Search Results (1,732)

Consolidated bioprocessing (CBP) is difficult to monitor because enzyme production, lignocellulose degradation, sugar release, and fermentation occur simultaneously under sparse measurement, feedstock variability, and plant–model mismatch conditions. This study proposes a computational sensor-set design framework for digital-twin-assisted CBP monitoring. A five-state virtual plant, consisting of active biomass, cellulolytic enzyme activity, residual insoluble substrate, soluble sugar, and ethanol, was used to evaluate all 16 ethanol-mandatory measurement packages formed from ethanol, sugar, biomass, enzyme, and residual-substrate proxy channels. Candidate sensor sets were assessed using finite-difference output sensitivities, Fisher-information-based state-observability and parameter-identifiability analyses, eigenvalue and parameter-correlation diagnostics, and paired Monte Carlo unscented Kalman filter soft-sensing reconstruction. Within the tested five-state virtual-plant benchmark and with the specified excitation schedule, noise assumptions, burden indices, and scoring objective, ethanol-only sensing provided the weakest support for state-aware CBP digital-twin reconstruction. At a $6\mathrm{h}$ sampling interval, the state-observability log-pseudodeterminant increased from 4.18 with ethanol-only sensing to 8.56 after adding soluble sugar and to 16.42 with full-proxy monitoring. The ethanol–sugar–biomass–substrate package also gave strong reduced state-observability performance, with log-pseudodeterminants of 15.12, 13.76, and 12.51 at 6, 12, and $24\mathrm{h}$, respectively. Biomass and enzyme proxies contributed strongly to parameter learning, and the ethanol–sugar–biomass–enzyme package gave the strongest active parameter-identifiability performance, with log-pseudodeterminants of 10.82, 9.06, and 6.67 at 6, 12, and $24\mathrm{h}$, respectively. In the paired soft-sensing analysis, full-proxy monitoring reduced the mean latent-state RMSE from 1.1899 to 0.3756, followed by ethanol–biomass–enzyme–substrate with 0.3843 and ethanol–sugar–biomass–substrate with 0.4121. The primary aggregate ranking identified ethanol–sugar–biomass–substrate as the best overall package, with a sensor-value score of 0.8432 and a burden index of 7.0, followed by full-proxy monitoring with a score of 0.8173 and a burden index of 10.0. Robustness tests showed that ethanol–sugar–biomass–substrate remained top-ranked under uniform noise scaling, full UKF missingness, delay and bias stress test conditions, most scoring-weight scenarios, and all tested sensor-specific burden workflows. Full-proxy monitoring remained a close competitor under independent sensor-specific noise variation conditions and became top-ranked for some alternative operating trajectories. The proposed framework provides a simulation-based method for prioritizing informative measurement packages before implementing CBP digital twins in laboratory and pilot-plant settings. Full article

Cultivated-meat production relies on robust animal cell-line engineering, scalable tissue-engineering strategies, and clearly defined regulatory standards. This review examines the developmental pipeline from primary tissue biopsy to large-scale expansion and regulatory evaluation, focusing on stable and safe immortalized cell platforms. We compare muscle satellite cells, mesenchymal stromal/adipogenic progenitors and induced pluripotent stem cells, highlighting trade-offs among proliferative capacity, lineage commitment, genomic stability, and food-safety considerations. We then analyze immortalization strategies, including spontaneous senescence bypass, telomerase reactivation and CRISPR-based checkpoint modulation, highlighting their impact on genomic stability and food-safety risks. Recent advances in serum-free media, extracellular matrix-mimetic biomaterials and staged co-culture protocols have enabled centimeter-scale tissues with improved texture and marbling; however, cost, reproducibility and scalability remain bottlenecks. Integrating multi-omics surveillance with life-cycle assessment reveals that environmental benefits (land, water and antibiotic reduction) are attainable only when energy inputs and growth-factor sourcing are optimized. Finally, we examine regulatory frameworks that distinguish food-grade immortalized cells from pharmaceutical substrates and genetically modified crops. By integrating cell biology, animal biotechnology, and bioprocess engineering, this review identifies technical priorities for advancing cultivated meat from laboratory development to industrial implementation, positioning genomic monitoring as an essential framework for assessing biological stability, functional predictability, and food-production suitability. Full article

