a balanced push–pull strategy in the shikimate pathway using feedback-resistant variants of DAHP synthase (ARO4) and chorismate mutase (ARO7), carbon flux from methanol-derived C3 and C4 precursors was effectively redirected toward aromatic biosynthesis. Shake-flask studies revealed strong gene-dosage-dependent p-CA production, but strains with high-copy numbers suffered metabolic burden under high-density fermentation. Fed-batch bioreactor cultivation demonstrated that a moderate-copy strain achieved the highest titer of 704 ± 6 mg/L, outperforming high-copy variants in robustness and scalability. This study establishes P. pastoris as a promising chassis for methanol-based aromatic production and highlights the critical trade-off between pathway amplification and cellular fitness in C1 biomanufacturing.

This study assesses the impact of physicochemical pretreatment, enzymatic hydrolysis, and co-culture fermentation strategies on bioethanol production from corn husk biomass (CHB). Under optimal alkali pretreatment conditions (1.75% alkali, 4.0 g substrate concentration, 120 °C, 10 h), 35% lignin removal was achieved, with 48% cellulose and 39% hemicellulose recovery. In contrast, acid pretreatment resulted in 30% lignin removal, 45% cellulose recovery, and 34% hemicellulose recovery, showing lower efficiency than alkali pretreatment. During ultrasonication alkali pretreatment enhanced cellulose and hemicellulose exposure up to 51 and 46% and delignification up to 49%. Enzymatic hydrolysis of pretreated corn husk biomass was performed using commercial enzymes [Celluclast 1.5 L (700 EGU or 854 U mL⁻¹) and Viscozyme (13.4 FBG/mL)] and isolated bacterial enzymes, including cellulase from Bacillus licheniformis (9.3 ± 0.3 U mL⁻¹) and xylanase from Enterobacter asburiae PQ396173 (7.0 ± 0.4 U mL⁻¹). The developed enzyme cocktail in ratio 3:2:3:1 (v/v; U mL⁻¹) (Celluclast: Viscozyme: native cellulase: native xylanse) using a cocktail of native and commercial enzymes, yielded total reducing sugar of 740 mg g⁻¹ glucose and 54.6 mg g⁻¹ xylose. Fermentation of hydrolysate prepared with commercial enzymes using monoculture of Saccharomyces cerevisiae and Pichia pastoris yielded 17.6 g L⁻¹ and 12.2 g L⁻¹ bioethanol separately. Co-cultured yeasts produced 26.8 g L⁻¹ ethanol at 96 h of incubation, exceeding monoculture yields. The fermentation with integration of commercial and isolated bacterial enzyme cocktails yielded the highest bioethanol output of 37.3 g L⁻¹ at 96 h incubation, indicating that enzymatic saccharification with a combination of commercial and native enzyme cocktails results in maximum bioethanol production.

Indigo, a ubiquitous vat dye in denim manufacturing, is characterized by its exceptionally low aqueous solubility, necessitating chemical reduction to its leuco form using hazardous agents such as sodium dithionite. This conventional process yields sulfite, sulfate, and sulfide byproducts, leading to significant environmental and toxicological concerns. To address these limitations, this study synthesized 1:1 molar ratio inclusion complexes of indigo with β-cyclodextrin (β-CD) and hydroxypropyl-β-cyclodextrin (HP-β-CD) to enhance solubility and stability without chemical intervention. The formation of these complexes was rigorously validated through UV–Vis, FT-IR, PXRD, TEM, and ¹H-NMR spectroscopy. Notably, the aqueous solubility of indigo was enhanced 3.58-fold and 5.55-fold for the β-CD and HP-β-CD complexes, respectively. Furthermore, both complexes demonstrated superior thermal and photostability, with HP-β-CD exhibiting the most pronounced effects. This cyclodextrin-assisted solubilization was successfully extended to naturally extracted Jeju Indigo, underscoring its broad applicability. Our findings suggest that cyclodextrin-based encapsulation offers a sustainable and effective alternative to conventional reduction-oxidation dyeing processes.

To achieve high-value utilization of brewer’s spent grains and to produce protein-rich food ingredients, brewer’s spent grains were upcycled by a liquid fungal fermentation and the fermentation conditions were optimized. Brewer’s spent grains (BSG) represent the most abundant by-product of the brewing industry. Although BSG are food-grade, their direct use in food is limited because of sensory changes of the products. In this study, screening experiments revealed that black beer spent grains could be efficiently upcycled by submerged fermentation with the edible fungus Pleurotus ostreatus. The conditions of the fermentation of BSG with P. ostreatus were optimized using response surface methodology, including the parameters substrate concentration, inoculum volume, initial pH value, and temperature. As no separation between BSG and mycelium was possible after the fermentation, ergosterol was used as a biomarker to determine the fungal growth. As optimum conditions, a BSG concentration of 17 g L^{− 1} dry matter, an inoculum volume of 4.4% (v/v), an initial pH of 9.3 and a temperature of 30 °C were identified. The fermentation with P. ostreatus increased the true protein content of the biomass compared to the spent grains and reduced the total fat content. The biological value was increased from 88 to 94 (reference standard is whole chicken egg with a biological value of 100). Tryptophan and lysine were limiting in the non-fermented spent grains, while after fermentation, the chemical score of lysine increased from 78 to 92, and tryptophan wasn’t limiting anymore. Fermentation by P. ostreatus enhanced the nutritional value of BSG, and the fermentation conditions were optimized by using response surface methodology.

