Search Results (2,004)

The use of eco-organic ingredients as a source of protein in aquaculture diets needs important attention due to the growing demand for organic seafood products. The present study evaluated the effects of fish meal substitution by different organic ingredients on the growth, body composition, retention efficiency, enzyme activity, and nutrient digestibility of white shrimp Penaeus vannamei. The four dietary formulations tested were formulated with organic ingredients and the fish meal was replaced by the following organic protein meals: Iberian pig viscera meal (PIG), trout by-product meal (TRO), insect meal (FLY), and organic vegetable meal (WHT), in addition to a control diet (CON) that included 15% fish meal. A growth trial was carried out for 83 days, raising 1 g shrimp to commercial size (20 g). Shrimp were stocked at 167 shrimp/m³ (15 individuals per 90 L tank). The results showed that the growth obtained by shrimp fed with TRO (19.27 g) and PIG (19.35 g) were similar in weight gain to the control diet (20.76 g), while FLY (16.04 g) and WHT (16.73 g) meals resulted in a significant lower final weight. The FLY diet showed significantly lower protein digestibility (68.89%) compared to the CON, PIG, TRO, and WHT diets, and significantly higher trypsin activity (0.17 mU/g) compared to shrimp fed with the PIG, TRO, and WHT diets. Shrimp fed with WHT have a significantly lower body weight percentage of protein (19.69%) than shrimp fed with the WHT and TRO diets, and some significant differences in dietary aminoacidic levels affecting amino acid body composition. These results indicate that Iberian pig viscera and trout by-product meal can successfully replace fish meal in Pacific white shrimp aquaculture. Full article

TasA gene, encoding a functional amyloid protein critical for biofilm formation and antimicrobial activity, was cloned from the endophytic strain Bacillus amyloliquefaciens BS-3, isolated from rubber tree roots. This study identified the shortest functional TasA variant (483 bp, 160 aa) reported to date, featuring unique amino acid substitutions in conserved domains. Bioinformatics analysis predicted a signal peptide (1–27 aa) and transmembrane domain (7–29 aa), which were truncated to optimize heterologous expression. Two prokaryotic vectors (pET28a and pCZN1) were constructed, with pCZN1-TasA expressed solubly in Escherichia coli Arctic Express at 15 °C, while pET28a-TasA formed inclusion bodies at 37 °C. Purified recombinant TasA exhibited potent antifungal activity, achieving 98.6% ± 1.09 inhibition against Colletotrichum acutatum, 64.77% ± 1.34 against Alternaria heveae. Notably, TasA completely suppressed spore germination in C. acutatum and Oidium heveae Steinmannat 60 μg/mL. Structural analysis via AlphaFold3 revealed that truncation enhanced protein stability. These findings highlight BS-3-derived TasA as a promising biocontrol agent, providing molecular insights for developing protein-based biopesticides against rubber tree pathogens. Full article

Background/Objectives: The clinical potential of antimicrobial peptides (AMPs) against dual threats like antimicrobial resistance (AMR) and cancer is often limited by their high host cell toxicity. Here, we focused on brevinin-2OS (B2OS), a novel peptide from the skin of Odorrana schmackeri with potent haemolytic activity. The objective was to study the structure–activity relationship and optimise the safety via targeted modifications. Methods: A dual-modification strategy involving C-terminal truncation and subsequent N-terminal D-amino acid substitution was employed. The bioactivities and safety profiles of the resulting analogues were evaluated using antimicrobial, haemolysis, and cytotoxicity assays. Result: Removal of the rana box in B2OS(1-22)-NH₂ substantially reduced haemolysis while maintaining bioactivities. Remarkably, the D-leucine substitution in [D-Leu²]B2OS(1-22)-NH₂ displayed a superior HC₅₀ value of 118.1 µM, representing a more than ten-fold improvement compared to its parent peptide (HC₅₀ of 10.44 µM). This optimised analogue also demonstrated faster bactericidal kinetics and enhanced membrane permeabilisation, leading to a greater than 22-fold improvement in its therapeutic index against Gram-positive bacteria. Conclusions: The C-terminal rana box is a primary determinant of toxicity rather than a requirement for activity in the B2OS scaffold. The engineered peptide [D-Leu²]B2OS(1-22)-NH₂ emerges as a promising lead compound, and this dual-modification strategy provides a powerful design principle for developing safer, more effective peptide-based therapeutics. Full article

