Search Results (3,624)

This study explored how combining supercritical fluid extraction (SFE) and enzymatic hydrolysis influences the structure and functionality of peptides recovered from filter-pressed shrimp waste. Freeze-dried press cake (PC) was defatted via SFE and hydrolyzed using Alcalase (ALC) and trypsin (TRYP). ALC-treated PC achieved the highest protein recovery (63.49%), extraction yield (24.73%), and hydrolysis degree (18.10%) (p < 0.05). SFE-treated hydrolysates showed higher zeta potential (−47.23 to −49.93 mV) than non-SFE samples (−25.15 to −38.62 mV) but had larger droplet sizes, indicating lower emulsion stability. SC-ALC displayed reduced fluorescence intensity and a red shift in maximum wavelength. TRYP hydrolysates reduced interfacial tension (20 mN/m), similar to sodium caseinate (Na-Cas, 13 mN/m), but with lesser effects. Dilatational rheology showed TRYP hydrolysates formed stronger, solid-like structures. These results emphasize protease efficacy over SFE for extracting functional compounds, enhancing shrimp waste valorization. Full article

Autoantibodies to ADAMTS13 are at the center of pathology of the immune-mediated thrombotic thrombocytopenic purpura. These autoantibodies can be either inhibitory (enzymatic function) or non-inhibitory, resulting in protein depletion. Under normal physiologic conditions, antibodies are generated in response to foreign antigens, which can include infectious agents; however, these antibodies may at times cross-react with self-epitopes. This is one of the possible mechanisms mediating formation of anti-ADAMTS13 autoantibodies. The process known as “antigenic mimicry” may be responsible for the development of these autoantibodies that recognize and bind cryptic epitopes in ADAMTS13, disrupting its enzymatic function over ultra large von Willebrand factor multimers, forming the seeds for platelet activation and microthrombi formation. In particular, specific amino acid sequences in ADAMTS13 may lead to conformational structures recognized by autoantibodies. Generation of these antibodies may occur more frequently among patients with a genetic predisposition. Conformational changes in ADAMTS13 between open and closed states can also constitute the critical change driving either interactions with autoantibodies or their generation. Nowadays, there is a growing understanding of the role that autoantibodies play in ADAMTS13 pathology. This knowledge, especially of functional qualitative differences among antibodies and the ADAMTS13 sequence specificity of such antibodies, may make possible the development of targeted therapeutic agents to treat the disease. This review aims to present what is known of autoantibodies against ADAMTS13 and how their structure and function result in disease. Full article

Selenium–polysaccharides possess antioxidant properties, making them promising materials for functional foods, pharmaceuticals, and clinical applications. This study examines the incorporation of selenium into polysaccharides via mycelial biosynthesis and its effects on structure and antioxidant activity. Polysaccharides obtained from Lentinula edodes-submerged cultures grown in Se-supplemented and non-supplemented media were analysed for Se content (RP-HPLC/FLD), structure (FT-IR, HPLC, and HPGPC-ELSD), and antioxidant activity (DPPH scavenging, reducing power, and Fe²⁺ chelation). Two low-molecular-weight Se–heteropolysaccharides (Se-FE-1.1 and Se-FE-1.2) containing ~80 and 125 µg/g Se were isolated, primarily composed of glucose, mannose, and galactose with β-glycosidic linkages. Se incorporation into polysaccharides selectively enhanced their antioxidant activity in the DPPH radical scavenging assay, with minimal effects observed in iron chelation and reducing power assays. Crude Se–polysaccharides displayed the highest antioxidant activity, suggesting an additional contribution from protein components. Our findings demonstrate that Se is effectively incorporated into polysaccharides, altering monosaccharide composition while preserving glycosidic linkages. The selective enhancement of radical scavenging suggests that selenium plays a specific role in antioxidant activity, primarily influencing radical scavenging mechanisms rather than interactions with metal ions. Further research is needed to clarify the mechanisms of selenium incorporation, the nature of its bonding within the polysaccharide molecule, and its impact on biological activity. Full article