Disruptions in the gut microbiome are linked to various diseases, but their roles in conditions such as age-related muscle loss (sarcopenia) and drug-induced microbial changes remain poorly understood. To address this gap, MyBioScope, a novel in vitro model using the DASbox^® mini bioreactor system and human stool samples, was developed to simulate the anaerobic environment of the gastrointestinal (GI) tract. Bioreactors containing 120–200 mL of cultivation media were inoculated with stool slurry, stabilized over 24 h, and maintained with a customizable feeding protocol for multi-day experiments. Samples were analyzed using 16S rRNA gene sequencing, quantitative PCR, and metabolomics. Four pilot studies were conducted to validate the platform and model specific disease states, including proton pump inhibitor-induced GI tract oralization and microbiome alterations associated with sarcopenia. The workflow incorporated an anaerobic stool collection kit for user-friendly, room-temperature sample transport and storage. Our results demonstrated consistent microbial community structure and metabolic activity within disease-mimicking conditions. MyBioScope enabled reproducible, controlled studies of gut microbial dynamics and provided a scalable tool for investigating disease-specific microbiome changes. This platform may support translational efforts to integrate microbiome insights into clinical research, therapeutic development, and personalized medicine. In conclusion, this novel bioreactor-based in vitro model, MyBioScope, shows strong potential for in-depth exploration of disease-specific microbiomes and can facilitate new ways for integrating the knowledge of the microbiome’s impact on human health and disease into clinical practice.

1,12-Dodecanediol is a high-value chemical widely used in the polymer and fine chemical industries. However, its industrial production is currently based on petroleum-derived processes associated with high energy consumption and environmental concerns. To address these limitations, microbial bioconversion of 1,12-dodecanedioic acid (C12 diacid) to 1,12-dodecanediol (C12 diol) has been investigated as a sustainable production route. In this pathway, carboxylic acid reductase (CAR) requires ATP and NADPH as essential cofactors, making efficient cofactor supply an important factor for achieving high conversion efficiency. In this study, a recombinant Escherichia coli–based biocatalytic system was developed to enhance C12 diol production through ATP regeneration. ATP availability was identified as an important factor for whole-cell bioconversion, and a polyphosphate kinase 2 (PPK2) from Erysipelotrichaceae bacterium was introduced to regenerate ATP from AMP, increasing the conversion yield from 22.0% to 31.8% at 40 mM substrate. Supplementation with sodium hexametaphosphate (SHMP, polyP₆) further improved diol production, reaching 19.5 mM C12 diol with a conversion yield of 48.8%. In the cell-lysate-based conversion, NADPH and NADH exhibited comparable conversion efficiencies up to 70 mM MgCl₂. Diol production was influenced by MgCl₂ concentration, with the highest conversion obtained at 100 mM MgCl₂ in the presence of NADPH, yielding approximately 28 mM C12 diol (~ 70% conversion) within 1 h. Overall, this study highlights the importance of ATP regeneration and cofactor supply for improving C12 diol production.

Human papillomaviruses (HPVs) are a major cause of cervical cancer, which ranks fourth among cancers in women worldwide. A prophylactic vaccine composed of virus-like particles (VLPs) formed by the major capsid protein L1 of human papillomavirus (HPV) effectively prevents HPV infection but provides limited cross-protection against other HPV subtypes, highlighting the importance of multivalent prophylactic vaccines. In this study, cultivation conditions for recombinant HPV58 L1 protein production in the yeast Hansenula polymorpha were optimized to enhance growth and the volumetric yield of L1 protein. The results indicated that induction with methanol (at 1% v/v) was necessary for HPV58 L1 production in SYN6 medium, whereas a cultivation temperature of 37 °C was optimal for growth and production of HPV58 L1 protein. Subsequently, SYN6 medium supplemented with 10 g/L of either Hy-Express™ System II or HySoy was evaluated in batch and fed-batch bioreactor cultivations. Fed-batch cultivation with HySoy supplementation under a constant feeding rate achieved an OD₆₆₀ of 117 (26.18 g-CDW/L), a volumetric L1 yield of 312 mg/L, and a productivity of 4.7 mg/L/h, which were significantly higher than those obtained with the control SYN6 medium (92 mg/L; 2.2 mg/L/h). These findings demonstrate that fed-batch cultivation with HySoy supplementation offers a practical and efficient strategy for HPV58 L1 production at the bioreactor scale.

