Search Results (1,721)

Introduction: Restrictive diets are increasingly encountered in pediatric practice and may be adopted voluntarily or prescribed for medical conditions. Although they can support normal growth when appropriately planned, exclusion of nutritionally important foods may increase the risk of nutrient inadequacy. This narrative review examined nutritional deficiencies and laboratory monitoring in children following plant-based, food-allergy elimination, gluten-free, ketogenic, and protein-restricted diets for inherited metabolic disorders. Methods: Targeted searches of PubMed, Scopus, and Web of Science were conducted through 30 June 2026 using pediatric, diet-specific, nutritional-status, and biomarker terms. Because this was a narrative review, the literature was selected and synthesized qualitatively rather than through a formal systematic-screening process; no fixed study count, duplicate independent screening, or formal risk-of-bias assessment was performed. Professional guidelines and position papers were prioritized when discussing monitoring considerations, while pediatric studies were used to describe dietary intake, biochemical findings, clinically manifest deficiency, and growth outcomes. Results: Nutritional risks differed according to the foods or nutrients restricted. Vitamin B12 and iron were major concerns in plant-based diets, whereas cow’s milk and multiple-food elimination increased the risk of inadequate calcium, vitamin D, iodine, protein, and energy intake. Gluten-free diets were commonly associated with low fiber, iron, folate, and B-vitamin intake, particularly when refined, non-fortified products predominated. Ketogenic dietary therapy required attention to selenium, vitamin D, bone-related minerals, carnitine in selected patients, and linear growth. In phenylketonuria and related disorders, nutritional adequacy depended strongly on protein-substitute adherence and appropriate provision of essential amino acids and micronutrients. Across all dietary patterns, laboratory results required interpretation in relation to dietary intake, growth, supplementation, inflammation, medication, and the underlying condition. Across dietary patterns, inadequate intake, biochemical abnormalities, clinically manifest deficiency, and impaired growth were considered related but distinct outcomes. Conclusions: Nutritional monitoring should be individualized and based on the actual dietary restriction and clinical risk. The principal contribution of this review is a practical, risk-based framework that links the specific dietary restriction and adequacy of replacement foods with growth, symptoms, supplementation, and targeted laboratory biomarkers. Full article

This study investigated how defatted silkworm pupae meal (DSPM) modulates flesh quality in pearl gentian grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂). A total of 360 size-uniform fish were randomly assigned to four dietary treatments for 8 weeks: D0, the fishmeal (FM) based control diet; and D1, D2, and D3, in which DSPM substituted 25%, 50%, and 100% of dietary FM, respectively, with three replicates per treatment and 30 fish per replicate. Compared with D0, D1 and D2 improved final body weight, weight gain rate, specific growth rate, and feed conversion ratio, whereas D3 reduced survival and feed utilization. For flesh quality, D2 showed the most favorable phenotype, characterized by higher crude protein, collagen, flavor-associated amino acids, pH, texture attributes, and muscle fiber density, together with lower ether extract, cooking loss, freezing loss, and shear force. DSPM substitution also increased unsaturated and polyunsaturated fatty acid proportions and improved lipid health indices. Moderate substitution, especially D2, enhanced oxidative stability by increasing SOD and CAT activities and reducing MDA accumulation. Non-targeted metabolomics combined with qPCR analysis of selected flesh quality-related genes suggested that these improvements were associated with osmotic regulation, collagen remodeling, purine metabolism, membrane lipid homeostasis, nutrient sensing, myogenesis, and antioxidant defense. Complete FM substitution impaired muscle structure, water retention, and redox balance. Thus, 50% FM substitution with DSPM effectively optimized grouper flesh quality in this study. Full article

