Search Results (25,436)

The escalating global threat of antimicrobial resistance (AMR) underscores the urgent need for innovative therapeutics. Bacteriophages (phages), natural bacterial predators, offer promising solutions, especially when harnessed through advances in artificial intelligence (AI). This review explores how AI-driven innovations are transforming phage biology, with an emphasis on three pivotal areas: (1) AI-enhanced structural prediction (e.g., AlphaFold); (2) deep learning functional annotation; (3) bioengineering strategies, including CRISPR-Cas. We further discuss applications extending to medical therapy, biosensing, agricultural biocontrol, and environmental remediation. Despite progress, critical challenges persist—including high false-positive rates, difficulties in modeling disordered protein regions, and biosafety concerns remain. Overcoming these requires experimental validation, robust computational frameworks, and global regulatory oversight. AI integration in phage research is accelerating the development of next-generation therapeutics to combat AMR and advance engineered living therapeutics. Full article

Improving agricultural by-product utilization can alleviate tropical feed shortages. This study used corn stover (CS, Zea mays L.) at the maturity stage as the material, with four silage treatments: control, lactic acid bacteria (LAB, Lactiplantibacillus plantarum), cellulase (AC, Acremonium cellulolyticus), and LAB+AC. After 60 days fermentation in plastic drum silos, the silos were opened for sampling. PacBio single-molecule real-time sequencing technology was used to study bacterial community structure, symbiotic network functionality, and pathogenic risk to clarify CS fermentation regulatory mechanisms. The CS contained 59.9% neutral detergent fiber and 7.1% crude protein. Additive-treated silages showed better quality than the control: higher lactic acid (1.64–1.83% dry matter, DM), lower pH (3.62–3.82), and reduced ammonia nitrogen (0.54–0.81% DM). Before ensiling, the CS was dominated by Gram-negative Rhizobium larrymoorei (16.30% of the total bacterial community). Functional prediction indicated that the microbial metabolism activity in diverse environments was strong, and the proportion of potential pathogens was relatively high (14.69%). After ensiling, Lactiplantibacillus plantarum as Gram-positive bacteria were the dominant species in all the silages (58.39–84.34% of the total bacterial community). Microbial additives facilitated the establishment of a symbiotic microbial network, where Lactiplantibacillus occupied a dominant position (p < 0.01). In addition, functional predictions showed an increase in the activity of the starch and sucrose metabolism and a decrease in the proportion of potential pathogens (0.61–1.95%). Among them, the synergistic effect of LAB and AC inoculants optimized the silage effect of CS. This study confirmed that CS is a potential high-quality roughage resource, and the application of silage technology can provide a scientific basis for the efficient utilization of feed resources and the stable development of animal husbandry in the tropics. Full article

TtgR, a transcriptional repressor from Pseudomonas putida, plays a key role in regulating multidrug resistance by controlling the expression of genes in response to various ligands. Despite its broad specificity, TtgR represents a promising candidate for the development of transcription factor (TF)-based biosensors. In this study, we utilized TtgR and its native promoter region (P_ttgABC) as genetic components to construct TF-based biosensors in Escherichia coli. By coupling TtgR and P_ttgABC with egfp, we developed a biosensor responsive to diverse flavonoids. To enhance the selectivity and specificity of the biosensor, we genetically engineered a TtgR-binding pocket. Engineered TtgR variants exhibited altered sensing profiles, enabling the development of biosensors with tailored ligand responses. Computational structural analysis and ligand docking provided insights into the interaction mechanisms between TtgR variants and flavonoids. Notably, biosensors based on wild-type TtgR and its N110F mutant were capable of quantifying resveratrol and quercetin at 0.01 mM with >90% accuracy. Although the precise molecular mechanisms involved remain unclear and further optimization is needed, the biosensors developed herein demonstrate strong potential for applications in numerous fields. This study lays the foundation for future research that could extend the utility of TtgR-based biosensors to synthetic biology, metabolic engineering, and beyond. Full article

