Search Results (339)

The demand for eco-friendly nanomaterial synthesis has increased interest in biological approaches. Yeast-mediated biosynthesis of gold nanoparticles (AuNPs) offers a sustainable alternative with potential biotechnological applications. This study developed a rapid screening method to identify oleaginous yeast strains able to synthesize AuNPs. A collection of 114 oleaginous yeasts from the LIBBA laboratory was screened. UV–Vis spectroscopy at 530–560 nm was used to assess nanoparticle formation, identifying 20 strains that effectively synthesize AuNP. Electron microscopy confirmed the presence of intracellular and extracellular nanoparticles, with variations in size and morphology. This screening and optimization approach effectively identified promising yeast candidates and refined biosynthesis conditions, providing a foundation for industrial-scale nanoparticle production. Full article

The environmental burden of conventional plastics has sparked interest in sustainable alternatives such as polyhydroxyalkanoates (PHAs). However, despite ample research in bioprocess development and the use of inexpensive waste streams, production costs remain a barrier to widespread commercialization. Complementary to this, genetic engineering offers another avenue for improved productivity. Cupriavidus necator stands out as a model host for PHA production due to its substrate flexibility, high intracellular polymer accumulation, and tractability to genetic modification. This review delves into metabolic engineering strategies that have been developed to enhance the production of poly(3-hydroxybutyrate) (PHB) and related copolymers in C. necator. Strategies include the optimization of central carbon flux, redox and cofactor balancing, adaptation to oxygen-limiting conditions, and fine-tuning of granule-associated protein expression and the regulatory network. This is followed by outlining engineered pathways improving the synthesis of PHB copolymers, PHBV, PHBHHx, and other emerging variants, emphasizing genetic modifications enabling biosynthesis based on unrelated single-carbon sources. Among these, enzyme engineering strategies and the establishment of novel artificial pathways are widely discussed. In particular, this review offers a comprehensive overview of promising engineering strategies, serving as a resource for future strain development and positioning C. necator as a valuable microbial chassis for biopolymer production at an industrial scale. Full article

White-Nose Syndrome (WNS) has devastated insectivorous bat populations, particularly in North America, leading to severe ecological and economic consequences. Despite extensive research, many aspects of the evolutionary history, mitochondrial genome organization, and metabolic adaptations of its etiological agent, Pseudogymnoascus destructans, remain unexplored. Here, we present a multi-scale genomic analysis integrating pangenome reconstruction, phylogenetic inference, Bayesian divergence dating, comparative mitochondrial genomics, and refined functional annotation. We show that P. destructans exhibits extensive mitochondrial genome rearrangements absent in its nonpathogenic relatives from the Leotiomycetes class, suggesting a potential link between mitochondrial evolution and pathogenic adaptation. Our divergence dating analysis reveals that P. destructans separated from its Antarctic relatives approximately 141 million years ago, before adapting to bat hibernacula in the Northern Hemisphere. Additionally, our refined functional annotation significantly expands the known functional landscape of P. destructans, revealing an extensive repertoire of previously uncharacterized proteins involved in carbohydrate metabolism and secondary metabolite biosynthesis—key processes that likely contribute to its pathogenic success. By providing new insights into the genomic basis of P. destructans adaptation and pathogenicity, our study refines the evolutionary framework of this fungal pathogen and creates the foundation for future research on WNS mitigation strategies. Full article

Background: Exposure to per- and polyfluoroalkyl substances (PFAS, including 7H-Perfluoro-4-methyl-3,6-dioxaoctanesulfonic acid (PFESA-BP2), perfluorooctanoic acid (PFOA), and hexafluoropropylene oxide (GenX), has been associated with liver dysfunction. While previous research has characterized PFAS-induced hepatic lipid alterations, their downstream effects on energy metabolism remain unclear. This study investigates metabolic alterations in the liver following PFAS exposure to identify mechanisms leading to hepatoxicity. Methods: We analyzed RNA sequencing datasets of mouse liver tissues exposed to PFAS to identify metabolic pathways influenced by the chemical toxicant. We integrated the transcriptome data with a mouse genome-scale metabolic model to perform in silico flux analysis and investigated reactions and genes associated with lipid and energy metabolism. Results: PFESA-BP2 exposure caused dose- and sex-dependent changes, including upregulation of fatty acid metabolism, β-oxidation, and cholesterol biosynthesis. On the contrary, triglycerides, sphingolipids, and glycerophospholipids metabolism were suppressed. Simulations from the integrated genome-scale metabolic models confirmed increased flux for mevalonate and lanosterol metabolism, supporting potential cholesterol accumulation. GenX and PFOA triggered strong PPARα-dependent responses, especially in β-oxidation and lipolysis, which were attenuated in PPARα^−/− mice. Mitochondrial fatty acid transport and acylcarnitine turnover were also disrupted, suggesting impaired mitochondrial dysfunction. Additional PFAS effects included perturbations in the tricarboxylic acid (TCA) cycle, oxidative phosphorylation, and blood–brain barrier (BBB) function, pointing to broader systemic toxicity. Conclusions: Our findings highlight key metabolic signatures and suggest PFAS-mediated disruption of hepatic and possibly neurological functions. This study underscores the utility of genome-scale metabolic modeling as a powerful tool to interpret transcriptomic data and predict systemic metabolic outcomes of toxicant exposure. Full article