Amino acids are the ‘building blocks’ of protein, including both feathers and whole-body protein, and serve numerous functional roles, including energy provision. Amino acid requirements for broiler chickens are expressed as ideal amino acid ratios relative to digestible lysine. However, ideal amino acid profiles in diets for broiler chickens are likely to remain elusive targets. This review considers the factors contributing to this situation. Just one complicating factor is that amino acids may be deposited as protein in either feathers or whole-body protein. However, in the partitioning of amino acids, it appears that preference may be given to feathering, which requires clarification. A second complicating factor is the transition of amino acids across enterocytes of the small intestinal gut mucosa, and small intestinal uptake of amino acids may be rate-limiting for growth performance. Protein-bound amino acids may be absorbed as oligopeptides or monomeric amino acids, and non-bound amino acids do not require digestion prior to their intestinal uptake. The transition of amino acids across the gut mucosa is involved because amino acids may be diverted into anabolic and/or catabolic pathways and are thereby denied entry to the portal circulation. The metabolic fate of amino acids in the gut mucosa may be subject to manipulation by nutritional strategies, but our comprehension of the relevant metabolism within avian enterocytes is inadequate. The post-enteral availability of twenty proteinogenic amino acids is complex with important implications for the efficiency of utilisation. Importantly, acceptably accurate amino acid profiles will be advantageous for sustainable chicken-meat production into the future. Full article

Peptides are the most extensively studied bioactive compounds derived from food. They are analyzed using, e.g., in silico strategy. The BIOPEP-UWM database has become a standard tool in computer-aided peptide research. The aim of this study was to equip this database with a tool enabling the annotation and processing of peptide or protein sequences containing modified amino acid residues as well as other residues. The most recent section of the BIOPEP-UWM, i.e., the repository of amino acids and modifications, apart from 20 proteinogenic amino acids, annotates non-amino acid moieties or residues subjected to enzymatic or chemical modifications (phosphorylation, oxidation, hydroxylation, acylation, etc.). This part of BIOPEP-UWM provides the following information: Compound ID, name, symbol in a special code, InChIKey identifier, SMILES representation, number in the PubChem database (CID), formula, and IDs in other databases. The search options include ID in the repository, name, symbol in a biological code, InChIKey, PubChem Compound identifier (CID), and chemical formula. Peptide or protein sequences annotated using symbols from the repository are utilized by all applications available in the BIOPEP-UWM database. The database meets contemporary trends involving modifications of amino acid residues in the bioinformatic analysis of peptides and proteins. Full article

Background/Aim: Fibroblast growth factor receptor 4 (FGFR4) is a tyrosine kinase involved in cell growth, proliferation, and angiogenesis. While FGFR1–3 are well studied in cancer, FGFR4 remains relatively understudied, and the distribution of its mutations across cancers and patient populations is not well defined. Materials and Methods: A retrospective pan-cancer analysis was performed using the AACR Project GENIE v12 database via cBioPortal. Tumors with somatic FGFR4 mutations were included, excluding copy number alterations and structural variants. Mutations were grouped by hotspot (amino acid 401) and major protein domains. Comparative analyses assessed cancer type distribution, demographics, mutation burden, and co-occurring genomic alterations using chi-square testing with multiple comparison correction. Results: A total of 4565 tumor samples (4283 patients) were analyzed. FGFR4 alterations were observed across diverse malignancies, most commonly non-small cell lung cancer, colorectal cancer, and melanoma. Mutations clustered primarily in the tyrosine kinase and immunoglobulin I-set domains, with no significant variation in distribution across cancer types. Sex was not associated with the mutation group, while race and ethnicity showed significant differences. The FGFR4 hotspot 401 group demonstrated a higher mutation burden, driven by a subset of hypermutated tumors, and showed enrichment for co-occurring alterations in chromatin remodeling, DNA repair, tumor suppressor, and receptor tyrosine kinase genes; however, sensitivity analyses indicated this association was largely attributable to mutation burden rather than a mutation-specific effect. Domain-based mutation groups had lower mutation burdens and fewer co-alterations. Conclusions: FGFR4 alterations occur across a broad range of cancers with consistent domain-level patterns. The hotspot 401 mutation shows a higher mutation burden and co-alteration frequency driven largely by a subset of hypermutated tumors, rather than acting as an isolated driver. Full article