Transglutaminase (TGase) improves protein structure by facilitating cross-linking reactions. However, the effects of TGase on the physicochemical properties of whey protein isolate (WPI)–soymilk complexes and their applications in yuba remain unclear. Therefore, the impacts of TGase concentration on the free sulfhydryl content, free amino content, particle size, and structure of WPI–soymilk complexes and their film-forming properties were studied. The results showed that the physicochemical properties of the composite soymilk were changed by the TGase-induced cross-linking reaction of protein. Compared with the composite soymilk without TGase modification, the particle size of the WPI–soymilk complexes increased from 707.99 ± 9.47 nm to 914.41 ± 2.8 nm as the TGase concentration increased, and the complexes remained relatively stable at low TGase concentrations. TGase modification changed the tertiary structure of the WPI–soymilk complexes. The composite yuba with 0.01% and 0.03% levels of TGase had a higher β-sheet content than composite yuba without addition of TGase. The surface hydrophobicity of composite soymilk was decreased by all the addition levels of TGase. Meanwhile, the TGase-modified composite protein with 0.03% TGase had the lowest free sulfhydryl (35.92 μg/g) and amino groups (0.46). Additionally, the tensile strength of the composite yuba with 0.05% TGase addition reached a peak of 1.66 ± 0.02 MPa, which was 7.8% higher than that of the composite yuba without TGase addition. The SEM results revealed that the composite yuba with 0.01–0.03% TGase addition exhibited a dense and non-porous film structure. Moreover, all the composite yuba with TGase addition had a reduced rate of yuba cooking loss. This study contributes to enhancing the yield and mechanical properties of traditional yuba. Full article

For 40 years, Intron Retention (IR) was dismissed as splicing noise and is now recognized as a dynamic and evolutionarily conserved mechanism of post-transcriptional gene regulation. Unlike canonical splicing, which excises all introns from pre-mRNAs, IR selectively retains intronic sequences, albeit at seemingly random places; however, current research now reveals that this process is strategic in its retention. IR influences mRNA stability, localization, and translational potential. Retained introns can lead to nonsense-mediated decay, promote nuclear retention, or give rise to novel protein isoforms that contribute to expanding proteomic and transcriptomic profiles. IR is finely regulated by splice site strength, splicing regulatory elements, chromatin structure, methylation patterns, RNA polymerase II elongation rates, and the availability of co-transcriptional splicing factors. IR plays critical roles in cell-type and tissue-specific gene expression with observed patterns, particularly during neuronal, cardiac, hematopoietic, and immune development. It also functions as a molecular switch during cellular responses to environmental and physiological stressors such as hypoxia, heat shock, and infection. Dysregulated IR is increasingly associated with cancer, neurodegeneration, aging, and immune dysfunction, where it may alter protein function, suppress tumor suppressor genes, or generate immunogenic neoepitopes. Experimental and computational tools like RNA-seq, RT-PCR, IRFinder, and IntEREst have enabled transcriptome-wide detection and validation of IR events, uncovering their widespread functional roles. This review will examine current knowledge on the function, regulation, and detection of IR, and also summarize recent advances in understanding its role in both normal and pathophysiological settings. Full article

Glycosylation, the enzymatic addition of glycans to proteins and lipids, is a critical post-translational modification that influences protein folding, stability, trafficking, immune modulation, and cell signaling. The vast structural diversity of glycans arising from differences in monosaccharide composition, branching, and terminal modifications such as sialylation, fucosylation, and sulfation underpins their functional specificity and regulatory capacity. This review provides a comprehensive overview of glycan biosynthesis, with a focus on N-glycans, O-glycans, glycosaminoglycans (GAGs), and glycolipids. It explores their essential roles in maintaining cellular homeostasis, development, and immune surveillance. In health, glycans mediate cell–cell communication, protein interactions, and immune responses. In disease, however, aberrant glycosylation is increasingly recognized as a hallmark of numerous pathological conditions, including cancer, neurodegenerative disorders, autoimmune diseases, and a wide range of infectious diseases. Glycomic alterations contribute to tumor progression, immune evasion, therapy resistance, neuroinflammation, and synaptic dysfunction. Tumor-associated carbohydrate antigens (TACAs) and disease-specific glycoforms present novel opportunities for biomarker discovery and therapeutic targeting. Moreover, glycan-mediated host–pathogen interactions are central to microbial adhesion, immune escape, and virulence. This review highlights current advances in glycomics technologies, including mass spectrometry, lectin microarrays, and glycoengineering, which have enabled the high-resolution profiling of the glycome. It also highlights the emerging potential of single-cell glycomics and multi-omics integration in precision medicine. Understanding glycome and its dynamic regulation is essential for uncovering the molecular mechanisms of disease and translating glycomic insights into innovative diagnostic and therapeutic strategies. Full article