Monascus purpureus is a filamentous fungus renowned for producing bioactive secondary metabolites, including lovastatin and azaphilone pigments. Lovastatin is valued for its cholesterol-lowering properties and cardiovascular benefits, while Monascus pigments exhibit anti-cancer, anti-inflammatory, and antimicrobial activities, underscoring their pharmaceutical and biotechnological relevance. This study evaluated the impact of carbohydrate-derived elicitors—mannan oligosaccharides, oligoguluronate, and oligomannuronate—on the enhancement of pigment and lovastatin production in M. purpureus C322 under submerged fermentation. Elicitors were added at 48 h in shake flasks and 24 h in 2.5 L stirred-tank fermenters. All treatments increased the production of yellow, orange, and red pigments and lovastatin compared to the control, with higher titres upon scale-up. OG led to the highest orange pigment yield (1.2 AU/g CDW in flasks; 1.67 AU/g CDW in fermenters), representing 2.3- and 3.0-fold increases. OM yielded the highest yellow and red pigments (1.24 and 1.35 AU/g CDW in flasks; 1.58 and 1.80 AU/g CDW in fermenters) and the highest lovastatin levels (10.46 and 12.6 mg/g CDW), corresponding to 2.03–3.03-fold improvements. These results highlight the potential of carbohydrate elicitors to stimulate metabolite biosynthesis and facilitate scalable optimisation of fungal fermentation. Full article

Tissue engineering enables autologous reconstruction of human tissues, addressing limitations in tissue availability and immune compatibility. Several tissue engineering techniques, such as self-assembly, rely on or benefit from extracellular matrix (ECM) secretion by fibroblasts to produce biomimetic scaffolds. Models have been developed for use in humans, such as skin and corneas. Ascorbic acid (vitamin C, AA) is essential for collagen biosynthesis. However, AA is chemically unstable in culture, with a half-life of 24 h, requiring freshly prepared AA with each change of medium. This study aims to demonstrate the functional equivalence of 2-phospho-L-ascorbate (2PAA), a stable form of AA, for tissue reconstruction. Dermal, vaginal, and bladder stroma were reconstructed by self-assembly using tissue-specific protocols. The tissues were cultured in a medium supplemented with either freshly prepared or frozen AA, or with 2PAA. Biochemical analyses were performed on the tissues to evaluate cell density and tissue composition, including collagen secretion and deposition. Histology and quantitative polarized light microscopy were used to evaluate tissue architecture, and mechanical evaluation was performed both by tensiometry and atomic force microscopy (AFM) to evaluate its macroscopic and cell-scale mechanical properties. The tissues produced by the three ascorbate conditions had similar collagen deposition, architecture, and mechanical properties in each organ-specific stroma. Mechanical characterization revealed tissue-specific differences, with tensile modulus values ranging from 1–5 MPa and AFM-derived apparent stiffness in the 1–2 kPa range, reflecting the nonlinear and scale-dependent behavior of the engineered stroma. The results demonstrate the possibility of substituting AA with 2PAA for tissue engineering. This protocol could significantly reduce the costs associated with tissue production by reducing preparation time and use of materials. This is a crucial factor for any scale-up activity. Full article