The self-assembly mechanisms of various complex biological structures, including viral capsids and carboxysomes, have been theoretically studied through numerous kinetic models. However, most of these models focus on the equilibrium aspects of a simplified kinetic description in terms of a single reaction coordinate, typically the number of proteins in a growing aggregate, which is often insufficient to describe the size and shape of the resulting structure. In this article, we use mesoscopic non-equilibrium thermodynamics (MNET) to derive the equations governing the non-equilibrium kinetics of viral capsid formation. The resulting kinetic equation is a Fokker–Planck equation, which considers viral capsid self-assembly as a diffusive process in the space of the relevant reaction coordinates. We discuss in detail the case of the self-assembly of a spherical (icosahedral) capsid with a fixed radius, which corresponds to a single degree of freedom, and indicate how to extend this approach to the self-assembly of spherical capsids that exhibit radial fluctuations, as well as to tubular structures and systems with higher degrees of freedom. Finally, we indicate how these equations can be solved in terms of the equivalent Langevin equations and be used to determine the rate of formation and size distribution of closed capsids, opening the door to the better understanding and control of the self- assembly process. Full article

(1) Background: MicroRNAs are non-coding RNA sequences that regulate cellular functions by targeting messenger RNAs and inhibiting protein synthesis. Identifying their target sites is vital to understanding their roles. However, it is challenging due to the high cost and time demands of experimental methods and the high false-positive rates of computational approaches. (2) Methods: We introduce a Multi-Input Neural Network (MINN) algorithm that integrates diverse biologically relevant features, including the microRNA duplex structure, substructures, minimum free energy, and base-pairing probabilities. For each feature derived from a microRNA target-site duplex, we create a corresponding image. These images are processed in parallel by the MINN algorithm, allowing it to learn a comprehensive and precise representation of the underlying biological mechanisms. (3) Results: Our method, on an experimentally validated test set, detects target sites with an AUPRC of 0.9373, Precision of 0.8725, and Recall of 0.8703 and outperforms several commonly used computational methods of microRNA target-site predictions. (4) Conclusions: Incorporating diverse biologically explainable features, such as duplex structure, substructures, their MFEs, and binding probabilities, enables our model to perform well on experimentally validated test data. These features, rather than nucleotide sequences, enhance our model to generalize beyond specific sequence contexts and perform well on sequentially distant samples. Full article

As a porous crystalline material, covalent organic frameworks (COFs) have attracted significant attention due to their extraordinary features, such as an ordered pore structure and excellent stability. Synthesized through the aldehyde amine condensation reaction, TpPa-1 COFs (Triformylphloroglucinol-p-Phenylenediamine-1 COFs) were blended with cellulose acetate (CA) to form a casting solution. The TpPa-1 COF/CA ultrafiltration membrane was then prepared using the non-solvent-induced phase inversion (NIPS) method. The influence of TpPa-1 COFs content on the hydrophilicity, stability and filtration performance of the modified membrane was studied. Due to the hydrophilic groups in TpPa-1 COFs and the network structure formed by covalent bonds, the modified CA membranes exhibited higher hydrophilicity and lower protein adsorption compared with the pristine CA membrane. The porous crystalline structure of TpPa-1 COFs increased the water permeation path in the CA membrane, improving the permeability of the modified membrane while maintaining an outstanding bovine serum albumin (BSA) rejection. Furthermore, the addition of TpPa-1 COFs reduced protein adsorption on the CA membrane and overcame the trade-off between permeability and selectivity in CA membrane bioseparation applications. This approach provides a sustainable method for enhancing membrane performance while enhancing the application of membranes in protein purification. Full article

Aldehyde dehydrogenases (ALDHs) are a gene family that relies on NAD +/NADP + proteins to oxidize toxic aldehydes to non-toxic carboxylic acids, and they play a crucial role in the growth and development of plants, as well as in their ability to withstand stress. This study identified 26 ALDH genes from six Glycyrrhiza uralensis gene families distributed on six chromosomes. By analyzing the phylogeny, gene structure, conserved motifs, cis-regulatory elements, collinearity of homologs, evolutionary patterns, differentiation patterns, and expression variations under drought stress, we found that the ALDH gene is involved in phytohormones and exhibits responsiveness to various environmental stressors by modulating multiple cis-regulatory elements. In addition, GuALDH3H1, GuALDH6B1, GuALDH12A2, and GuALDH12A1 have been identified as playing a crucial role in the response to drought stress. By analyzing the expression patterns of different tissues under drought stress, we discovered that GuALDH3I2 and GuALDH2B2 exhibited the most pronounced impact in relation to the drought stress response, which indicates that they play a positive role in the response to abiotic stress. These findings provide a comprehensive theoretical basis for the ALDH gene family in Glycyrrhiza uralensis and enhance our understanding of the molecular mechanisms underlying ALDH genes in licorice growth, development, and adaptation to drought stress. Full article

