Search Results (14,363)

Background/Objectives: Dolphins inhabiting coastlines can be influenced by anthropogenic factors. As biochemical changes accumulate in blubber over weeks to months, blubber metabolites may be informative biomarkers of molecular adaptations to environmental changes. Methods: We investigated the blubber metabolomic signatures of live free-ranging bottlenose dolphins for the first time. This exploratory study analyzed blubber samples from 35 common bottlenose dolphins (Tursiops truncatus) in South Texas waters using untargeted ultra-high-performance liquid chromatography-Orbitrap metabolomics. Results: Blubber samples exhibited distinct temporal and spatial metabolic patterns. Pathway enrichment analyses comparing detected metabolites (n = 2777) revealed that dolphins sampled in the spring had enhanced lipid quality and immune regulation, while dolphins sampled in the summer showed stress-associated metabolic responses. Dolphins inhabiting areas previously reported to experience heavy vessel traffic and contaminant burdens exhibited enriched immune- and inflammation-associated pathways. Dolphins that visually appeared to have poorer body condition exhibited metabolite profiles suggestive of increased protein catabolism. Dolphins in extreme salinity conditions had more abundant membrane maintenance and endocrine pathways. Conclusions: Dolphins from each system exhibited distinct metabolic signatures that may be associated with differing physiological responses, highlighting the potential utility of blubber biomarkers for assessing physiological adaptations in free-ranging marine mammals. Improved understanding of habitat-specific physiological responses offers critical insights into how cumulative impacts may affect the health and adaptive capacity of vulnerable species in dynamic coastal ecosystems. Full article

Autophagy is a carefully regulated catabolic process that utilizes assemblies of specific sets of macromolecules operating at multiple stages of the pathway. Discoveries in recent years show that autophagy markedly relies on liquid-liquid phase separation (LLPS). Here, we present parameters that indicate the plasticity of autophagy proteins and their probability to undergo LLPS in macroautophagy and microautophagy. We show that microautophagy is an extremely LLPS-friendly pathway. Several mechanisms involving proteins in the autophagy machinery that drive LLPS on various types of membranes to regulate this process or that undergo LLPS as autophagic cargo are described in detail. We also summarize the factors that modulate the LLPS potential of autophagy proteins. A high probability of autophagy-related proteins to undergo spontaneous LLPS shown here can direct future research on the role of protein droplets in autophagy. Full article

The longissimus dorsi (LD) and biceps femoris (BF) muscles are important meat-producing regions in camels. Investigating differences in meat quality and proteomic profiles between the LD and BF muscles in Junggar Bactrian camels can provide a molecular basis for regulating camel meat quality and genetic improvement. In this study, 20 healthy adult male Junggar Bactrian camels were selected. Following slaughter, muscle samples were collected from the splenius (SP), triceps brachii (TB), LD, external oblique (EO), gluteus medius (GM), and BF. Meat quality parameters (pH, meat color, shear force, drip loss, and cooking loss) were measured. The LD exhibited the highest meat quality among the six cuts, in contrast to the BF, which showed the lowest. Proteomic analysis of LD and BF from 6 Junggar Bactrian camels was conducted to identify proteins associated with meat quality, yielding 81 differentially expressed proteins (DEPs). Gene Ontology (GO) enrichment analysis highlighted several significantly enriched terms among the DEPs (p < 0.05), including calcium-dependent phospholipid binding, zinc ion binding, and metal ion binding. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis (p < 0.05) further indicated notable enrichment in cytoskeletal organization, 2-oxocarboxylate metabolism, and the citric acid cycle. DEPs associated with meat quality were identified, including tubulin α-chain-like 3 and synaptic function regulator FMR1 isoform X15, which can serve as candidate DEPs for shear force. Protein phosphatase 1 regulatory subunit 14C isoform X1 can serve as a candidate differentially expressed protein for pH. Protein phosphatase 1 regulatory subunit 14C isoform X and anchoring protein repeat domain 1 can serve as candidate DEPs for cooking loss. Membrane-associated protein A4 and membrane-associated protein A7 isoform X1, as well as the transcriptional activator of cytochrome c oxidase 1, can serve as candidate DEPs for color a*. These data may serve as a reference for further studies on how different cuts affect meat quality and for practical efforts to improve camel meat quality. Full article