Streptococcus agalactiae (SA) is a severe prevalent pathogen, resulting in high morbidity and mortality in the global tilapia industry. With increasing bacterial resistance to antibiotics, alternative strategies are urgently needed. This study aims to investigate the antibacterial activity and the underlying mechanisms of the natural product xanthohumol (XN) against SA infection in tilapia (Oreochromis niloticus). The results showed that XN could significantly reduce the bacterial loads of SA in different tissues (liver, spleen and brain) after treatment with different tested concentrations of XN (12.5, 25.0 and 50.0 mg/kg). Moreover, XN could improve the survival rate of SA-infected tilapia. 16S rRNA gene sequencing demonstrated that the alpha-diversity index (Chao1 and Shannon_e) was significantly increased in the XN-treated group (MX group) compared to the SA-infected group (CG group) (p < 0.05), and the Simpson diversity index significantly decreased. The Bray–Curtis similarity analysis of non-metric multidimensional scaling (NMDS) and principal coordinate analysis (PCA) showed that there were significant differences in microbial composition among groups. At the phylum level, the relative abundance of the phyla Actinobacteria, Proteobacteria and Bacteroidetes decreased in the MX group compared to the CG group, while the relative abundance of the phyla Fusobacteria, Firmicutes and Verrucomicrobia increased. Differences were also observed at the genus level; the relative abundance of Mycobacterium decreased in the MX group, but the abundance of Cetobacterium and Clostridium_sensu_stricto_1 increased. Metabolomics analysis revealed that XN changed the metabolic profile of the liver and significantly enriched aspartate metabolism, glycine and serine metabolism, phosphatidylcholine biosynthesis, arginine and proline metabolism, glutamate metabolism, urea cycle, purine metabolism, methionine metabolism, betaine metabolism, and carnitine synthesis. Correlation analysis indicated an association between the intestinal microbiota and metabolites. In conclusion, XN may be a potential drug for the prevention and treatment of SA infection in tilapia, and its mechanism of action may be related to the regulation of the intestinal microbiota and liver metabolism. Full article

Cordycepin, a bioactive adenosine analog, holds promise in pharmaceutical and health product development. However, large-scale production remains constrained by the limitations of natural producers, Cordyceps spp. Herein, we report the reconstruction of the first genome-scale metabolic model (GSMM) for a cordycepin-producing strain of recombinant Aspergillus oryzae. The model, iNR1684, incorporated 1684 genes and 1947 reactions with 93% gene-protein-reaction coverage, which was validated by the experimental biomass composition and growth rate. In silico analyses identified key gene amplification targets in the pentose phosphate and one-carbon metabolism pathways, indicating that folate metabolism is crucial for enhancing cordycepin production. Nutrient optimization simulations revealed that chitosan, D-glucosamine, and L-aspartate preferentially supported cordycepin biosynthesis. Additionally, a carbon-to-nitrogen ratio of 11.6:1 was identified and experimentally validated to maximize production, higher than that reported for Cordyceps militaris. These findings correspond to a faster growth rate, enhanced carbon assimilation, and broader substrate utilization by A. oryzae. This study demonstrates the significant role of GSMM in uncovering rational engineering strategies and provides a quantitative framework for precision fermentation, offering scalable and sustainable solutions for industrial cordycepin production. Full article

The mismatch between the rapid expansion of breeding scale and outdated techniques has hindered the development of the sea cucumber (A. japonicus) industry. Our previous work revealed that ecological seedling breeding can produce red-colored A. japonicus, a phenotype not observed in traditional artificial breeding, where individuals are typically green. To investigate the molecular and genetic basis of this novel red coloration, we compared the growth conditions of red sea cucumbers and green sea cucumbers, as well as the differences in the pigment composition, gene expression and metabolites of their body walls. Red individuals showed higher body length and weight, and elevated levels of astaxanthin, lutein, canthaxanthin, and β-carotene in the body wall. Transcriptomic and metabolomic analyses identified differentially expressed genes and metabolites associated with pigmentation. In particular, FMO2 and WDR18, involved in the cytochrome P450 drug metabolism pathway, were significantly upregulated in red individuals and are known to play roles in pigment biosynthesis and light signal perception. Key metabolites such as astaxanthin and fucoxanthin were implicated in body color formation. Moreover, genes in the arachidonic acid metabolism pathway were highly expressed, suggesting that dietary factors may contribute to pigment synthesis and accumulation. These findings provide novel insights into the mechanisms underlying body color variation in A. japonicus and offer potential for improved breeding strategies. Full article