Ribulose bisphosphate carboxylase (RuBisCO) is the primary regulator of carbon fixation in the plant kingdom. Although the large subunit (RBCL) is the site of catalysis, RuBisCO efficiency is also influenced by the sequence divergence of the small subunit (RBCS). This project compared the RBCS gene family in C3 and C4 grasses to identify genetic targets for improved crop photosynthesis. Triticeae/Aveneae phylogeny groups exhibited a syntenic tandem duplication array averaging 326.1 Kbp on ancestral chromosomes 2 and 3, with additional copies on other chromosomes. Promoter analysis revealed a paired I-box element promoter arrangement in chromosome 5 RBCS of H. vulgare, S. cereale, and A. tauschii. The I-box pair was associated with significantly enhanced expression, suggesting functional adaptation of specific RBCS gene copies in Triticaeae. H. vulgare-derived pan-transcriptome data showed that RBCS expression was 50.32% and 28.44% higher in winter-type accessions compared to spring types for coleoptile (p < 0.05) and shoot, respectively (p < 0.01). Molecular dynamics simulations of a mutant H. vulgare Rubisco carrying a C4-like amino acid substitution (G59C) in RBCS significantly enhanced the stability of the Rubisco complex. Given the known structural efficiency of C4 Rubisco complexes, G59C could serve as an engineering target for enhanced RBCS in economically crucial crop species which, in comparison, possess less efficient Rubisco complexes. Full article

Açaí (Euterpe oleracea) seeds account for up to 95% of the fruit’s weight and are commonly discarded during pulp processing. Roasted açaí seed extract (RASE) has recently emerged as a caffeine-free coffee substitute, although its composition and functionality remain underexplored. This study characterized commercial açaí seed powder and evaluated the effect of temperature on the recovery of total phenolic content (TPC) in the aqueous extract using a Central Composite Rotatable Design (CCRD). An intermediate extraction condition (6.0 ± 0.5 g 100 mL⁻¹ at 100 °C) was selected, resulting in 21.78 mg GAE/g TPC, 36.23 mg QE/g total flavonoids, and notable antioxidant capacity (FRAP: 183.33 µmol TE/g; DPPH: 23.06 mg TE/g; ABTS: 51.63 mg TE/g; ORAC: 31.46 µmol TE/g). Proton Nuclear Magnetic Resonance (¹H NMR) analysis suggested the presence of amino acids, carbohydrates, and organic acids. During in vitro digestion, TPC decreased from 54.31 to 17.48 mg GAE 100 mL⁻¹ when RASE was combined with goat milk. However, higher bioaccessibility was observed with skimmed (33%) and semi-skimmed (35%) cow milk. These findings highlight RASE as a phenolic-rich, antioxidant beverage with functional stability when prepared with boiling water. This is the first study to report the phytochemical profile of RASE and its interactions with different milk types, supporting its potential as a coffee alternative. Full article

Background and objectives: Adducins are cytoskeletal proteins essential for membrane stability, actin–spectrin network organization, and cell signaling. Mutations in the genes ADD1, ADD2, and ADD3 have been linked to hypertension, neurodevelopmental disorders, and cancer. However, no comprehensive in silico saturation mutagenesis study has systematically evaluated the pathogenic potential and structural consequences of all possible missense mutations in adducins. This study aimed to identify high-risk variants and their potential impact on protein stability and function. Methods: We performed computational saturation mutagenesis for all possible single amino acid substitutions across the adducin proteins family. Pathogenicity predictions were conducted using four independent tools: AlphaMissense, Rhapsody, PolyPhen-2, and PMut. Predictions were validated against UniProt-annotated pathogenic variants. Predictive performance was assessed using Cohen’s Kappa, sensitivity, and precision. Mutations with a prediction probability ≥ 0.8 were further analyzed for structural stability using mCSM, DynaMut2, MutPred2, and Missense3D, with particular focus on functionally relevant domains such as phosphorylation and calmodulin-binding sites. Results: PMut identified the highest number of pathogenic mutations, while PolyPhen-2 yielded more conservative predictions. Several high-risk mutations clustered in known regulatory and binding regions. Substitutions involving glycine were consistently among the most destabilizing due to increased backbone flexibility. Validated variants showed strong agreement across multiple tools, supporting the robustness of the analysis. Conclusions: This study highlights the utility of multi-tool bioinformatic strategies for comprehensive mutation profiling. The results provide a prioritized list of high-impact adducin variants for future experimental validation and offer insights into potential therapeutic targets for disorders involving ADD1, ADD2, and ADD3 mutations. Full article