This study aimed to optimize the ultrasound-assisted extraction (UAE) of polysaccharides from fermented Astragalus membranaceus (FAPS) and to investigate the physicochemical properties and antioxidant activities of the extracted polysaccharides. Using a combination of single-factor experiments and response surface methodology based on a Box–Behnken design, we improved the extraction of crude FAPS without deproteinization. Under optimal conditions (50 °C, 60 min, 8 mL/g, 480 W), the yield of crude FAPS obtained by UAE (7.35% ± 0.08) exceeded the yield from convectional hot water extraction (6.95% ± 0.24). After protein removal, the FAPS was subjected to comprehensive chemical analyses, including HPLC, HPGPC, FT-IR, UV spectroscopy, and a Congo red assay. The results showed that FAPS had a significantly higher carbohydrate content compared to the non-fermented group (95.38% ± 6.20% vs. 90.938% ± 3.80%), while the protein content was significantly lower than that of the non-fermented Astragalus polysaccharides (APS) group (1.26% ± 0.34% vs. 6.76% ± 0.87%). In addition, FAPS had a higher average molecular weight and a lower Mw/Mn ratio compared to APS. The primary monosaccharides in FAPS were identified as Glc, Ara, Gal and GalA, with a molar ratio of 379.72:13.26:7.75:6.78, and FAPS lacked a triple helix structure. In vitro, antioxidant assays showed that FAPS possessed superior antioxidant properties compared to APS. These results emphasize the significant potential of FAPS as an antioxidant, possibly superior to that of APS. The results of this study suggest that fermentation and UAE offer promising applications for the development and utilization of Astragalus membranaceus for human and animal health. Full article

Identifying reliable biomarkers in peripheral blood is critical for advancing the diagnosis and management of multiple sclerosis (MS), particularly given the invasive nature of cerebrospinal fluid (CSF) sampling. This review explores the role of B cells and immunoglobulins (Igs), particularly IgG and IgM, as biomarkers for MS. B cell oligoclonal bands (OCBs) in the CSF are well-established diagnostic tools, yet peripheral biomarkers remain underdeveloped. Emerging evidence highlights structural and functional variations in immunoglobulin that may correlate with disease activity and progression. A recent novel discovery of blood IgG aggregates in MS patients that fail to bind Protein A reveals promising diagnostic potential and confirms previous findings of the unique features of immunoglobulin G in MS and the potential link between the superantigen Protein A and MS. These aggregates, enriched in IgG1 and IgG3 subclasses, exhibit unique structural properties, including mutations in the framework region 3 (FR3) of IGHV3 genes, and are associated with complement-dependent neuronal apoptosis. Data based on ELISA have demonstrated that IgG aggregates in plasma can distinguish MS patients from healthy controls and other central nervous system (CNS) disorders with high accuracy and differentiate between disease subtypes. This suggests a role for IgG aggregates as non-invasive biomarkers for MS diagnosis and monitoring. Full article

Background: Programmed cell death protein 1 (PD-1), encoded by the PDCD1 gene, is critical in immune checkpoint regulation and cancer immune evasion. Variants in PDCD1 may alter its function, impacting cancer susceptibility and disease progression. Objectives: This study evaluates the structural, functional, and regulatory impacts of non-synonymous single-nucleotide polymorphisms (nsSNPs) in the PDCD1 gene, focusing on their pathogenic and oncogenic roles. Methods: Computational tools, including PredictSNP1.0, I-Mutant2.0, MUpro, HOPE, MutPred2, Cscape, Cscape-Somatic, GEPIA2, cBioPortal, and STRING, were used to analyze 695 nsSNPs in the PD1 protein. The analysis covered structural impacts, stability changes, regulatory effects, and oncogenic potential, focusing on conserved domains and protein–ligand interactions. Results: The analysis identified 84 deleterious variants, with 45 mapped to conserved regions like the Ig V-set domain essential for ligand-binding interactions. Stability analyses identified 78 destabilizing variants with significant protein instability (ΔΔG values). Ten nsSNPs were identified as potential cancer drivers. Expression profiling showed differential PDCD1 expression in tumor versus normal tissues, correlating with improved survival in skin melanoma but limited value in ovarian cancer. Regulatory SNPs disrupted miRNA-binding sites and transcriptional regulation, affecting PDCD1 expression. STRING analysis revealed key PD-1 protein partners within immune pathways, including PD-L1 and PD-L2. Conclusions: This study highlights the significance of PDCD1 nsSNPs as potential biomarkers for cancer susceptibility, advancing the understanding of PD-1 regulation. Experimental validation and multi-omics integration are crucial to refine these findings and enhance theraputic strategies. Full article