Phytoremediation is a green economic method to address soil cadmium (Cd) pollution, and Solanum americanum is considered a potential phytoremediation candidate. However, the underlying Cd response mechanisms of S. americanum remain unclear. In the current study, a hydroponic experiment with 160 μmol/L Cd stress was conducted, physiological and molecular indices were measured to explore the response of S. americanum leaves to Cd stress at different time points (0, 3, and 7 days). Our findings revealed that Cd stress inhibited plant growth. Moreover, Cd stress significantly increased Cd accumulation, as well as Chla content, Chla/b, activities of SOD and POD, and elevated MDA content in the leaves. Furthermore, transcriptomics, proteomics, and metabolomics analyses revealed 17,413 differentially expressed genes (DEGs), 1421 differentially expressed proteins (DEPs), and 229 differentially expressed metabolites (DEMs). Meanwhile, integrative analyses of multi-omics data revealed key proteins involved in response to Cd stress, including POD, PAL, F5H, COMT, and CAD for phenylpropanoid biosynthesis, as well as GAPA, FBP, and FBA for photosynthesis pathways. Additionally, conjoint analyses highlighted that upregulated phenylpropanoid metabolism and photosynthesis alleviated Cd toxicity, playing vital roles in enhancing Cd tolerance in leaves. A conceptual molecular regulatory network of leaves in the response to Cd toxicity was proposed. This comprehensive study will provide detailed molecular-scale insights into the Cd response mechanisms in S. americanum. Full article

The sustainable and economically viable production of microalgae biomass for biofuels and high-value bioproducts is highly dependent on precise, multi-parametric monitoring of cultivation systems. This review provides a comprehensive overview of current approaches and technological advances in multi-sensor systems applied to photobioreactors, including flow cytometry, IR spectroscopy, RGB sensors, in situ microscopy, and software-based sensors. The integration of artificial intelligence (AI), the Internet of Things (IoT) and metaheuristic algorithms into monitoring systems is also discussed as a promising way to optimise key ecological, physicochemical, and biological parameters in real time. The report highlights critical factors that influence biomass growth and product yield, such as nutrient concentrations, light intensity, CO₂ levels, pH and temperature. In addition, current technological limitations are highlighted, and future strategies for improving monitoring accuracy, automating cultivation, and improving the biosynthesis of metabolites are outlined. Through a synthesis of the literature and technological trends, this work contributes to the development of smart photobioreactor systems and provides actionable insights to improve large-scale, highly efficient microalgae cultivation in energy and environmental biotechnology. Full article

This study investigated the potential of Yarrowia lipolytica, an oleaginous yeast, for producing lipid-rich biomass and its application in food technology. According to EFSA guidelines, lipid-rich biomass is recognized as a novel food with potential nutritional and technological value. However, cost-effective and scalable production of such biomass remains a challenge. The yeast was cultured in a nitrogen-limited medium using a cost-containment strategy based on the use of waste carbon sources, such as post-frying oil and untreated tap water. The composed batch culture approach studied in the experiments presented an example that reduces the cost of yeast biomass biosynthesis. This research aimed to characterize the biomass to assess its nutritional quality and suitability for food applications. Cultures were conducted in a laboratory bioreactor with a working volume of 4 litres. Key kinetic parameters were determined, including biomass yield (X), maximum lipid concentration (Lmax), lipid yield, protein yield relative to substrate and the specific rate of lipid synthesis or protein content and other cellular components. The biomass of Y. lipolytica demonstrated a high lipid content (39.43–50.53%), with significant levels of protein (24.16–27.03%) and unsaturated fatty acids, including oleic acid (62.73–66.44%) and linoleic acid (19.40–21.40%). Lipid-rich biomass produced in cultures with shorter times (20 h), which ended in the logarithmic growth phase, exhibited lower oxidative stability than longer cultures (65 h), which ended in the stationary growth phase. The results of this study highlighted that waste carbon sources and untreated tap water did not significantly impact the biomass yield or the nutritional profile, but did affect the stability of the produced oil. The biomass of Y. lipolytica, containing over 20% lipids, could serve as a promising raw material for food technology, providing a sustainable alternative to traditional vegetable oils. This work makes an important contribution to the development of alternative lipid sources by integrating waste processing in bioreactor-scale culture and kinetic modelling. Full article