The volumetric mass transfer coefficient ($k_{L}a$) governs the design, operation, and scale-up of aerobic bioprocesses, yet its dependence on reactor geometry, impeller design, operating conditions, and fluid properties limits prediction by empirical correlations. Machine learning (ML) improves accuracy but faces two barriers in bioprocess practice: selecting the best model among many candidates requires expertise, and small, highly multicollinear data make models chosen based on test error alone prone to overfitting. Using a browser-based, no-code platform, we trained 14 regression algorithms under an identical pipeline on a published $k_{L}a$ dataset, and introduced a composite objective, the generalization-penalized error (GPE), which is the test RMSE plus the absolute train–test RMSE gap. Minimizing GPE rather than test RMSE expanded the top statistically equivalent group to include not only boosting ensembles but also simpler, interpretable models, indicating that black-box models hold no clear advantage once train–test consistency is assessed. Sensitivity analysis showed that tree models produce discontinuous responses, whereas algebraic learning via elastic net (ALVEN) yields smooth surfaces. Shapley additive explanations (SHAP) and an ontology graph, interpreted by a retrieval-augmented language-model agent, identified rotational speed and gas flow rate as dominant, reproducing the established mass transfer mechanism. The framework offers a reproducible, interpretable, expertise-light route to bioprocess model selection. Full article

The main objective of this study was to generate protein-polyphenol microparticles on the basis of pea and rice proteins in combination with pomegranate juice. Protein microparticles were prepared as a freeze-dried powder and evaluated for total polyphenols and proanthocyanidins using spectrophotometric methods, and for individual polyphenols using the HPLC method. In addition, they were assessed for antioxidant activity, and IR spectra were recorded to establish structural changes in proteins upon adsorption of pomegranate polyphenols. The potential of the formulated microparticles to inhibit colon cancer cell proliferation (SW1116 and Colo205) was also investigated and compared with pomegranate juice. The adsorption capacity of total polyphenols for both protein matrices were 47%. All compounds had a higher affinity for the pea protein matrix except gallic acid. The highest affinity for proteins had punicalagin, with 88% and 80% for pea and rice proteins, respectively. The microparticles demonstrated antioxidant potential using DPPH, ABTS, FRAP, and CUPRAC methods. Both pomegranate juice and protein microparticles exhibited high antioxidant potential and inhibitory effects on both types of colon cancer cells. Screening of IR spectra of protein microparticles revealed the adsorption of pomegranate polyphenols through changes in protein structures, particularly in regions characteristic of proteins. Full article

Olive mill wastewater (OMW), due to its high organic load and phenolic content, represents both a major environmental challenge and a promising low-cost substrate for microbial bioprocesses. In this study, lipid production by Yarrowia lipolytica using OMW was optimized through a mixed-level Taguchi experimental design. The effects of OMW dilution (%), nitrogen supplementation, NaCl concentration, sterilization, and carbon source (glucose or glycerol) were evaluated in terms of biomass production, lipid accumulation, and fatty acid composition. The results demonstrated a clear inverse relationship between biomass formation and lipid accumulation. The highest lipid content (33.49%) was achieved under nitrogen-limited conditions combined with a high OMW dilution. After 168 h of fermentation, the calculated lipid yield was 0.51 g/L. Biomass and lipid productivities were calculated as 0.22 g/L/day and 0.073 g/L/day, respectively. ANOVA analysis revealed that nitrogen concentration was the dominant factor affecting lipid production (67.71%), followed by NaCl concentration (18.83%). In contrast, OMW dilution, sterilization, and carbon source type were not statistically significant (p > 0.05), indicating that lipid production can be effectively performed under non-sterile conditions with flexible substrate utilization. Fatty acid analysis revealed that the produced lipids were rich in oleic acid (C18:1n9c), reaching up to 57.97%, with unsaturated fatty acids generally accounting for the majority of the total fatty acid composition. Although the carbon source had a limited effect on lipid yield, it contributed to variations in fatty acid composition, suggesting the possibility of tailoring lipid quality through substrate selection. Full article