The emergence of multidrug-resistant pathogens has driven the development of novel antimicrobial peptides (AMPs) as therapeutic alternatives. Lactolisterin LBU (LBU) is a bacteriocin with promising activity against Gram-positive bacteria, including Staphylococcus aureus. In this study, we designed and evaluated a panel of amino acid variants of LBU to investigate domain–activity relationships and improve activity. Peptides were commercially synthesized, and their effect was evaluated for minimal inhibitory concentration (MIC), minimal bactericidal concentration (MBC), hemolytic activity, cytotoxicity, in vivo toxicity, and virulence modulation. AlphaFold3 structural prediction of LBU revealed a four-helix topology with amphipathic and hydrophobic segments. Helical wheel projections identified helices I and IV as amphipathic, suggesting their potential involvement in membrane interaction and activity. Glycine-to-alanine substitutions at helix I markedly increased antimicrobial activity but altered toxicity profiles. In contrast, changes at helix junctions and kinks reduced antimicrobial activity. We also showed differential regulation of virulence genes upon sub-MIC treatment. Overall, rational substitution enabled identification of residues critical for activity and toxicity, providing insights into therapeutic tuning of lactolisterin-based peptides. Full article

Three-finger toxins (3FTxs) are the largest group of nonenzymatic toxins found in snake venoms. Among them, neurotoxins that target nicotinic acetylcholine receptors are the most well-studied ligands. In addition to the classical neurotoxins, several other new classes have been characterized for their structure, receptor subtype, and species selectivity. Here, we systematically analyzed over 700 amino acid sequences of three-finger neurotoxins that interact with nicotinic acetylcholine receptors. Based on the amino acid residue substitutions in the functional sites and structural features of various classes of neurotoxins, we have classified them into over 150 distinct subgroups. Currently, only a small number of typical examples representing these subgroups have been studied for their structure, function, and subtype selectivity. The functional site residues responsible for their interaction with specific receptor subtypes of several toxins are yet to be identified. The molecular details of each subgroup representative toxin with its target receptor will contribute towards the understanding of subtype- and/or interface-selectivity. Thus, this review will provide new impetus in the toxin research and pave the way for the design of potent, selective ligands for nicotinic acetylcholine receptors. Full article

The phosphorylation of Rab10 (pT73-Rab10) by LRRK2 promotes the establishment of epithelial cell polarity by controlling the trafficking to the primary cilia membrane of cilia-resident proteins and signaling proteins. Previous studies have identified a site in the globular tail domain of MYO5A that specifically binds to only the phosphorylated form of Rab10. In this work, we have demonstrated that pT73-Rab10 does not associate with the globular tail of MYO5B. We have mapped the putative binding site to a required three amino acids (MEN, 1473–1475) in the MYO5A globular tail domain that are not found in the MYO5B globular tail. Substitution of the MEN amino acid sequence found in MYO5A into the paralogous position in the MYO5B globular tail conferred the ability to associate with pT73-Rab10. The results demonstrate that the interactors with MYO5A and MYO5B are not completely overlapping and that the interaction of pT73-Rab10 is specific to the MYO5A globular tail domain. Full article