This study systematically evaluated substrate-dependent variations in yield, nutritional composition, mineral profiles, taste-active compounds, electronic tongue profile, and metabolome of A. bisporus cultivated on corn stover-based substrates (CM1, CM2, CM3) and wheat straw-based substrate (WM4). Corn stover-based substrates supported the cultivation of A. bisporus, yielding 20.56–25.63 kg/m², comparable to WM4 (24.23 kg/m²). Biological efficiency of the corn stover treatments ranged from 80.32% to 88.58%; CM1 and CM2 were comparable to WM4 (91.35%), whereas CM3 showed a significantly lower biological efficiency than WM4 (p < 0.05). Crude protein and mineral elements (Cu, Fe, Zn) were substantially higher in mushrooms from corn stover-based substrates, whereas crude polysaccharide content was greater in WM4. Taste profile analysis revealed that corn stover-based substrates elevated umami and sweet amino acids alongside 5′-GMP and 5′-UMP, leading to enhanced equivalent umami concentration (EUC) and umami perception by the electronic tongue, while WM4 supported higher 5′-AMP accumulation. Non-targeted metabolomics analysis (CM3 vs. WM4) identified 3997 metabolic features. KEGG pathway enrichment analysis revealed that these substrate-dependent metabolic alterations were primarily driven by pathways such as the biosynthesis of amino acids, nucleotide metabolism, and 2-oxocarboxylic acid metabolism, underlying the metabolic adaptation of A. bisporus. These findings provide new insights into the compositional characteristics and quality formation of A. bisporus cultivated on corn stover-based substrates. Full article

Dietary protein is essential for poultry performance, influencing egg production, growth, immunity, and physiological functions. However, the high cost and environmental impact of soybean meal has encouraged the development of reduced crude protein (CP) diets supplemented with crystalline amino acids (AAs), coupled with the reduced cost and improved availability of synthetic AA. This strategy enables precise AA balancing, improves nitrogen utilization, and reduces nitrogen excretion and ammonia emissions. Among these strategies, supplementation with arginine (Arg), an indispensable AA in chickens, is particularly important due to its critical roles in protein synthesis, reproductive function, and eggshell formation. In addition, functional Arg precursors, such as guanidinoacetic acid (GAA) and citrulline (Cit), can further enhance Arg availability while supporting energy metabolism and hormonal regulation. Despite these benefits, excessive protein reduction without adequate AA balance can impair laying performance, particularly in aged hens. Furthermore, nutrient digestibility remains a key limitation in reduced protein (RP) diets, as non-starch polysaccharides present in cereal-based feeds can reduce nutrient availability. The inclusion of exogenous enzymes, such as xylanase and β-glucanase, can improve digestibility, while phytase supplementation further enhances nutrient utilization by increasing phosphorus availability and mitigating the anti-nutritional effects of phytate; however, responses are often inconsistent. Another critical factor is maintaining an optimal energy-to-protein ratio, as imbalances may lead to increased fat deposition and reduced productive performance. While supplementation of key limiting AAs (lysine, methionine, and threonine) supports protein reduction, other AAs, such as Arg, isoleucine, and valine, may become limiting in RP diets. Hence, this review explores developments toward RP diets by highlighting three key strategies: enzyme supplementation to enhance nutrient digestibility, inclusion of functional Arg sources to improve performance and bone quality, and optimization of the energy–protein ratio in RP diets through precise AA formulation, with the overall aim to improve the sustainability of the poultry industry. Full article

Non-covalent forces are the primary drivers of biomolecular interactions. They also represent a key factor in the unexpected tendency for proteins, peptides, and even individual amino acids to self-assemble into precise supramolecular assemblies, often characterized by a β-rich, amyloid-like structure. Studies carried out in the last few decades have shown that peptides/proteins self-assembly not only has structural consequences but also generates spectroscopic properties whose origin remains debated. Here, we investigated the spectroscopic properties of four peptides, GAIIGL, NNQQ, SSTSAA, and GNNQQNG (a derivative of the frequently studied GNNQQNY peptide), devoid of aromatic residues, whose crystallographic characterization has been seminal in elucidating the basis of the aggregation process. The spectroscopic behavior of these peptides was analyzed in two different media and in the solid state, highlighting the conditions that favor UV–visible fluorescence emission. These investigations have also prompted the use of this fluorescence as a potential diagnostic tool in nanomedicine. Importantly, the identification of intrinsic fluorescence signatures in these amyloid-like assemblies may support the development of label-free optical approaches for the early detection and monitoring of aggregation-related pathological processes. For all peptides, the emitted fluorescence spans a rather wide range of wavelengths. Although centered in the blue region, a significant signal is also observed in the green region, independent of their physical state. The structural analysis of the solid used to collect the spectroscopic data reveals features related to the packings in the crystal state. This observation suggests that their three-dimensional crystal structures may serve as reliable models for studies aimed at correlating structural and spectroscopic features. Full article