Saccharina japonica (S. japonica) is a large-scale intertidal aquatic plant that exhibits characteristics such as rhizoid, holdfast, and blade differentiation. It demonstrates remarkable environmental adaptability. However, compared with higher plants, details about its phytohormone content, distribution, synthesis, and accumulation remain poorly understood. In this study, the phytohormone contents distribution and expression patterns of synthetic genes in different parts of S. japonica, including the rhizoid, petiole, basis, middle, and tip, were analyzed in detail by combining targeted metabolomics and transcriptomics analyses. A total of 20 phytohormones were detected in S. japonica, including auxin, abscisic acid (ABA), cytokinin (CTK), ethylene (ETH), gibberellin (GA), jasmonate acid (JA), and salicylic acid (SA), with significant site-differentiated accumulation. ABA and JA were significantly enriched in the tips (28.01 ng·g⁻¹ FW and 170.67 ng·g⁻¹ FW, respectively), whereas SA accumulated specifically only in the rhizoid. We also identified 12 phytohormones, such as gibberellin A1, methyl jasmonate, and trans-zeatin for the first time in S. japonica. Transcriptomic profiling revealed the tissue-specific expression of phytohormone biosynthesis genes, such as CYP735A (CTK synthesis), in the rhizoids and LOX/NCED (JA/ABA synthesis) in the tips. Key pathways, such as carotenoid biosynthesis and cysteine methionine metabolism, were found to be differentially enriched across tissues, aligning with hormone accumulation patterns. Additionally, an enrichment analysis of differentially expressed genes between various parts indicated that different parts of S. japonica performed distinct functions even though it does not have organ differentiation. This study is the first to uncover the distribution characteristics of phytohormones and their synthetic differences in different parts of S. japonica and elucidates how S. japonica achieves functional specialization through non-specific phytohormone regulation despite lacking organ differentiation, which provides an important theoretical basis for research on the developmental biology of macroalgae and their mechanisms of response to adversity. Full article

Cytochromes P450 (CYPs) form one of the largest enzyme superfamilies, with similar structural folds yet biological functions varying from synthesis of physiologically essential compounds to metabolism of myriad xenobiotics. Sterol 14α-demethylases (CYP51s) represent a very special P450 family, regarded as a possible evolutionary progenitor for all currently existing P450s. In metazoans CYP51 is critical for the biosynthesis of sterols including cholesterol. Here we determined the crystal structures of ligand-free CYP51s from the abyssal fish Coryphaenoides armatus and human-. Comparative sequence–structure–function analysis revealed specific structural elements that imply elevated conformational flexibility, uncovering a molecular basis for faster catalytic rates, lower substrate selectivity, and intrinsic resistance to inhibition. In addition, the C. armatus structure displayed a large-scale repositioning of structural segments that, in vivo, are immersed in the endoplasmic reticulum membrane and border the substrate entrance (the FG arm, >20 Å, and the β4 hairpin, >15 Å). The structural distinction of C. armatus CYP51, which is the first structurally characterized deep sea P450, suggests stronger involvement of the membrane environment in regulation of the enzyme function. We interpret this as a co-adaptation of the membrane protein structure with membrane lipid composition during evolutionary incursion to life in the deep sea. Full article

Pyrus bretschneideri ‘Xinli No.7’, a progeny of Pyrus sinkiangensis ‘Korla Fragrant Pear’, is an early-maturing, high-quality pear (Pyrus spp.) cultivar. As a dominant variety in China’s pear-producing regions, it holds significant agricultural importance. Investigating its male sterility (MS) mechanisms is critical for hybrid breeding and large-scale cultivation. Integrated cytological, physiological, and transcriptomic analyses were conducted to compare dynamic differences between male sterility (MS, ‘Xinli No.7’) and male-fertile (MF, ‘Korla Fragrant Pear’) plants during anther development. Cytological observations revealed that, compared with ‘Korla Fragrant Pear’, the tapetum of ‘Xinli No.7’ exhibited delayed degradation and abnormal thickening during the uninucleate microspore stage. This pathological alteration compressed the microspores, ultimately leading to their abortion. Physiological assays demonstrated excessive reactive oxygen species (ROS) accumulation, lower proline content, higher malondialdehyde (MDA) levels, and reduced activities of antioxidant enzymes (peroxidase and catalase) in MS plants. Comparative transcriptomics identified 283 co-expressed differentially expressed genes (DEGs). Functional enrichment linked these DEGs to ROS-scavenging pathways: galactose metabolism, ascorbate and aldarate metabolism, arginine and proline metabolism, fatty acid degradation, pyruvate metabolism, and flavonoid biosynthesis. qRT-PCR validated the expression patterns of key DEGs in these pathways. A core transcriptome-mediated MS network was proposed, implicating accelerated ROS generation and dysregulated tapetal programmed cell death. These findings provide theoretical insights into the molecular mechanisms of male sterility in ‘Xinli No.7’, supporting future genetic and breeding applications. Full article