Low temperatures limit the yield and stability of autumn-sown oats; thus, investigating cold resistance physiological responses is essential. In this study, we compared a cold-resistant variety (‘Aiwo’) and a cold-sensitive variety (‘Hewang’). ‘Aiwo’ exhibited a significantly higher overwintering survival rate (96.9%) and superior physiological traits, including elevated levels of soluble proteins, proline, putrescine, unsaturated fatty acids, and glutathione, alongside greater ATPase activity and reduced ROS levels. Exogenous putrescine application suggested a potential role of Put in alleviating lipid peroxidation. Metabolomic analysis showed that the arginine–proline and cysteine–methionine pathways were enriched among DAMs associated with ‘Aiwo’, accompanied by the accumulation of stress-protective metabolites. These metabolic changes may contribute to improved energy balance and membrane stability under low-temperature conditions. Our findings suggest that proline, putrescine, and glutathione are candidate physiological indicators associated with the cold-resistant phenotype, which may facilitate future screening of cold-resistant oat germplasm. Full article

The outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has emerged as one of the most significant global health crises in recent history. Coronaviruses are a diverse group of RNA viruses classified into alpha, beta, gamma, and delta genera, with SARS-CoV-2 belonging to the beta-coronavirus family. The virus exhibits high transmissibility and causes a wide spectrum of clinical manifestations ranging from mild respiratory symptoms to severe complications such as acute respiratory distress syndrome, multi-organ failure, and death, particularly among elderly and immunocompromised individuals. Structurally, SARS-CoV-2 possesses a large single-stranded RNA genome encoding major structural proteins, including spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins, which play critical roles in host-cell recognition and viral infection. Understanding the molecular mechanisms of virus–host interactions, especially protein–protein interactions (PPIs), is essential for uncovering viral pathogenesis and identifying potential therapeutic targets. Traditional experimental techniques for PPI detection, such as yeast two-hybrid and affinity purification methods, are often expensive, labor-intensive, and prone to inaccuracies. Consequently, computational approaches based on machine learning (ML) and deep learning (DL) have gained significant attention for efficient and scalable PPI prediction. These methods use diverse biological information, including protein sequences, structural features, genomic data, Gene Ontology annotations, and interaction networks, to model complex biological relationships. This survey reviews computational approaches to PPI prediction, highlighting ML- and DL-based techniques, methodological advances, performance evaluation practices, and limitations that affect benchmark comparability. It also discusses biological databases and data sources commonly used in PPI studies and explicitly considers how models trained in coronavirus-centered settings may generalize to other viral families with different mechanisms of host interaction. Full article

Accessory proteins of SARS-CoV-2 play crucial roles in viral pathogenesis, yet their structural properties remain elusive. ORF7b, a small accessory protein comprising only 43 amino acids, is widely assumed to parallel the structure–function relationships of its SARS-CoV ortholog based solely on sequence homology. In this study, we challenge this paradigm through direct physicochemical and structural characterization. Sequence analysis and electrostatic profiling reveal that the SARS-CoV-2 protein is a macromolecular polyanion with a net charge of −4 at neutral pH, featuring a diffuse negative surface that is highly responsive to pH changes. Complete 3D structures generated via ab initio modeling display a helical core flanked by two highly fluctuating, disordered termini. Residue Interaction Network (RIN) topology and Normal Mode Analysis (NMA) identified specific hinges governing these flexible extremities. Furthermore, the calculated dipole moment vector is tilted outward by 24°, misaligning with the central axis. Molecular dynamics simulations suggest that while the soluble structure is highly stable in water, it undergoes severe distortions and insufficient solvation within a membrane-mimetic environment. Thermodynamic association profiles and verified interactomic data from BioGRID reveal a strong propensity for ORF7b to participate in liquid–liquid phase transitions alongside human and viral partners. Taken together, these unique properties suggest that ORF7b operates as a dynamic peripheral membrane protein rather than a sedentary transmembrane component, providing a fresh framework for future therapeutic targeting. Overall, these in silico findings shift the current paradigm on ORF7b2 topology and provide a robust, physically grounded framework that identifies specific molecular priorities for future in vitro and in vivo validation. Full article