In this study, biochar was prepared from Flammulina velutipes residues, and then loaded with Bacillus megaterium YZS-M06, to construct a composite material (BCB treatment) with synergistic remediation function. The improvement effect of this material on coastal sandy soil and its regulatory mechanism on the growth of Ipomoea pes-caprae were investigated. The findings demonstrated that F. velutipes residue-based biochar loaded with B. megaterium YZS-M06 (BCB) exerted a pronounced synergistic effect on the amelioration of chemical properties in coastal sandy land. After 30 days of cultivation, BCB treatment significantly increased soil total nitrogen (0.65 g/kg), total potassium (12.89 g/kg), and available potassium (81.75 mg/kg), as well as urease and phosphatase activities by 221% and 210% relative to the control. It also optimized the soil bacterial community, markedly enriching Bacillus from 46.58% to 57.85% relative abundance, reshaping microbial networks, and restructuring key ecological diversity–function pathways. These combined improvements in soil physicochemical properties and microbial structure effectively promoted I. pes-caprae growth. BCB treatment enhanced root length by 101% and root number by 63%, activated leaf antioxidant systems, mitigated membrane lipid peroxidation, and boosted osmolyte accumulation, thereby systematically strengthening the plant’s stress resistance. F. velutipes residue-based biochar loaded with B. megaterium YZS-M06, through the synergistic interaction of “biochar-functional bacteria”, substantially improved soil chemical properties, optimized microbial community architecture, enhanced stress tolerance of I. pes-caprae, and promoted plant growth. This study combines the resource utilization of agricultural waste F. velutipes residues with functional microbial enhancement. Through the synergistic mechanism of biochar-functional bacteria, the dual goals of coastal sandy soil improvement and plant growth promotion were achieved, providing a new technical route and theoretical basis for ecological restoration in extreme habitats.

Sustainable biofuels have spurred interest in cyanobacterial ethanol production, yet large-scale application is severely hindered by microbial contamination—a devastating challenge that lacks universally effective, biocompatible mitigation strategies. Traditional methods such as pH manipulation or antibiotic application are often physiologically incompatible, environmentally unsustainable, or ineffective against diverse contaminant consortia.

Here, we propose and validate alginate encapsulation as a physical barrier strategy to address this challenge. Alginate, a biodegradable polysaccharide derived from brown algae, forms a porous hydrogel matrix that encapsulates cyanobacterial cells. This matrix blocks direct contact, uptake or ingestion by microbial contaminants while allowing the efficient diffusion of gases (CO₂, O₂), light, and nutrients to maintain photosynthetic and metabolic functions. Using our previously engineered, high-performance ethanol-producing strain (EP), we find that unprotected cultures rapidly collapse and cease ethanol production upon inoculation with a contaminant consortium, with cumulative ethanol yield falling to undetectable levels, whereas encapsulated cells sustain normal growth and photosynthetic activity under identical contamination pressure. After rinsing and re-cultivation, the encapsulated biomass partially restored ethanol productivity, achieving a cumulative titer of 320 mg/L over 4 days post-recovery. This suggests that the protective strategy is non-invasive and enables functional recovery of the production system following contamination exposure.

This study demonstrates that alginate encapsulation represents a promising strategy to mitigate microbial contamination, with the potential to enhance the technical resilience and operational stability of cyanobacterial biofuel production.

White rot fungi obtain nutrients from fibrous substrates through the radical secretion of extracellular ligninolytic enzymes (LE) and spent mushroom substrate (SMS), a by-product of commercial cultivation, is a valuable bioresource of LE. This study aims to compare various techniques for dehydrating and preserving the Pleurotus ostreatus SMS extract in terms of enzymatic activity and ability to improve the fiber rumen degradability (NDFD) of extract-treated wheat straw. To convert the extract into stable enzyme powder, it was concentrated before being dried using freeze, spray and vacuum drying processes. The different extracts reconstituted from powders were evaluated for residual LE activity after multiple successive freeze-thaw cycles, as well as their ability to improve wheat straw NDFD. To produce extracts, fresh SMS was suspended in acetate buffer, homogenized and filtered. A portion of the original extract was stored (− 20 °C) and the remainder was concentrated up to 50% of volume by cross-flow filtration. The concentrated extract was divided into four aliquots to be used without processing or spray, vacuum or freeze drying. Extracts were evaluated for total, Mn and lignin peroxidases and laccases (LAs) enzymatic activity and were subjected to four freezing-thawing cycles. Wheat straw was incubated in reconstituted extracts before being tested for in vitro NDFD. Compared to the original extract, reductions of LE were 2–30% in concentrated and 10–36, 4–48 and 74–84% in freeze, vacuum and spray dried, respectively. LE of extracts decreased with the number of freeze-thaw cycles, apart from the spray dried extract. The NDFD of all extract-treated straws resulted higher (P < 0.05) than the control, apart from the spray-dried extract and had a high linear relationship with LAs of extracts (R² 0.87, P < 0.01). Results support the potential of extract preparations from fungal SMS to be a promising bioresource useful for improving the NDFD of high-fiber forages, such as straw.