This study investigated the effects of microwave puffing-induced soy protein structural modification on the dynamic changes in physicochemical properties and umami formation during soybean paste fermentation. The results indicated that optimal microwave puffing (400 W, 90 s) disrupts protein non-covalent bonds, depolymerizes protein aggregates, exposes the internal hydrophobic groups to enhance surface hydrophobicity, forms a loose porous structure, and creates favorable conditions for enzymatic hydrolysis during soybean paste fermentation. Conversely, excessive treatment (400 W, >90 s) induced protein re-aggregation and inhibited proteolysis, as confirmed by SEM. Furthermore, microwave puffing (400 W, 90 s) promoted Aspergillus oryzae growth and protease activity, and significantly improved physicochemical properties of soybean paste, including lower pH and higher contents of total acid (5.8%), amino acid nitrogen (11.8%), small peptides (13.3%), and reducing sugars (14.95%) (p < 0.05), plus a brighter, redder color. LC-MS/MS revealed microwave puffing (400 W, 90 s) reshaped the peptide profile of soybean paste, increasing the relative abundance of the umami amino acids (Glu, Asp) and sweet amino acid (Ala) and decreasing proportions of the bitter amino acids in the peptides. Sensory and electronic tongue analyses confirmed enhanced umami and weaker bitterness and saltiness. These findings demonstrate that microwave puffing (400 W, 90 s) effectively improves the quality and flavor characteristics of soybean paste, providing technical support for high-quality fermented soybean products. Full article

The narrow-clawed crayfish (Pontastacus leptodactylus), a non-native species accidentally introduced into China’s Irtysh River Basin, has formed a wild population with aquaculture potential, but its natural diet and protein utilization remain poorly understood. This study investigated its feeding ecology and digestive responses to protein sources to support ecological assessment and feed formulation. Intestinal contents and muscle samples from wild crayfish were analyzed using eDNA metabarcoding and fatty acid signature analysis. In vitro digestibility of 10 protein ingredients was evaluated with crude digestive enzyme extracts, and a 4-week trial compared an all-plant-protein diet (PPD) with an all-animal-protein diet (APD). eDNA indicated an omnivorous diet dominated by planktonic taxa, especially Rotifera, and fatty acid biomarkers suggested contributions from diatoms, dinoflagellates, phytoplankton, zooplankton, and benthic organisms. Soybean meal and soy protein concentrate showed high dry matter digestibility, whereas fishmeal and krill meal had high crude protein digestibility and amino acid release. Compared with PPD, APD increased feed intake, apparent nutrient digestibility, hemolymph nutritional indicators, villus height, and intestinal trypsin and lipase activities; however, intestinal integrity was preserved in both groups, and most intestinal antioxidant indices did not differ significantly. These findings indicate that animal proteins enhance nutrient utilization in P. leptodactylus, while selected plant proteins may serve as partial alternatives. Full article