Sarcopenia is characterized by progressive loss of skeletal muscle mass and function and is a major contributor to frailty, disability, and mortality in older adults. Store-operated calcium entry (SOCE) is a crucial regulator of skeletal muscle calcium homeostasis, and impaired SOCE has been linked to age-related muscle weakness. Here, we identify the synaptophysin family member synaptophysin-like protein 2, also known as mitsugumin 29 (MG29; encoded by the human gene SYPL2 and the mouse ortholog Mg29), as a key organizer of triad membrane cholesterol and lipid signaling required for normal SOCE during aging. Using Mg29^−/− mice as a model of accelerated sarcopenia, together with RNA interference against Mg29 in adult muscle and primary myotubes, we quantified changes in muscle morphology, contractile function, SOCE activity, and targeted lipidomic profiles. Reduced MG29 expression led to decreased muscle fiber cross-sectional area, reduced specific force, blunted SOCE, and marked alterations in membrane cholesterol content and fatty acid-derived lipid mediators. Cholesterol depletion by methyl-β-cyclodextrin in wild-type myotubes produced SOCE defects similar to those observed in aged wild-type and young Mg29⁻/⁻ muscles, indicating that MG29-dependent maintenance of membrane cholesterol is required for normal SOCE. Acute Mg29 knockdown also altered myogenic differentiation, the expression of calcium-handling and stress-response genes, and the release and consumption of specific polyunsaturated fatty acid-derived lipid mediators. Together, these findings identify MG29 as a critical regulator of SOCE and lipid signaling in skeletal muscle and suggest that its age-related decline contributes to sarcopenia by disrupting triad membrane organization and excitation–contraction coupling. Full article

Mitochondria-targeting metal complexes (MTMCs) are a mechanistically distinct class of metallopharmaceuticals. Unlike first-generation platinum drugs that form nuclear DNA adducts, MTMCs exploit organelle-specific vulnerabilities such as hyperpolarised mitochondrial membrane potential (ΔΨm), elevated reactive oxygen species (ROS), limited mitochondrial DNA (mtDNA) repair capacity, and redox-dependent enzymes such as thioredoxin reductase (TrxR). We systematically searched PubMed, Web of Science, Scopus, and Google Scholar databases for studies published between 2016 and 2026, applying predefined inclusion criteria that included subcellular localization evidence and functional bioenergetic endpoints. The search identified 147 studies covering Pt(II/IV), Ru(II/III), Au(I/III), Ir(III), Os(II), Re(I), and V(IV/V) complexes and metal–organic framework nanoplatforms. Mechanistic evidence converges on four intramitochondrial target categories: inhibition of ETC (Electron Transport Chain) Complexes I/III with consequent ATP depletion; ROS overproduction, coupled with glutathione and TrxR depletion; outer mitochondrial membrane permeabilization and intrinsic apoptotic cascade activation; and mtDNA damage within a compartment limited to base excision repair. Multi-modal cell death—the co-occurrence of apoptosis, ferroptosis, necroptosis, and autophagic cell death—was a recurrent finding across the reviewed studies. This review thoroughly surveys the latest trends in MTMC drug design (metals, ligand structures, and mechanisms of action) and summarises analytical techniques for speciation, pharmacokinetics, safe monitoring, and resistance, while critically analysing translational barriers and clinical failures. To address the field’s inconsistent terminology, we introduce an explicit localization evidence hierarchy that distinguishes mitochondria-targeting complexes (through quantitative ICP-MS fractionation or co-localization with defined Pearson/Manders coefficients) from simply mitochondria-localising or mitochondria-perturbing agents, and we apply it throughout. We also point out that the idea of selectivity being purely driven by membrane voltage (ΔΨm) and thermodynamics is constrained by membrane and protein binding, as well as the transmembrane pH gradient, kinetic limitations, and demonstrated heterogeneity of cancer-cell membrane potential, and, as such, the functional mitochondrial effects must not be equated with mitochondrial accumulation. Since elemental quantification cannot distinguish intact complex from protein adducts and decomposition products, speciation-aware pharmacokinetics emerges as a prerequisite for a credible exposure–response interpretation. The translational progress will depend less on new chemotypes than on this analytical and pharmacokinetic rigour, together with organelle-level safety monitoring and biomarker-guided patient selection. Full article