The rapid evolution of SARS-CoV-2 has underscored the need for a detailed understanding of antibody binding mechanisms to combat immune evasion by emerging variants. In this study, we investigated the interactions between Class I neutralizing antibodies—BD55-1205, BD-604, OMI-42, P5S-1H1, and P5S-2B10—and the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein using multiscale modeling, which combined molecular simulations with the ensemble-based mutational scanning of the binding interfaces and binding free energy computations. A central theme emerging from this work is that the unique binding strength and resilience to immune escape of the BD55-1205 antibody are determined by leveraging a broad epitope footprint and distributed hotspot architecture, additionally supported by backbone-mediated specific interactions, which are less sensitive to amino acid substitutions and together enable exceptional tolerance to mutational escape. In contrast, BD-604 and OMI-42 exhibit localized binding modes with strong dependence on side-chain interactions, rendering them particularly vulnerable to escape mutations at K417N, L455M, F456L and A475V. Similarly, P5S-1H1 and P5S-2B10 display intermediate behavior—effective in some contexts but increasingly susceptible to antigenic drift due to narrower epitope coverage and concentrated hotspots. Our computational predictions show strong agreement with experimental deep mutational scanning data, validating the accuracy of the models and reinforcing the value of binding hotspot mapping in predicting antibody vulnerability. This work highlights that neutralization breadth and durability are not solely dictated by epitope location, but also by how binding energy is distributed across the interface. The results provide atomistic insight into mechanisms driving resilience to immune escape for broadly neutralizing antibodies targeting the ACE2 binding interface—which stems from cumulative effects of structural diversity in binding contacts, redundancy in interaction patterns and reduced vulnerability to mutation-prone positions. Full article

The suppressive regulator of cell fusion, suppressyn, is specifically expressed in the human placenta and is thought to play a crucial role in trophoblast fusion or syncytialization. Previous studies have suggested that alterations in its expression are associated with aberrant placental development, such as the immature placental morphology observed in Down syndrome, and may contribute to the pathogenesis of fetal growth restriction. While syncytialization in trophoblasts is an essential process for normal placental development, the precise molecular causes of its dysregulation remain poorly understood. In the present study, we aimed to elucidate the potential contribution of genomic variation to the loss of suppressyn function, extending previous analyses of expression abnormalities in perinatal disorders. Through sequence analysis, (1) we identified six polymorphisms within the coding region of the suppressyn gene, and (2) discovered that certain deletions and specific amino acid substitutions result in a complete loss of suppressyn-mediated inhibition of cell fusion. Although these mutations have not yet been reported in disease-associated genomic databases, our findings suggest that comprehensive genomic studies of perinatal and other disorders may reveal pathogenic variants of suppressyn, thereby uncovering novel genetic contributions to placental dysfunction. It is also anticipated that these findings might direct the development of therapeutic strategies targeting loss-of-function mutations. Full article

The H1N1 swine influenza viruses CQ91 and CQ445, isolated from pigs in China, exhibited distinct virulence in mice despite sharing similar genomic constellations. CQ91 demonstrated higher pathogenicity (MLD₅₀: 5.4 log₁₀ EID₅₀) and replication efficiency in mice compared to CQ445 (MLD₅₀: 6.6 log₁₀ EID₅₀). Through reverse genetics, we found that the attenuation of CQ445 was due to a single substitution of glutamic acid (E) with lysine (K) at position 343 in the PB2 protein. Introducing the CQ445-PB2 (343K) into CQ91 significantly reduced viral replication and pathogenicity in mice, while replacing CQ445-PB2 with CQ91-PB2 (343E) restored virulence. In vitro studies showed that the K343E mutation impaired viral replication in MDCK and A549 cells and reduced polymerase activity in minigenome assays. Mechanistically, the amino acid at position 343 in the PB2 affects the transcription stage of the viral replication process. Structural modeling indicated that the charge reversal caused by E343K altered local electrostatic interactions without major conformational changes. Phylogenetic analysis revealed that PB2-343E is highly conserved (>99.9%) in human and swine H1/H3 influenza viruses, suggesting that PB2-343E confers an adaptive advantage. This study identifies PB2-343E as a critical determinant of influenza virus pathogenicity in mammals, highlighting its role in host adaptation. Full article