Commercially relevant processing conditions, including protein concentration, pH and shearing and their impact on the solubility, heat stability, and secondary structure of faba bean proteins (FBPIs), were studied. Most of the examined properties, including protein solubility and heat stability, were due to the simultaneous effects of pH and concentration. The shearing rate played a crucial role in determining the heat stability of FBPI during thermal processing through protein molecular activities, such as inter- and/or intramolecular force interactions. Under the heat treatment conditions (temperature of 95 °C and time of 30 min), the shearing rate of 1000 s⁻¹ enhanced the heat stability, compared to 100 s⁻¹. Meanwhile, concentration and pH shift contributed to the conformation of various protein structures of faba bean protein isolates. This study revealed that these structural changes involve the unfolding of the protein’s native tertiary structure, which likely exposes hydrophobic and sulfhydryl (–SH) groups, ultimately leading to protein aggregation. It also provided a comprehensive understanding of faba bean protein functionality by studying various interactions of FBPI proteins under thermal processing systems. Full article

With the recent development of accurate protein structure prediction tools, virtually all protein sequences now have an experimental or a modeled structure. It has therefore become essential to develop fast algorithms capable of detecting non-covalent interactions not only within proteins but also in protein-protein, protein-DNA, protein-RNA, and protein-ligand complexes. Interactions involving aromatic compounds, particularly their $\pi$ molecular orbitals, hold unique significance among molecular interactions due to the electron delocalization, which is known to play a key role in processes such as protein aggregation. In this paper, we present PInteract, an algorithm that detects $\pi$-involving interactions in input structures based on geometric criteria, including $\pi$-$\pi$, cation-$\pi$, amino-$\pi$, His-$\pi$, and sulfur-$\pi$ interactions. In addition, it is capable of detecting chains and clusters of $\pi$ interactions as well as particular recurrent motifs at protein-DNA and protein-RNA interfaces, called stair motifs, consisting of a particular combination of $\pi$-$\pi$ stacking, cation/amino/His-$\pi$ and H-bond interactions. Full article

Diet and gut microbiota are significant determinants of host health, but how dietary quality modulates gut microbiota in Blastocystis-colonised individuals remains underexplored. We studied two contrasting cohorts: university students (FACSA, n = 46) and institutionalised children with their caregivers (PAVILA, n = 37), representing distinct dietary and sociodemographic contexts. Eight participants from each cohort tested positive for Blastocystis; however, two PAVILA samples could not be sequenced, resulting in a final microbiota subcohort of 14 individuals (FACSA n = 8, PAVILA n = 6). Dietary quality was assessed using the Healthy Eating Index-2020 (HEI-2020), and faecal microbiota was characterised through 16S rRNA sequencing. Alpha and beta diversity were analysed, and genus-level transformed data were further evaluated using permutational multivariate analysis of variance (PERMANOVA), principal coordinates analysis (PCoA), and distance-based redundancy analysis (db-RDA). The FACSA cohort exhibited higher microbial richness and diversity (Shannon and Simpson indexes, p < 0.01) compared to PAVILA, with marked differences in microbial composition (PERMANOVA R² = 0.39, p = 0.002). Total diet quality correlated with microbial structure (R² = 0.26, p = 0.016), with protein (R² = 0.23, p = 0.017) and vegetable components (R² = 0.17, p = 0.044) as primary contributors. Multivariate analysis showed that higher protein and vegetable intakes were associated with genera such as Sellimonas, Murimonas, Alistipes, and Desulfovibrio (FACSA group). In contrast, Hydrogenoanaerobacterium, V9D2013_group, and Haemophilus were linked to lower-quality diets (PAVILA group). Our results indicate that diet quality significantly influences gut microbiota composition in individuals colonised by Blastocystis, underscoring its potential as a target for nutritional interventions in vulnerable populations. Full article