Phycobiliproteins (PBPs) are a family of pigment-proteins renowned for their exceptional light-harvesting, fluorescent, and antioxidant properties. Among cyanobacteria, Spirulina stands out as one of the richest natural sources of PBPs, particularly phycocyanin (PC) and allophycocyanin (APC), yet the large-scale production of analytical-grade PBPs remains hampered by an inherently complex downstream process that relies on multiple purification steps, compromising both yield and scalability. This work presents a streamlined strategy to obtain analytical-grade PC, combining ultrasound-assisted extraction (UAE) with an aqueous ionic liquid (IL) solution and a single hydrophobic interaction chromatography (HIC) step, integrated within a biorefinery framework. The proposed approach yielded analytical-grade PC with a recovery of up to 50.44% and enhanced APC purity up to 10.57-fold. Furthermore, the IL was successfully reused in both extraction and purification steps without compromising yield or purity. The environmental performance of the proposed process was assessed through a cradle-to-gate life cycle assessment (LCA), with system boundaries encompassing the following biorefinery stages: cultivation, harvesting and drying, PC extraction and purification, post-processing, and spent biomass valorization via anaerobic digestion. The LCA identified the main environmental hotspots and guided the proposal of targeted process improvements—particularly HIC salt substitution and increased IL recovery—which reduced environmental impacts by 65.9–89.8% across most categories. The proposed strategy was further benchmarked against two model scenarios for analytical-grade PC production, one conventional and one innovative, revealing its relative advantages and limitations. Overall, this work demonstrates a viable pathway for producing high-purity PC that balances process efficiency with environmental sustainability, supporting the development of greener microalgae-based bioprocesses. Full article

Plant-derived bioactive compounds, such as polyphenols and saponins, possess significant pharmacological value. However, conventional extraction methods often suffer from low efficiency, poor bioavailability, and environmental burdens. Aspergillus-based biotransformation has emerged as a superior platform for overcoming these limitations due to their robust secretomes, versatile metabolic networks, and the GRAS (Generally Recognized as Safe) status of specific industrially relevant species (e.g., A. oryzae and A. niger). Existing literature frequently focuses on isolated compounds or general fungal processes. To fill this gap, this review systematically links specific Aspergillus enzymatic systems to an “enzymatic hydrolysis–transformation–synthesis” closed-loop framework, which is essential for industrial-scale valorization. In this review, we summarize recent advances in the biotransformation of phytochemicals by A. niger, A. oryzae, and A. nidulans. These fungi utilize specialized enzymes—including β-glucosidases, cellulases, and glycosidases—to enable precise hydrolysis, deglycosylation, and detoxification under mild conditions. We highlight representative transformations that demonstrate markedly enhanced bioactivity and solubility. Key examples include the conversion of polydatin to resveratrol (>90% yield) and ginsenoside Rb1 to ginsenoside compound K (94.4% conversion rate). Although industrial applications span the food, pharmaceutical, and cosmetic sectors, significant challenges persist in solid-state fermentation (SSF) scale-up, strain stability, target compound over-degradation, and downstream purification. Genetic engineering, process optimization and hybrid bioprocessing are highlighted as promising strategies to overcome these limitations and realize sustainable, high-value production of natural bioactive metabolites. Full article

Mesenchymal stromal cells (MSCs) are central to regenerative medicine and advanced therapies. However, the absence of consensus on reporting kinetic parameters, such as population doubling level (PDL), population doubling time (PDT), and the reliance on passage number alone obscures biological age and manufacturing history, and limits correlation of potency with expansion dynamics. Here, we clarify the distinctions among passages, PDL, PDT, and replication rate; we synthesize evidence that identical passage numbers can conceal multifold differences in cumulative doublings, with downstream effects on transcriptomic stability, and immunomodulatory performance. We further highlight culture determinants, oxygen tension, seeding density, media formulation, surface/bioreactor systems, and early niche mimetic stimuli, that shape proliferative kinetics and cellular aging trajectories in WJ-MSCs. Critically, we propose extracellular vesicles (EVs) as sensitive functional readouts of bioprocess stress and expansion history: EV quantity can increase while functional bioactivity declines, and EV miRNA cargo captures cell state programs not evident from minimal identity markers. To address these gaps, we recommend a reporting framework that incorporates: (1) culture conditions, (2) passage number and PDL at harvest, and (3) functional consequences of expansion. Adopting kinetic metrics beyond passage number will harmonize data capture and enable pooled analyses, accelerating clinical translation while safeguarding patient outcomes. Full article