Extracellular vesicles (EVs) are membrane-enclosed nanoparticles that mediate intercellular communication in the immune system by transferring proteins, nucleic acids, and lipids. Their biocompatibility, nanoscale size, and capacity for cell-type-selective delivery have stimulated growing interest in engineering EVs as therapeutic platforms. In this review, we discuss recent advances in EV engineering for immune regulation, focusing on surface display, cellular targeting, and cargo loading strategies. A central concept is that engineered EVs should not be viewed simply as delivery vehicles, but as programmable immune interfaces. EVs can integrate antigen specificity, target-cell recognition, therapeutic cargo delivery, and defined immunostimulatory or tolerogenic signals within a single nanoscale particle. By combining these modular elements, engineered EVs can be designed to direct immune responses in a context-dependent manner. We examine how this principle is being applied to cancer immunotherapy, immune suppression, and antigen-specific tolerance induction, including antigen-presenting EVs, cytotoxic and RNA-loaded EVs, checkpoint-modulatory EVs, MSC-derived EVs, and engineered platforms for autoimmune and inflammatory diseases. We also discuss the clinical translation of engineered EV therapeutics, with emphasis on manufacturing, characterization, potency assays, biodistribution, safety, and regulatory challenges. Together, current advances suggest that programmable EV immune interfaces may provide a versatile foundation for next-generation cancer immunotherapy and antigen-specific immune regulation. Full article

Eosinophils are highly granulated white blood and tissue cells that play complex roles in the immune system including host protection against helminthic parasites, viruses, fungi, and bacteria. These bone marrow-derived cells cause tissue damage in a range of diseases and disorders, particularly in allergy, asthma, and chronic rhinosinusitis with nasal polyps. Eosinophils are recruited to tissues in response to chemotactic signals, and during inflammation, they release a plethora of mediators, including immunoregulatory cytokines, through multiple pathways involving degranulation, respiratory burst, lipid mediator release, exosome release, and extracellular trap formation. Degranulation from eosinophils has been implicated as a major effector mechanism in airway diseases, particularly late phase asthma responses and in nasal polyps from patients with chronic rhinosinusitis. In degranulation responses, eosinophils release numerous granule proteins by classical exocytosis, compound exocytosis, piecemeal degranulation, and cytolysis, which refers to cell lysis through membrane rupture and cell destruction. Cytolysis can lead to suicidal extracellular trap formation, which is a regulated form of cell death involving the release of extracellular DNA traps and granule proteins. Granule release from eosinophils is dependent on activation of specific and tightly regulated intracellular signaling pathways, including Rac and Rab guanosine triphosphatases, soluble NSF attachment protein (SNAP) receptors (SNAREs), Cdk5 kinase, and actin dynamics. These observations have shown selective and nonredundant roles for signaling in degranulation responses. In this review, we explore findings from the literature on the mechanisms controlling granule-derived mediator release from eosinophils. Full article