Supercritical CO₂ extraction was applied to Heliotropium arbainense to evaluate how extraction pressure influences phytochemical composition and biological activity. Extractions of phenolic and flavonoid were performed at two pressures (200 and 550 bar), by using Supercritical CO₂. Phenolic and flavonoid compounds, were determined by HPLC analysis. Higher pressure extraction (550 bar) resulted in a greater extraction yield and a marked enrichment of phenolic and flavonoid compounds. Gallic acid (1496.01 µg/g) was the most prevalent component under SFE 1, followed by catechin (859.51 µg/g), rutin (824.55 µg/g), and coumaric acid (559.93 µg/g). Both extracts exhibited broad antimicrobial activity against Gram-positive and Gram-negative bacteria as well as Candida albicans, with consistently lower MIC and MBC/MFC values observed for the high-pressure extract. Cytotoxic evaluation against SKOV3 ovarian cancer cells revealed a clear dose-dependent reduction in cell viability. The calculated IC₅₀ values further confirm the greater cytotoxic potency of extract at 550 bar, with a lower IC₅₀ (153.04 ± 0.4 µg/mL) compared to extract at 200 bar (183.18 ± 2.29 µg/mL) against SKOV3 cells. However, flow cytometry revealed that extract at 200 bar produced slightly higher early apoptosis (43.79% vs. 43.39%) and greater necrosis (21.83% vs. 13.29%) in SKOV3 ovarian cells overall. Anti-inflammatory activity, assessed by protein denaturation inhibition, was observed for both extracts, with the lower-pressure extract showing slightly stronger inhibitory efficiency. Pressure-dependent supercritical CO₂ extraction significantly influenced the phytochemical richness and biological performance of H. arbainense. These findings highlight the importance of extraction conditions in maximizing the functional potential of plant-derived bioactive compounds and support further investigation of H. arbainense as a source of biologically active phenolics.

This review develops a region-specific Multi-Criteria Decision Analysis (MCDA)-based screening framework for evaluating food-processing residues for biochar applications, offering a transparent and replicable decision-support tool for policymakers and bioeconomy stakeholders in Turkey and beyond. Using Turkey as a region-specific case context, ten underutilized residues—boza fermentation residue, tarhana fines, rosehip seed cake, mulberry syrup press-cake, carob syrup pulp residue, pumpkin seed oil cake, saffron floral by-products, fig-jam seed fraction, lupin brining sediment, and date syrup filter cake—were compiled from the literature and characterized in terms of moisture, ash, organic fractions, higher heating value, and macro-mineral composition. Drawing on thermochemical fundamentals, the review synthesizes how these traits influence biochar properties relevant to fuel use, soil amendment, pollutant adsorption, anaerobic digestion (AD) enhancement, and composite materials, and qualitatively links residue groups to suitable conversion windows such as hydrothermal carbonization and low- or high-severity slow pyrolysis. To convert this information into a transparent screening tool, all indicators were normalized via min–max transformation and aggregated into four mechanistic proxies capturing fuel quality, nutrient release, an adsorption-oriented screening proxy, and AD compatibility. A Simple Additive Weighting (SAW) method was then used to calculate 0–1 suitability scores and 0–100 indices for five application domains: fuel, soil amendment, adsorption/remediation, AD enhancement, and composite/material use. Under the selected criteria and weighting assumptions, rosehip seed cake, pumpkin seed oil cake, carob syrup pulp residue, and fig-jam seed fraction emerged as comparatively high-priority feedstocks, whereas saffron floral by-products and lupin brining sediment showed consistently low relative suitability. By linking feedstock chemistry to application-oriented screening scores, the framework supports rapid comparison of residue-to-application pathways while acknowledging that rankings may evolve as additional performance data, logistical constraints, or alternative weighting scenarios are incorporated.

This study evaluated the anti-acne potential of extracellular proteins derived from Lactobacillus gasseri (LG-EPs) by integrating physicochemical characterization, antibacterial assessment, cellular assays, and an in vivo sebaceous gland model. LG-EPs were obtained by ammonium sulfate precipitation and characterized using gel permeation chromatography/light scattering (GPC/LS) and liquid chromatography–tandem mass spectrometry (LC–MS/MS). The molecular weight of LG-EPs was mainly distributed between 1.0 × 10⁴ and 2.0 × 10⁴ g/mol, and peptide analysis identified four peptides with antimicrobial potential and twelve peptides with antioxidant potential. LG-EPs exhibited direct antibacterial activity against acne-associated bacteria, with MIC and MBC values of 600 µg/mL against Cutibacterium acnes and MIC and MBC values of 700 µg/mL and 1 mg/mL, respectively, against Staphylococcus aureus. Growth-curve and biofilm adhesion assays further showed that LG-EPs inhibited bacterial proliferation and adhesion. In LPS-stimulated HaCaT cells, LG-EPs reduced the secretion of pro-inflammatory cytokines, including IL-6, IL-8, IL-1β, and TNF-α, while increasing the expression of barrier-related factors such as AQP3, FLG, and LOR. In a golden hamster model, topical LG-EP treatment decreased sebum production and downregulated the transcription of lipogenesis-related genes, including SREBP-1, FAS, and ACC1. These effects were associated with reduced transcript levels of PI3K, AKT, and mTOR, while the anti-sebum effect was accompanied by increased AMPK transcription. Overall, LG-EPs showed multi-target anti-acne potential through antibacterial, anti-inflammatory, barrier-protective, and sebum-suppressive effects.