Macrobrachium nipponense holds significant economic importance in freshwater aquaculture in China, where larger body weight and longer body length are directly associated with higher market demand and improved commercial value. Consequently, identifying genes associated with growth traits is a priority for enhancing economic returns. Previous studies have predicted that the cAMP-dependent protein kinase type I regulatory subunit-like (PKA-R1) may be involved in the growth regulation of M. nipponense. In this study, we functionally characterized the Mn-PKA-R1 gene to investigate its potential involvement in growth and molting regulation in M. nipponense through qPCR analysis and RNA interference (RNAi). The open reading frame of Mn-PKA-R1 spanned 3345 base pairs, encoding a protein of 1114 amino acids. The Mn-PKA-R1 amino acid sequence showed the highest identity with that of Macrobrachium rosenbergii, followed by Penaeus vannamei. Tissue distribution analysis revealed that Mn-PKA-R1 was ubiquitously expressed across all examined tissues, with the highest transcript level detected in the testis, suggesting a potential association with testis-related physiological functions. Functional validation via RNA interference showed that repeated dsPKA-R1 treatment was associated with reduced molting frequency and relative body weight compared with the non-targeting dsRNA control group. From day 14 to day 42, the relative body weight compared with day 0 in the non-targeting dsRNA control group was significantly higher than that in the dsPKA-R1-injected group. Additionally, the molting frequency in the non-targeting dsRNA control group was significantly higher than that in the dsPKA-R1-injected group at days 7, 14, 21, 28, and 35. These findings suggest that Mn-PKA-R1 may participate in the regulation of growth and molting in M. nipponense under the tested experimental conditions. This study provides preliminary functional evidence for the involvement of Mn-PKA-R1 in growth-related traits in M. nipponense. Full article

Background/Objectives: Ovarian cancer (OC) is a leading cause of cancer-related mortality in women, largely driven by late-stage diagnosis. Five-year survival is just 30% for advanced-stage (III-IV) disease but exceeds 90% for early-stage disease, underscoring the critical need for effective early detection tools. Current standard-of-care biomarkers show limited sensitivity for early-stage OC and lack specificity in symptomatic populations. Most biomarker studies in OC serum evaluate single molecular classes or compare OC to healthy controls, limiting understanding of coordinated biological alterations in circulating proteins, lipids, and metabolites in clinically relevant populations. Methods: We performed integrated multi-omics profiling of serum from a retrospective, case–control cohort of women presenting with vague abdominal symptoms (VAS), including early- and late-stage OC, borderline tumors, benign gynecologic conditions including adnexal masses, GI disorders, and healthy controls. Protein biomarkers were quantified by ELISA, lipidomic profiling was performed by untargeted LC-MS, and ganglioside and metabolomic profiling were performed by semi-targeted LC-MS with metabolite annotation performed against a curated reference library. Results: Consistent with known limitations for early-stage OC detection, CA125 and HE4 levels overlapped substantially with benign gynecologic conditions. Additional proteins also showed limited separation in their expression between early-stage OC and symptomatic controls. In contrast, OC showed unique lipid and metabolite profiles: phospholipids and glycerolipids were decreased, and sphingolipid composition was altered. Borderline and benign conditions exhibited lipid profiles that fall between healthy and OC groups, suggesting a continuum of metabolic changes rather than distinct states between OC and non-OC controls. Sphingolipid alterations included changes in ceramides and sphingomyelins, along with broader dysregulation of ganglioside profiles, including an elevated GD2;O2-to-GD1;O2 ratio. Metabolic profiling showed decreased amino acids and enriched cysteine metabolism in OC, consistent with altered redox balance, along with changes in fatty acids and acyl-carnitines, suggesting altered lipid metabolism and inflammatory mechanisms. Lower levels of glycolytic and TCA cycle intermediates in OC suggested altered mitochondrial metabolism and energetic reprogramming. Pairwise comparisons revealed a gradient of significance between groups, with differences between OC and healthy controls across lipid classes (LPC, PC, PE, TG, SM), gangliosides (GD1, GD2, GD2/GD1 ratio), and metabolites (amino acids, Cys/CySS, TCA cycle); borderlines occupied an intermediate space. Integration of these datasets revealed coordinated cross-omics relationships, identifying links between metabolite, lipid, and protein features. Together, these connections highlight structured, system-level alterations related to lipid remodeling, redox balance, immune signaling, and energy metabolism that no single modality would have revealed in isolation. Conclusions: This study presents an integrated analysis of the lipidome, gangliosome, metabolome, and protein biomarkers within a single clinically relevant symptomatic cohort enriched with multiple stages and subtypes of OC. This multi-omics framework demonstrates that molecular alterations in OC are biologically interconnected across molecular classes. While these findings are discovery-based and require independent validation prior to clinical application, they support the development of clinically deployable multi-omics biomarker strategies for early detection and potential pathways for therapeutic intervention. Full article