The Dongting Lake wetland is an important habitat for rodents. In order to understand the structural characteristics of rodent communities and the effect of groundwater level on them, this study explored the changes in rodent community structure in four different habitats (Carex, Reeds, Carex + Reeds, and Poplar) from 2003 to 2023. Meanwhile, the relationships between groundwater level, nutrient composition of Carex brevicuspis, and structural characteristics of rodent communities were analyzed. The results showed that the advantages of rodent species in the four different habitats are different, and the community structure of rodents has undergone significant changes in recent years. A significant correlation between groundwater level and the nutrient composition of C. brevicuspis was found. Further analysis shows a significant correlation between the nutritional components of C. brevicuspis and the population structure of rodents. Crude protein, total phosphorus, and dry matter were three key plant nutrient indicators that were significantly correlated with both capture rate and the community diversity index (p < 0.05). Total phosphorus and crude protein were significantly negatively correlated with capture rate and Simpson’s index (p < 0.05), but significantly positively correlated with Pielou’s index and Shannon–Wiener’s index (p < 0.05), while the dry matter was completely opposite. The research conclusions suggest that different habitats and groundwater levels affect different characteristics of rodent community structures, and that plant nutrients are likely to be the mediator. Full article

The Pichia system has been exploited for decades as a host for recombinant protein production, but there is still an information gap regarding problems that may arise with its use. The application of strains based on the methanol-induced alcohol oxidase 1 (AOX1) promoter may represent a safety issue, and its performance varies among strains. In this study, the ability of a Komagataella phaffii Mut^S KM71H strain to produce recombinant cutinases was evaluated and compared to that of the more widely used Mut⁺ X-33 strain. The effects of the nature of the cutinase (ANCUT1 and ANCUT3, from Aspergillus nidulans), methanol level, and inoculum concentrations were evaluated in shake flasks containing a complex medium. Higher activities and volumetric cutinase productivity were observed at lower induction cell densities (0.5%) for the Mut^S KM71H aox1::pPICZα-A-ANCUT1 strain, while a higher one (2%) yielded better results in KM71H aox1::pPICZα-A-ANCUT3. The best inoculum and inducer conditions for both strains yielded similar results. The behavior of the different cutinases in the Mut^S or Mut⁺ genetic background was opposed: strain KM71H aox1::pPICZα-A-ANCUT3 produced 19% more activity than strain X-33 aox1::pPICZα-A-ANCUT3, while the ANCUT1 containing strain produced significantly higher activity in the X-33 Mut⁺ strain. These results indicate that Mut^S strains are viable host options without the complications of rapidly growing methanol strains. The effect of the gene structure being expressed is a phenomenon that needs further exploration. Full article