Polyurethane (PU) is an industrially versatile polymer whose environmental persistence pose significant waste management challenges. Although several PU-degrading microorganisms have been reported, studies evaluating degradation across chemically distinct PU substrate remain limited. The present study explores PU biodegradation potential of a soil-borne fungus Fusarium parceramosum, with two chemically different PU substrates—Impranil (PU dispersion), and PU foam—under unoptimized conditions. The fungus achieved 92% degradation of Impranil within 192 h, and 31.29% weight loss of PU foam over 60 d. Degradation kinetics were evaluated using zero-order, first-order, Langmuir, and Freundlich models, with zero-and first-order models showing best fit with experimental data. Enzymatic assay revealed significant urease and aliphatic carbamate-hydrolyzing activities associated with degradation. For Impranil, urease and aliphatic carbamate-hydrolyzing activities were 202.03 U/mL and 412.47 U/mL, respectively, whereas for PU foam they were 338.12 U/mL and 284.17 U/mL, respectively. Structural and chemical alterations were confirmed through SEM, FTIR, XRD and GC–MS analysis. Metabolite identification indicated the formation of degradation intermediates, suggesting their possible involvement in subsequent microbial processes. Overall, this study provides the first evidence of dual-substrate specificity of Fusarium parceramosum highlighting its potential in sustainable waste management approaches.

Ultraviolet B (UVB) radiation is the primary cause of photodamage to the skin, triggering the oxidative stress, mitochondrial dysfunction, and impaired barrier integrity. We extracted polysaccharides from Passiflora edulis Sims peel via microbial fermentation (PP-FP) and characterized their structural properties using fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), and molecular weight analyses. Photoprotective effects were evaluated in UVB- irradiated HaCaT cells and BALB/c mice dorsal skin by measuring of oxidative stress markers, mitochondrial function, DNA damage, and skin barrier proteins. PP-FP contains a furanose ring structure, exhibits an irregular, loosely layered morphology with attached filamentous and porous structures, and shows a number-average molecular weight (Mn) of 3.519 kDa and a weight-average molecular weight (Mw) of 6.66 kDa. In UVB-irradiated HaCaT cells, PP-FP (500 µg/mL) significantly enhanced cell migration capacity (achieving 79.39% wound closure at 48 h), reduced reactive oxygen species (ROS) accumulation, alleviated mitochondrial membrane potential aberrations, and decreased interleukin-17 (IL-17) release by 63%. Concurrently, it markedly elevated key skin barrier protein levels in HaCaT cells, notably enhancing filaggrin (FLG, 1.82-fold) and lamellar oligomerizing protein (LOR, 2.04-fold) expression. Furthermore, PP-FP maintained epidermal thickness, suppressed formation of DNA damage marker γ-H2AX, downregulated matrix metalloproteinase-3/9 (MMP3/9) expression by 40–50%, and effectively preserving epidermal barrier function. This study demonstrates that fermentation-derived Passiflora edulis Sims polysaccharides mitigate UVB damage through a dual mechanisms—antioxidant protection and barrier reinforcement—providing a sustainable strategy to repurpose agricultural byproducts for high-efficacy skincare formulations.

To address the challenges of high-density animal cell culture, this study developed a high-density culture system comprising a single-use bioreactor (SUB) with a nominal volume of 500 mL and a pulsed tangential flow filtration (ITF) unit. The reactor can be configured with two layers of 35 mm diameter impellers—either double Elephant Ear (EE-EE) or Elephant Ear combined with Ribbon (EE-RB). The flow field characteristics were rigorously characterized through CFD simulations (60–240 rpm; 90–480 mL) validated by experimental data. Engineering analysis revealed the system’s robust culture environment: ${k}_{L}a$ values ranging from 2 to 15 h⁻¹ (60–180 rpm; 200–400 mL; 30–150 mL/min aeration), $P/V$ values from 0.1 to 10 W/m³, and mixing times between 1 and 10 s. Crucially, the system maintains a mild shear environment with an average shear strain rate (SSR) below 25 s⁻¹, fully within the physiological tolerance range for mammalian cells. This low-shear, high-mass-transfer design was validated through perfusion cultures of CHO and HEK293 cells. The system achieved exceptionally high cell densities of 8.32 × 10⁷ cells/mL and 1.17 × 10⁸ cells/mL, respectively, with cell viability consistently exceeding 90%, demonstrating its suitability for high-intensity biopharmaceutical production.

Using biochar as a carrier to enhance the adaptability and survival of inoculated microorganisms under harsh environmental conditions is considered as a promising strategy. However, the immobilization performance and underlying mechanisms of microorganisms on different biochars remain insufficiently understood. In this study, a series of biochars were prepared from various feedstocks and at different temperatures, and their capacities to immobilize Bacillus subtilis (B.subtilis) were evaluated. The results demonstrated that high-temperature (700 °C) biochars exhibited 14.40%–60.00% greater loading capacity for B.subtilis, compared to low-temperature (400 °C) biochars. Analyses of surface morphology, functional groups, hydrophobicity, and Zeta potential before and after immobilization indicated that B.subtilis loading significantly altered the surface properties of biochar, including increases in C and N contents, enhanced richness and diversity of functional groups, and a transformation from hydrophobicity to hydrophilicity. Adsorption kinetics and isotherm modeling revealed that the immobilization process was dominated by chemical adsorption, characterized by monolayer adsorption on a homogeneous surface. Interface interaction analysis further confirmed that the electrostatic interaction, hydrogen bonding, and hydrophobic forces between the functional groups of biochar and those on B.subtilis cells synergistically facilitated microbial immobilization. Based on these findings, a two-stage adsorption process of B.subtilis on biochar was proposed: initial surface adhesion and pore filling, followed by extracellular polymer and surface functional group complexation. Biochar properties, including specific surface area, pore volume, Zeta potential, hydrophobicity, C/N ratio, and surface functional groups, were further identified as key factors influencing immobilization. Finally, the salt tolerance of B.subtilis was significantly enhanced when immobilized on biochars, particularly corn straw biochars with large specific surface areas and developed pore structures. This improved salt tolerance suggests that the biochar-based microbial fertilizers could serve as a promising approach for the amelioration of salt-alkaline soil.