It is well known that the host response to different human and animal coronaviruses infection is regulated by the aryl hydrocarbon receptor, a ligand-activated transcription factor. The present study investigates the expression of the aryl hydrocarbon receptor during bovine coronavirus infection, through in vitro and in silico investigations. The in vitro studies demonstrate that the aryl hydrocarbon receptor and as well as its targets, CYP1A1 and CYP1B1, were significantly activated by bovine coronavirus infection in bovine cells (MDBK). During infection, the pretreatment of cells with non-cytotoxic doses of CH223191, a selective inhibitor of the aryl hydrocarbon receptor, resulted in a significant reduction in virus yield and a downregulation in the viral spike protein expression. These findings occurred in the presence of the inhibition of aryl hydrocarbon receptor signaling. Our results reveal that the bovine coronavirus acts on viral replication, upregulating the aryl hydrocarbon receptor and its downstream target proteins, CYP1A1 and CYP1B1. In addition, following the in silico studies, the three-dimensional structural model of the bovine aryl hydrocarbon receptor in complex with the antagonist CH223191 indicates that the molecular mechanism, by which the PASB and TAD domains of the receptor interact with the inhibitor, is mainly driven by an extensive network of hydrophobic interactions, with a series of hydrogen bonds contributing to stabilizing the complex. Interestingly, bioinformatic analyses revealed that the PASB and TAD domains in the human and bovine aryl hydrocarbon receptor present high similarity at the primary sequence and three-dimensional structure levels. Taken together, these findings represent a fundamental step for the development of innovative drugs targeting AhR as a potential object for CoVs therapy. Full article

Viroids represent obligate plant pathogens composed exclusively of non-protein coding small single-stranded RNAs that cause high economic losses worldwide. A field survey was carried out to assess the incidence of the peach latent mosaic viroid (PLMVd) in southeastern Kazakhstan, the region of the country where fruit trees are mainly grown. Of 246 stone fruit trees, 20 (8.13%) were infected with the PLMVd. The incidence of the PLMVd in the peach (19.23%; 15/78) was significantly higher than that in the apricot (6.76%; 5/74; p = 0.0234). Eight of the detected viroids were cloned and used for full-genome sequencing. The nucleotide sequence similarity of the selected isolates found in Kazakhstan was 83.9–100%. A phylogenetic analysis indicated three clusters for the Kazakhstani isolates of the PLMVd. Three groups of Kazakhstani viroids differed in their predicted secondary structure. During the survey, the PLMVd was detected and genetically characterized for the first time in Kazakhstan. The obtained results indicate the need to develop state control measures for the PLMVd, including regular monitoring surveys. We identified several SNPs of the PLMVd that had not been previously described. The results may be useful in optimizing diagnostic approaches for detecting stone fruit viroids and preventing their spread through propagation material. Full article