Spinal health depends on the dynamic interplay between mechanical forces, biochemical signaling, and cellular behavior. This review explores how key molecular pathways, including integrin, yeas-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ), Piezo, and Wingless/Integrated (Wnt) with β-catenin, actively shape the structural and functional integrity of spinal tissues. These signaling mechanisms respond to physical cues and interact with inflammatory mediators such as interleukin-1 beta (IL-1β), interleukin-6 (IL-6), and tumor necrosis factor alpha (TNF-α), driving changes that lead to disc degeneration, vertebral fractures, spinal cord injury, and ligament failure. New research is emerging that shows scaffold designs that can directly harness these pathways. Further, new stem cell-based therapies have been shown to promote disc regeneration through targeted differentiation and paracrine signaling. Interestingly, many novel bone and ligament scaffolds are modulating anti-inflammatory signals to enhance tissue repair and integration, as well as prevent scaffold degradation. Neural scaffolds are also arising. These mimic spinal biomechanics and activate Piezo signaling to guide axonal growth and restore motor function. Scientists have begun combining these biological platforms with brain–computer interface technology to restore movement and sensory feedback in patients with severe spinal damage. Although this technology is not fully clinically ready, this field is advancing rapidly. As implantable technology can now mimic physiological processes, molecular signaling, biomechanical design, and neurotechnology opens new possibilities for restoring spinal function and improving the quality of life for individuals with spinal disorders. Full article

Norovirus–bacterial interactions influence viral replication and immune responses, yet the molecular details that mediate binding of these viruses to commensal bacteria are unknown. Studies with other enteric viruses have revealed that LPS and other lipid/carbohydrate structures facilitate virus–bacterial interactions, and it has also been shown that human noroviruses (HuNoVs) can interact with histo-blood group antigen (HBGA)-like compounds on the surface of bacterial cells. Based on these findings, this study hypothesized that carbohydrate-based compounds were the ligands that facilitated binding of both human and murine noroviruses (MNV) to bacteria. Using glycan microarrays, competitive inhibition assays, and a panel of bacterial mutants, the project assessed the influence of specific glycans on viral attachment to bacteria. Protein-based interactions were also examined. The results supported previous work which demonstrated that HuNoVs strongly bind HBGA-like glycans, while MNV displayed distinct binding to other glycans including aminoglycosides and fucosylated structures. Ultimately, this work demonstrates that HuNoVs have more limited binding requirements for bacterial attachment compared to MNV, and the MNV binding to bacteria may involve both specific structures as well as electrostatic interactions. Given the importance of commensal bacteria during viral infection, defining the molecular mechanisms that mediate virus–bacteria interactions is critical for understanding infection dynamics and may be useful in the development of disease therapeutics and novel technologies for viral detection from food and environmental sources. Full article

Fenofibrate (FF), a lipid-lowering drug, may decrease the risk of cardiovascular diseases in some pathological settings, yet data on its cardiac effects in physiological aging is scarce. To determine FF and age effects on the heart’s morphology and expression of metabolism-related genes, we treated young and old male rats for 30 days with 0.1% or 0.5% FF. FF did not affect serum activities of LDH and creatine kinase in both age groups. Upon FF treatment the structure of the heart muscle did not change in young rats; however, 0.5% FF increased the abundance of collagen fibers in old rats, and lipid accumulation in cardiomyocytes in young and old animals. FF increased immunoreactivity of the hypertrophy marker NPPA that was more pronounced in old than in young rats, while VEGFB immunoreactivity did not change. FF upregulated phospho-AMPK and PGC1α protein levels only in the cardiac muscle of old rats, while in both age groups it mildly increased the expression of selected fatty acid oxidation genes. We conclude that the cardiac muscle response to FF is dose-dependent and influenced by age. The observed negative impact of high-dose FF in the hearts of aged rats underscores the importance of dose optimization in the elderly. Full article

Peptides derived from protein sources in food exhibit a diverse array of biological activities. The screening, preparation, and functional investigation of bioactive peptides have become a focal area of research. This review summarizes the status of peptide activity mining, including the latest research progress in protein sources, peptide functions, and processing conditions. It critically evaluates the limitations of current bioactive peptide screening methods, including the drawbacks of traditional methods and molecular simulations. The potential of using molecular simulation for the virtual screening of potentially bioactive peptides is summarized. This includes virtual enzymatic digestion, molecular docking, simulation of non-thermal processing technologies, and the construction of organelle/cell models. The driving role of artificial intelligence in molecular simulation is also discussed. In addition, the structural information, mechanism, and structural analysis technique of action of the popular target proteins of foodborne bioactive peptides are summarized to provide a better reference for virtual-reality combinations. Full article