Temperature is a key factor driving microbial community succession and volatile flavor compound formation during the fermentation of cigar tobacco leaves (CTLs). This study systematically investigated microbial community dynamics, co-occurrence networks, and volatile flavor compound (VFCs) profiles of CTLs from Dominica and Yunnan under a 20–60 °C fermentation gradient. High-throughput sequencing identified Staphylococcus, Oceanobacillus, and thermophilic fungi as core microbes potentially associated with aroma formation. Dominica CTLs exhibiting higher microbial diversity than Yunnan CTLs. Dominica CTLs produced abundant esters, alcohols and ketones across different temperature stages, whereas Yunnan CTLs accumulated more pyrazines, indole and terpenoids at high temperatures (≥ 50 °C). Co-occurrence network analysis revealed temperature-driven shifts in microbial interactions: Dominica CTLs formed balanced networks with mixed positive/negative correlations at low temperatures, while Yunnan CTLs developed stable networks dominated by positive correlations at high temperatures. PERMANOVA indicated significant differences in microbial community structure among temperature gradients (R² = 0.78, p < 0.001). Spearman correlation analysis suggested that core microbes (e.g., Staphylococcus) were significantly correlated with the accumulation of key VFCs (e.g., esters, alcohols). These findings propose a conceptual temperature–microbe–VFC interaction framework, providing theoretical support for optimizing CTL fermentation processes.

The past few years have witnessed an exponential rise in the development of carbon quantum dots (CQDs) derived from natural biomasses, rendering them a green and multifunctional platform for sensor applications. This comprehensive review provides a critical assessment of advancements between 2021 and 2025 in the syntheses, physicochemical characterizations, and sensing applications of biomass-derived CQDs. Different precursors—e.g., fruit peels, leaves, and agricultural waste—have been effectively transformed into highly fluorescent CQDs using hydrothermal, microwave-assisted, and pyrolytic routes, with synthesis times as short as 10 min for certain microwave procedures. The structural studies exhibit quasi-spherical morphologies (2–10 nm) and partial graphitization, and the optical studies confirm excitation-dependent fluorescence with quantum yields as high as 30%, particularly in nitrogen- and sulfur-doped systems. Biomass-derived CQDs have shown superb selectivity and sensitivity to a broad spectrum of analytes. For example, CQDs synthesized from Solanum nigrum leaves reported detection limits as low as 8 nM for Fe³⁺, while CQDs synthesized from pitaya peels enabled sensitive detection of antibiotics via aggregation-induced emission effects. Environmental targets such as glyphosate, NH₃, and CH₂O have also been detected at nanomolar levels, employing mechanisms like static/dynamic fluorescence quenching, electron transfer, and FRET. Despite these advances, there are still challenges in large-scale production, standardization of fabrication protocols, and integration of CQDs into real-time sensing platforms. In the future, the work is going to be further developed through the adoption of green synthesis approaches, regulatory standardizations, and integration of CQDs into wearable and portable diagnostic devices. Such developments point to the prospects of biomass-sourced CQDs as green, cost-effective, and ultrasensitive nanomaterials for next-generation chemical, biological, and environmental sensors.

In Uruguay, Pinus taeda is the dominant conifer in industrial plantations, generating large volumes of knot-containing offcuts during processing. These residues are highly enriched in extractives, offering opportunities for valorization within a circular bioeconomy. This study examined the recovery of bioactive compounds from P. taeda knotwood through ethanol extraction, process optimization, Gas Chromatography coupled with Mass Spectrometry and Flame Ionization Detection (GC–MS/FID) analysis, and antifungal evaluation. The effects of extraction temperature, ethanol concentration, and liquid–solid (L/S) ratio on extraction yield, total phenolic content, and FRAP antioxidant activity were assessed, and response models were developed to identify optimal conditions. Maximum extraction yield (20.8%) occurred at 47 °C, 100% ethanol concentration, and L/S of 8.3. The highest phenolic content (5.7 g gallic acid equivalents/100 g) was predicted at 61 °C, 100% ethanol, and L/S 15, while the greatest antioxidant capacity (15.8 mmol ascorbic acid equivalents/100 g) was achieved at 75 °C and L/S 15, independently of ethanol concentration. Two extraction conditions, representing the best compromise among yield, phenolics, and antioxidant performance, were selected for further characterization and antifungal tests. GC–MS/FID analysis showed that stilbenes and terpenoids dominated the extracts. Antifungal assays against Trametes versicolor and Gloeophyllum trabeum revealed strong inhibition, reaching up to 65% and 97% after seven days. Overall, the results demonstrate that P. taeda knotwood residues can be efficiently valorised via ethanolic extraction to obtain bioactive fractions with high antioxidant and antifungal activity, supporting sustainable and circular approaches for wood protection.