In Mexico, cheese whey (CW) is commonly treated as a dairy wastewater despite its high lactose and nutrient content. This study evaluated cheese whey (CW) and ultrafiltered cheese whey (UF-CW) as low-cost substrates for the cultivation of the probiotic strains Lactobacillus acidophilus and Lactococcus lactis. The proposed bioprocess simultaneously enables the production of probiotic biomass and lactic acid, a high-value platform chemical with broad applications in the food, pharmaceutical, and biopolymer industries. In the first experimental trials, in which CW and UF-CW were used solely as media, fermentations lasted 36 h at 30 and 37 °C, with initial pH levels of 5 and 7. CW demonstrated a greater capacity to support the growth of lactic acid bacteria. Thus, to increase the fermentative capability of UF-CW, it was supplemented with yeast extract (YE) or corn steep liquor (CSL), and CaCO₃ was added to stabilize pH, as low pH values inhibit growth and lactic acid production. The proposed strategy notably improved microbial growth in UF-CW, increasing Lc. lactis and L. acidophilus populations from 8.3 and 8.2 Log₁₀ CFU/mL to 9.3 Log₁₀ CFU/mL, respectively. The findings suggest that dairy wastewater can be effectively repurposed as a low-cost cultivation medium for these bacteria. ASPEN simulation analyses demonstrated that lactose conversion efficiency and final product concentration were key factors affecting process performance and economic feasibility. Among the evaluated scenarios, a 45% lactose-to-lactic acid conversion yielded the most economically favorable process performance compared with conversions of 10% and 25%. Future research should focus on enhancing fermentation yields and adopting more efficient downstream recovery techniques. Full article

Food waste is a readily digestible and fermentable feedstock for waste to energy bioprocesses. Approximately one third of food is wasted, thus making improvements in food waste valorization is essential for a circular economy. Laboratory results must be reproducible and as representative of scaled performance as possible to facilitate knowledge sharing between research groups. Food waste used in laboratory studies is often collected in situ or overly simplistic synthetic mixtures are used. Food waste collected in situ from any one local source at a single time point (e.g., grab samples from a cafeteria or restaurant) are not reproducible or nationally representative; additionally, overly simple synthetic mixtures are reproducible, but lack the complexity of real food waste and are not nationally representative. Thus, an adequately complex, reproducible, and nationally representative food waste recipe is needed to standardize the feedstocks used in laboratory scale food waste digestion and fermentation studies. In this work, we developed a food waste recipe made from widely and commercially available ingredients which is based on national-scale food wastage data in the United States. The nationally representative food waste mixture was 45.4% carbohydrates, 32.5% lipids, and 13.4% proteins. The biomethane potential was 495 ± 44 mL CH₄/g VS and the food waste mixture was suitable for use in low-pH bench-scale arrested anaerobic digesters. This design approach can be adapted for other regions and countries where food loss data are available. Full article

The replacement of synthetic dyes has gained increasing attention due to stricter regulatory policies and growing health concerns. Microbial carotenoids represent a promising alternative to artificial food colorants; however, their large-scale production is limited by the high cost of raw materials. In this context, the valorization of lignocellulosic biomass offers a strategy to develop low-cost substrates for microbial bioprocesses. Sotol bagasse (SB), an underutilized lignocellulosic residue generated during sotol production, was composed of 24% cellulose, 14% hemicellulose, and 42% lignin. A non-thermal plasma pretreatment, optimized through response surface methodology, achieved up to 29% of lignin removal. Subsequent enzymatic hydrolysis yielded a total sugar concentration of 28 g/L. The resulting hydrolysate supported the growth of Rhodotorula glutinis, yielding 4.4 g/L of biomass and 0.91 mg/L of carotenoids. To the best of our knowledge, this is the first report describing the use of non-thermal plasma as a pretreatment strategy for sotol bagasse, demonstrating its potential as a chemical-free approach for lignocellulosic valorization and sustainable microbial carotenoid production. Full article