The enzyme ABH2, one of nine human DNA dioxygenases of the AlkB family, belongs to the superfamily of Fe(II)/α-ketoglutarate-dependent dioxygenases and plays a crucial role in the direct reversal repair of nonbulky alkyl lesions in DNA nucleobases. ABH2 has broad substrate specificity, directly oxidizing DNA damages such as N¹-methyladenine, N³-methylcytosine, 1,N⁶-ethenoadenine, 3,N⁴-ethenocytosine, and a number of others. In our investigation, we sought to uncover the subtleties of the mechanisms governing substrate specificity in ABH2 by focusing on several critical amino acid residues situated in its active site. To gain insight into the function of this enzyme, we performed a functional mapping of its active site region, concentrating on pivotal residues, participating in forming a damaged binding pocket of the enzyme (Val99 and Ser125), as well as the residues directly involved in interactions with damaged bases, namely Arg110, Phe124, Arg172, and Glu175. To support our experimental data, we conducted a series of molecular dynamics simulations, exploring the interactions between the ABH2 mutant forms, bearing corresponding substitutions and DNA substrates, and harboring various types of methylated bases, specifically N¹-methyladenine or N³-methylcytosine. The comparative studies revealed compelling data indicating that alterations in most of the studied amino acid residues significantly influence both the binding affinity of the enzyme for DNA and its catalytic efficiency. Intriguingly, the findings suggest that the mutations impact the catalytic activity of ABH2 to a greater extent than its ability to associate with DNA strands. Collectively, these results show how changes to the active site affect molecular dynamics and reaction kinetics, improving our understanding of the substrate recognition process in this pivotal enzyme. Full article

This paper summarizes the results of multi-year studies performed by our research team, focusing on an analysis of protein recoding mediated by messenger RNA editing by ADAR adenosine deaminases. Searching for ADAR-mediated protein recoding was performed in the central nervous system of the model organisms, fruit fly and mouse, as well as in the human proteomic datasets. The proteogenomic approach has made it possible to identify dozens of editing events in the proteome, thus validating the results of transcriptomic studies. The observed recoding events in animals, ranging from insects to mammals, mainly affect the cytoskeletal components and proteins involved in synaptic transmission. In humans, recoding changes are most often observed in the central nervous system or tumor tissues. Over 15 million editing sites have been identified in humans; only a few thousand of those can potentially yield amino acid substitutions. Using a proteogenomic approach, dozens of protein recoding sites are identified, demonstrating their origin in ADAR RNA editing. Moreover, this revealed that the level of recoding at specific sites is not directly related to the abundance of ADAR enzymes per se or their target proteins. The recoding processes probably have differential regulation of interactions at the mRNA level that is yet to be clarified. Full article

Coronavirus non-structural protein 1 (nsp1) is a pathogenic determinant of Betacoronaviruses. Previous studies demonstrated that the nsp1 of various coronaviruses induces host shutoff through a variety of mechanisms; however, there is little information on the function of bovine coronavirus (BCoV) nsp1. We aimed to characterize the host gene expression suppression function of BCoV nsp1. We first confirmed that the expression of BCoV nsp1 in MAC-T cells, a bovine mammary epithelial cell line, suppressed host and reporter gene expression. Subsequently, lysine and phenylalanine at amino acid positions 232 and 233, respectively, were identified as key residues required for this suppressive effect. Expression levels of housekeeping genes are comparable in cells expressing wild-type BCoV nsp1 and a mutant with alanine substitutions at positions 232 and 233 (BCoV nsp1-KF). Wild-type BCoV nsp1 localized to both the cytoplasm and nucleus; however, BCoV nsp1-KF exhibited prominent nuclear accumulation with dot-like structures. Using confocal microscopy and co-sedimentation analysis, we identified an association between wild-type BCoV nsp1, but not BCoV nsp1-KF, and ribosomes, suggesting that ribosome binding is required for BCoV nsp1-mediated suppression of host gene expression. This is the first study of the characterization of host gene expression suppression by BCoV nsp1. Full article