The transition from fossil fuels to low-carbon bio-based energy systems is increasingly constrained by the efficiency, scalability, and integration of conversion technologies. Addressing this challenge, this review critically analyzes microbial biofuel production through a conversion-centric and systems-level framework, emphasizing how feedstock diversity, pretreatment chemistry, enzymatic deconstruction, and microbial metabolism collectively govern overall process performance. This review evaluates how pretreatment strategies modulate biomass recalcitrance, hydrolysate chemical ecologies, inhibitor profiles, and redox balance, thereby imposing fundamental constraints on enzymatic efficiency, microbial conversion yields, and emissions outcomes. Advances in enzymatic hydrolysis are assessed in terms of bond-specific catalysis, enzyme synergy, and persistent bottlenecks arising from substrate heterogeneity, lignin enzyme interactions, and non-productive binding, while microbial engineering strategies from robust monocultures to synthetic consortia and cell-free systems are examined through techno-economic and metabolic flux perspectives. It further highlights the emerging role of artificial intelligence and multi-omics integration in enabling predictive optimization of pretreatment severity, enzyme cocktails, and metabolic routing, moving beyond empirical process tuning. This article establishes a unified framework for integrated “microbial lignocellulose-to-fuel” pathways, demonstrating how coordinated advances in conversion technologies are essential for achieving scalable, economically viable, and environmentally sustainable bioenergy systems.

Agro‑industrial brans are abundant residues that can be valorized as low‑cost feedstocks for microbial bioprocesses within a circular‑economy framework. Here, we investigated the use of corn, soybean, rice and wheat bran hydrolysates as sole nutrient sources (no detoxification and no supplementation) for carotenoid production by the yeast Rhodotorula mucilaginosa. After standardizing total fermentable sugars to 10–12 g/L, the yeast successfully consumed mixed sugars and produced biomass and carotenoids in all hydrolysates. Rice bran hydrolysate led to the highest carotenoid titer (28.41 ± 0.23 mg/L) and the highest specific carotenoid content (1.11 ± 0.05 mg_carotenoids/g_{dry cells}), whereas soybean bran hydrolysate favored biomass formation (29.74 ± 0.18 g/L). UV–Vis/FTIR analyses of the pigment-rich extract showed spectral features consistent with carotenoids (absorption maxima at 480–490 nm and characteristic FTIR bands), supporting the qualitative identification of a carotenoid mixture. Finally, a cradle‑to‑gate life cycle assessment (LCA) showed that the RBH scenario presented the lowest impacts across the evaluated categories, with electricity demand during fermentation as the main hotspot. Overall, rice bran emerges as a promising residue for sustainable carotenoid bioproduction coupling process performance and environmental benefits. This study highlights the valorization of agro-industrial residues as an efficient strategy to reduce production costs and environmental impact, contributing to the development of more sustainable biotechnologies for carotenoid synthesis and beyond.

Medicinal plants have long served as important sources of therapeutic agents owing to their diverse bioactive constituents and multi-target pharmacological properties. In particular, plant-derived compounds have attracted increasing attention for the management of chronic inflammatory and metabolic diseases, including atherosclerosis. However, the molecular mechanisms by which medicinal plants modulate the cellular heterogeneity and intercellular communication networks within atherosclerotic plaques remain insufficiently understood. Despite the widespread implementation of lipid-lowering therapy, the persistence of residual inflammatory risk, driven by immunometabolic network dysregulation, remains a cardinal therapeutic challenge in atherosclerosis (AS) management. While Perilla frutescens exhibits well-documented anti-inflammatory properties, the precise molecular targeting within the atherosclerotic plaque microenvironment and the regulatory mechanisms governing intercellular communication networks remain poorly elucidated. To address this gap, we established a multi-scale integrative computational framework synergizing network pharmacology, human atherosclerotic plaque single-cell transcriptomic (scRNA-seq) profiling, and ensemble machine learning algorithms (LASSO and random forest) for systematic identification of robust therapeutic targets. Subsequently, molecular docking coupled with 100-ns all-atom molecular dynamics (MD) simulations validated the binding affinity and thermodynamic stability of drug–target complexes. The study successfully analyzed the cellular heterogeneity lineage of plaques and identified a core feature set of 10 genes including HIF1A, PPARG and ITGB1, which specifically mapped the differentiation trajectory of macrophages to foam cells. External validation in an independent cohort demonstrated superior diagnostic performance of this signature (AUC = 0.996). Cellular communication network dissection revealed the foam cell-driven SPP1–ITGB1 signaling axis as a pivotal conduit orchestrating inflammatory crosstalk. Molecular docking demonstrated pronounced binding affinity between luteolin, the principal bioactive constituent of Perilla frutescens, and ITGB1 (binding energy: − 8.9 kcal/mol). MD simulations further corroborated the efficacy of luteolin in stabilizing ITGB1 conformation via a "conformational-locking" mechanism (RMSD equilibration within 0.10–0.20 nm), thereby abrogating pathological cell adhesion signaling transduction. Collectively, this study provides a high-resolution molecular atlas of Perilla frutescens-mediated AS intervention, systematically elucidating the mechanistic paradigm whereby luteolin attenuates vascular inflammation through targeted disruption of the SPP1–ITGB1 communication axis. These findings underscore the therapeutic targeting of cell adhesion receptors as a translationally promising strategy for mitigating residual inflammatory risk in AS.