Microplastic pollution has become a significant environmental concern due to its persistence and widespread impact across ecosystems. These plastic particles (1 μm to 5 mm), originating from larger plastic debris or industrial sources, accumulate in diverse habitats, affecting biodiversity and human health. Microplastics resist natural degradation, posing challenges to both ecological sustainability and waste management strategies. Although numerous studies have explored microbial degradation, most existing research focuses primarily on bacteria, leaving the role of filamentous fungi comparatively underexplored. This represents a significant research gap, because fungi secrete a variety of extracellular enzymes, including laccases, peroxidases, and esterases, which play crucial roles in the breakdown of synthetic polymers. These enzymes facilitate the depolymerization of microplastics by targeting polymer chains and increasing their susceptibility to further microbial degradation. However, the underlying enzymatic mechanisms and their effectiveness in microplastic remediation remain insufficiently characterized. Here, we critically review the potential of filamentous fungi for microplastic biodegradation, emphasizing their oxidative and hydrolytic enzyme systems, biosurfactant production, and mechanisms of adsorption and mineralization. The novelty of this review lies in consolidating the most recent mechanistic insights into fungal-driven depolymerization pathways, integrating them with advances in genetic engineering, bioprocess scale-up, and regulatory perspectives, areas rarely combined in previous reviews. We identify current limitations related to environmental applicability, enzyme accessibility, and the lack of standardized protocols, and propose strategies to overcome these challenges through enzyme immobilization, microbial consortia design, and synthetic biology approaches. By addressing these gaps, filamentous fungi may contribute to the development of sustainable strategies for plastic pollution mitigation and support circular economy approaches toward polymer biodegradation. Full article

Paclitaxel (Taxol), a taxane diterpenoid from Taxus species, is a clinically important microtubule-stabilizing anticancer agent widely used in chemotherapy. However, its supply remains limited by precursor scarcity and the molecule’s structural complexity. The biosynthetic pathway from geranylgeranyl diphosphate (GGPP) to paclitaxel is estimated to involve 19 to 23 enzymatic steps. Recent multi-omics approaches have substantially elucidated this pathway, yet key mechanistic questions persist, notably the formation of the oxetane ring. Complete heterologous biosynthesis is further hampered by poor cytochrome P450 (CYP) expression in non-native hosts and insufficient metabolic flux. This review synthesizes advances across four themes: (1) progressive elucidation of the biosynthetic pathway, with emphasis on the CYP-mediated oxygenation cascade and oxetane ring formation; (2) genomic and regulatory insights from Taxus genome assemblies, transcription factor networks, and spatial multi-omics; (3) metabolic engineering in microbial hosts, including Escherichia coli, Saccharomyces cerevisiae, and non-conventional chassis; and (4) plant-based heterologous production platforms. Critical bottlenecks are identified, including unresolved enzymatic steps, CYP functional expression, flux partitioning, and bioprocess scale-up. Strategies to overcome these challenges are discussed. Full article

Lignocellulosic biorefineries are limited by the high cost of cellulolytic enzymes. Consolidated bioprocessing (CBP), which integrates saccharification and fermentation in one step, offers a solution to this challenge. In this study, a cellulase-hyperproducing mutant of Talaromyces pinophilus, Y117, was generated from the parental strain TP117 via sequential ultraviolet irradiation and NTG (N-methyl-N′-nitro-N-nitrosoguanidine) mutagenesis. Enzymatic secretion and lignocellulose degradation capacities were evaluated, focusing on agricultural residues, particularly corncob. Y117’s performance was compared with TP117 and Trichoderma reesei Rut-C30 (TR30) under high-solids fermentation. Furthermore, the lactate dehydrogenase A (ldhA) gene from Rhizopus oryzae was heterologously expressed in Y117 to direct hydrolyzed sugars toward lactic acid (LA). Y117 exhibited significantly enhanced enzymatic secretion, achieving FPase activity of 8.9 IU/mL and a substrate utilization rate of 72.2% at 125 g/L corncob solids. Y117 outperformed TP117 and TR30 in cellulase, xylanase, and CMCase activities, as well as growth under high-solids fermentation conditions. In the LA fermentation process, Y117 produced 14.20 g/L LA, a notable improvement compared to TP117 (5.33 g/L) and TR30 (2.71 g/L). While LA productivity and yield currently remain below bacterial benchmarks, the unique CBP capability of Y117 provides a foundation for further metabolic engineering toward industrial viability. The engineered T. pinophilus Y117 demonstrates promising potential as a CBP platform for efficient straw-to-LA conversion, providing a sustainable approach for third-generation biobased materials production. Full article