Grass carp (Ctenopharyngodon idella) is a major freshwater aquaculture species in China, but its growth is limited under intensive high-density farming. This study aimed to investigate the characteristics of plasma exosomes associated with distinct growth performance by isolating and characterizing exosomes from fast- and slow-growing grass carp after nine months of culture. Exosomes showed typical morphology and expressed characteristic markers (CD63, CD81, TSG101). Small RNA sequencing identified 3325 miRNAs, with 177 highly abundant miRNAs differentially expressed: immune-related miRNAs were upregulated, while development-inhibitory miRNAs were downregulated in fast-growing fish. Target gene enrichment highlighted pathways in neural and skeletal development and amino acid metabolism. Integrative analysis across tissues revealed 26 miRNAs with coordinated expression patterns between plasma exosomes and brain, liver, or muscle, validated by qPCR. DIA proteomics quantified 4203 proteins, identifying 843 differentially enriched proteins linked to immune response, energy metabolism, and endoplasmic reticulum stress. Notably, TYMP was upregulated in muscle and exosomes, while several proteins (e.g., GYG2, BHMT) showed coordinated downregulation across tissues and exosomes in large fish. These results provide comprehensive evidence of exosome-mediated cross-tissue communication in teleosts and suggest a potential role for plasma exosomal miRNAs and proteins as non-invasive biomarkers correlated with growth status in aquaculture. Full article

The combination of computational and experimental methods has become indispensable for optimization and rational enzyme design. Recently, the development of artificial intelligence (AI)-based tools has further streamlined enzyme engineering pipelines, enabling more accurate designs, while reducing the number of variants required for experimental validation. However, due to the intricate complexity of enzymatic systems, significant challenges must be addressed before we take the next step to fully optimize the use of these AI-guided enzyme design methodologies. These challenges include un-curated datasets, the need to consider both the static and dynamic structure of enzymes, and the requirement for effective interdisciplinary collaborations to ensure the integration of computational and experimental approaches. Here, we present recent advances in AI-based computational enzyme design, discussing the main challenges in the field and how a combination with classical physics-based methods could help overcome them. We further explore novel trends that could completely modulate the future of protein design and provide our outlook on the key concepts and future opportunities that will shape the next steps of enzyme design. Full article

Porcine epidemic diarrhea virus (PEDV) continues to undergo genetic evolution and remains a major etiological agent of enteric disease in swine, causing significant economic losses worldwide. This study investigated the molecular epidemiology and genetic characteristics of PEDV circulating in Chongqing, China, between 2022 and 2024. A total of 296 diarrheic piglet samples collected from nine regions were screened using RT-qPCR, of which 48.31% (143/296) tested positive for PEDV. A subset of positive samples was subjected to S gene amplification and sequencing, yielding 15 complete sequences. Phylogenetic analysis revealed that all sequenced strains clustered within the G2c lineage and showed high nucleotide similarity (93.37–94.09%) to the classical CV777 strain. Recombination analysis indicated potential recombination events among field strains involving S-INDEL and G2b-like parental lineages, although these findings are based on a limited number of sequences. Sequence analysis identified multiple amino acid substitutions within the COE antigenic region, while other neutralizing epitopes (SS2, SS6, and 2C10) remained largely conserved. In addition, variation in predicted N-glycosylation sites was observed among some strains. Structural modelling suggested that these changes may influence spike protein conformation and antigenic properties; however, these interpretations are based on in silico analysis and require experimental validation. Overall, the findings indicate ongoing genetic evolution of PEDV in Chongqing and suggest circulation of G2c-associated variants in diarrheic piglets. However, given the limited and non-random nature of sequencing, these results may not fully represent the broader viral population. Continued large-scale molecular surveillance and functional studies are needed to better understand PEDV evolution and to support the development of improved control strategies and vaccines. Full article