This study aimed to elucidate the core therapeutic targets and mechanisms of action of rosehip extract (FRLE) in IgA nephropathy (IgAN) by integrating bioinformatics, machine learning, and computational simulation techniques to simultaneously analyze the therapeutic effects of FRLE on IgAN. Through screening differentially expressed genes in IgAN patients and identifying potential target proteins of the core components of FRLE, 118 overlapping targets were ultimately determined as the gene set involved in the synergistic interaction between the two. Through triple machine learning validation, FGR and LDHB were identified as core target proteins, with Ellagic acid, Rutin, and Hyperoside as the core active components. In IgAN patients, LDHB was significantly downregulated, while FGR was significantly upregulated. Both demonstrated excellent diagnostic efficacy and were closely associated with the renal immune microenvironment. Molecular docking and molecular dynamics simulations confirmed that the core components could stably bind to FGR and LDHB. In summary, FRLE targets and modulates FGR and LDHB through its core components, intervening in inflammatory pathways and immune microenvironment imbalance, thereby providing a theoretical basis for subsequent experiments and clinical translation.

Renal fibrosis is a progressive injury contributing to renal function deterioration. Mounting evidence has underscored the profound impact of gut microbiota metabolites on host health and disease, yet their underlying mechanisms against renal fibrosis remain unclear. The aim of this study was to fully elucidate their therapeutic potential in the context of renal fibrosis.

The targets of gut microbiota metabolites were identified in gutMGene. The diseases targets were obtained from the OMIM, GeneCards and DisGeNet databases. The STRING and DAVID platform were employed to identify the core targets and pathways. Gut Microbiota-Targets-Pathway-Metabolites (G-T-P-M) network was constructed to screen the core metabolites. Molecular docking was used to assess the interactions between the targets and metabolites.

A total of 47 overlapping targets related to gut microbiota metabolites and renal fibrosis were acquired. The bioinformatics analysis indicated that the targets were enriched in the regulation of TNF pathway and Toll-like receptor pathway. The PPI network (Protein-Protein Interaction) identified JUN, IL6, IL1B and AKT1 as the core targets. The G-T-P-M network revealed that Propionate, Butyrate and 3-Indolepropionic acid were identified as the core non-toxic and promising core metabolites. The core metabolites showed stable binding affinity with the core targets.

The findings highlight that gut microbiota metabolites represent a promising therapeutic option for combating renal fibrosis by modulating multiple targets and pathways, providing a theoretical foundation for the future studies exploring gut microbiota as targeted strategies in the prevention and treatment of renal fibrosis.

Hepatocellular carcinoma (HCC) is a global health challenge with limited therapeutic options. The effectiveness of conventional medication like cisplatin is often compromised by their severe toxicity. This study investigated carob pod aqueous extract (CPAE), a polyphenol-rich natural product, as a potential adjunct therapy to enhance efficacy and mitigate cisplatin toxicity in a preclinical HCC animal model.

A rat model of HCC was established using diethylnitrosamine (DEN) and carbon tetrachloride (CCl₄). Forty-two Wistar rats were divided into seven groups, receiving various treatments: control, CPAE, vehicle, HCC only, HCC+CPAE, HCC+cisplatin, and HCC+CPAE+cisplatin. Liver and kidney function, metabolic profiles, oxidative stress/antioxidant parameters, gene and protein expression (AMPK, PGC-1α, TFAM, SIRT1, iNOS, NF-κB, IκK, p53, SREBP-2), histopathology, and statistical analyses were performed.

HCC induction caused significant liver dysfunction, metabolic disturbances, oxidative stress, alongside dysregulation of AMPK/PGC-1α/TFAM and NF-κB/iNOS pathways. CPAE, alone or with cisplatin, markedly ameliorated these changes, improving liver and kidney function, restoring antioxidant status, reducing the tumor marker AFP, suppressing pro-inflammatory and oncogenic signaling, and enhancing histological architecture. Furthermore, Combination therapy demonstrated synergistic benefits, with CPAE reducing cisplatin-induced nephrotoxicity and enhancing its antitumor efficacy, primarily via modulation of mitochondrial biogenesis, redox balance, and inflammatory signaling.

CPAE exhibits potent hepatoprotective and anti-HCC activity, especially when combined with cisplatin. This combination modulates mitochondrial and inflammatory pathways while mitigating cisplatin-induced toxicity. These finding position CPAE as a promising natural adjuvant for integrative HCC management. Further translational studies are warranted to validate these findings and explore clinical applicability.