LEA_5 domain-containing proteins constitute a small family of late embryogenesis-abundant proteins that are essential for seed desiccation tolerance and dormancy. However, their roles in non-seed storage organs such as underground tubers are largely unknown. This study presents the first genome-scale analysis of the LEA_5 family in tigernut (Cyperus esculentus L.), a Cyperaceae plant producing desiccation-tolerant tubers. Four LEA_5 genes identified from the tigernut genome are twice of two present in model plants Arabidopsis thaliana and Oryza sativa. A comparison of 86 members from 34 representative plant species revealed the monogenic origin and lineage-specific family evolution in Poales, which includes the Cyperaceae family. CeLEA5 genes belong to four out of five orthogroups identified in this study, i.e., LEA5a, LEA5b, LEA5c, and LEA5d. Whereas LEA5e is specific to eudicots, LEA5b and LEA5d appear to be Poales-specific and LEA5c is confined to families Cyperaceae and Juncaceae. Though no syntenic relationship was observed between CeLEA5 genes, comparative genomics analyses indicated that LEA5b and LEA5c are more likely to arise from LEA5a via whole-genome duplication. Additionally, local duplication, especially tandem duplication, also played a role in the family expansion in Juncus effuses, Joinvillea ascendens, and most Poaceae plants examined in this study. Structural variation (e.g., fragment insertion) and expression divergence of LEA_5 genes were also observed. Whereas LEA_5 genes in A. thaliana, O. sativa, and Zea mays were shown to be preferentially expressed in seeds/embryos, CeLEA5 genes have evolved to be predominantly expressed in tubers, exhibiting seed desiccation-like accumulation during tuber maturation. Moreover, CeLEA5 orthologs in C. rotundus showed weak expression in various stages of tuber development, which may explain the difference in tuber desiccation tolerance between these two close species. These findings highlight the lineage-specific evolution of the LEA_5 family, which facilitates further functional analysis and genetic improvement in tigernut and other species. Full article

Chalcone isomerase (CHI) is not only an enzyme related to flavonoid biosynthesis, but also one of the key enzymes in the flavonoid metabolic pathway. In this study, members of the CHI gene family were identified in the whole genome of sweet potato. Bioinformatics methods were used to analyze the physical and chemical properties, systematic evolution, conserved domain, chromosome location, cis-acting elements of the promoter, and so on, of CHI gene family members. In addition, the tissue site-specific expression of CHI gene family members and their expression patterns under three kinds of abiotic stress were analyzed. The results showed that five members of IbCHI gene family were identified in sweet potato, which were unevenly distributed on four chromosomes. The protein secondary structure and tertiary structure were consistent, and there was a conservative domain related to chalcone isomerase. The prediction of subcellular localization showed that it was mainly located in cytoplasm and chloroplast. Systematic evolution showed that the members of sweet potato CHI gene family could be divided into Type I-IV, and the Type I gene IbCHI1 showed CHI catalytic activity in transgenic callus. The collinearity gene pairs were identified between sweet potato and allied species. Its promoter contains light response elements, hormone response elements, and stress response elements. The results of real-time fluorescence quantitative PCR (qRT-PCR) analysis showed that the expression of the IbCHI gene was tissue-specific and that the catalytic genes IbCHI1 and IbCHI5 serve as primary responders to abiotic stress, while the non-catalytic members IbCHI3 and IbCHI4 may fine-tune metabolic flux or participate in low-temperature, salt, and drought stress signaling. This study can provide a theoretical basis for a follow-up functional genomics study of the chalcone isomerase gene family in sweet potato. Full article

Sorghum (Sorghum bicolor) is an essential bioenergy crop. Cellulosic and non-cellulosic polysaccharides, which can be transformed into biofuels, comprise most of its biomass. Many glycosyltransferases (GT) families, including GT43, are involved in the biosynthesis of xylan in plants’ primary and secondary cells. In this study, the GT43 gene family was identified, and its secondary structure and a three-dimensional (3D) model were constructed. Additionally, subcellular localization, detection of motifs, and analyses of its phylogenetic tree, physiochemical properties, protein–protein interaction network, gene structure, functional domain, gene duplication, Cis-acting elements, sequence logos, multiple sequence alignment, and gene expression profiles were performed based on RNA-sequence analyses. As a result, eleven members of the GT43 gene family were identified, and the phylogenetic tree of the GT43 gene family showed that all GT43 genes had evolutionary relationships with sorghum. Analyses of gene structure, motifs, sequence logos, and multiple sequence alignment showed that all members of the GT43 protein family were highly conserved. Subcellular localization showed all members of the GT43 protein family were localized in different compartments of sorghum. The secondary structure of the GT43 genes comprised different percentages of α-helices, random coils, β-turns, and extended strands. The tertiary structure model showed that all GT43 proteins had similar 3D structures. The results of the current study indicated that members of the GT43 gene family (Sobic.010G238800, Sobic.003G254700, and Sobic.001G409100) were highly expressed in internodes of the sorghum plant, based on RNA-Sequencing. The framework used in this study will be valuable for advancing research aligned with modern technology requirements and for enhancing understanding of the relationships among GT43 genes in Sorghum bicolor. Full article