Background: Cellular senescence is accompanied by mitochondrial dysfunction and decline in type I collagen production, contributing to age-related tissue deterioration. However, the post-transcriptional mechanisms underlying senescence-associated collagen decline remain poorly understood. Methods: Here, we investigated the effects of chlorella hot water extract (CHWE) on mitochondrial function and collagen production in senescent human fibroblasts. Results: CHWE restored mitochondrial membrane potential, ATP production, and redox balance through upregulation of SOD2. Notably, CHWE increased collagen protein levels without altering COL1A1 mRNA, indicating post-transcriptional regulation. miRNA profiling across young, senescent, and CHWE-treated senescent fibroblasts revealed that miR-193a-5p was upregulated during senescence (1.73-fold) and normalized by CHWE treatment. Functional validation confirmed that miR-193a-5p mimic suppressed COL1A1 protein. These findings identify a senescence–miR-193a-5p–COL1A1 axis in which age-dependent miR-193a-5p accumulation represses collagen translation, and CHWE reverses this process. By simultaneously restoring mitochondrial bioenergetic capacity and relieving miRNA-mediated translational repression, CHWE promotes efficient collagen recovery in senescent cells through complementary mechanisms. Conclusions: This study reveals a translational regulatory mechanism of collagen decline during cellular aging and highlights CHWE as a functional food supplement and a potential multi-target agent for age-related tissue deterioration. Full article

The vascular endothelial glycocalyx (EGX) is a gel-like, negatively charged mesh of membrane-bound proteoglycans, glycosaminoglycans, glycoproteins and adsorbed plasma proteins that covers the luminal surface of the endothelium and orchestrates vascular homeostasis through regulation of permeability, leukocyte trafficking, mechanotransduction and anti-thrombotic signalling. Progressive thinning, heterogeneous remodelling and accelerated shedding of the EGX are now recognised as hallmarks of vascular ageing and early drivers of age-related cardiovascular disease. Here, we synthesise current evidence linking EGX integrity to biological ageing, with emphasis on age-dependent remodelling of heparan-sulfate proteoglycans, endothelial progenitor-cell dysfunction, and the heightened susceptibility of the aged EGX to oxidative, inflammatory and infectious insults. We discuss signalling pathways driving EGX shedding—including the IQGAP1/PAR1-2/PI3K/Akt axis—and clinical correlates such as vulnerable coronary plaque in older patients with coronary artery disease and microvascular endotheliopathy in severe COVID-19. Finally, we review emerging anti-ageing strategies targeting the EGX, including direct oral anticoagulants, glycocalyx-mimetic and nitric-oxide-releasing biomaterials, bioinspired antithrombogenic surfaces and microbiome-based modulation, and consider their translational potential for extending cardiovascular healthspan. Full article

Objectives: The ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the current treatment limitations—particularly the emergence of drug resistance and the reduced efficacy of some existing drugs against new variants—highlight the need for novel antiviral strategies with novel action mechanisms. Fusion inhibitors that disrupt six-helix bundle (6-HB) formation during viral entry represent a promising approach. Posaconazole, an antifungal agent, has been identified as a weak fusion inhibitor, but suffers from poor membrane permeability and modest activity. This study aimed to enhance its antiviral potency by conjugating it with cell-penetrating polyarginine peptides and to investigate the mechanism of action. Methods: A series of posaconazole-polyarginine conjugates were synthesized via click chemistry. Antiviral activity was evaluated using pseudotyped SARS-CoV-2 Omicron XDV in HEK293T cells. Mechanisms were investigated by circular dichroism, native PAGE, size-exclusion HPLC, molecular docking, and isothermal titration calorimetry. Metabolic stability was assessed using hepatic microsomes. Results: Posa-R8 exhibited potent antiviral activity comparable to the clinical candidate EK1, with minimal cytotoxicity. Mechanistic studies confirmed that Posa-R8 binds the HR2 region of the spike protein, disrupts 6-HB formation, and inhibits membrane fusion. It also showed strong lipid bilayer affinity and improved phase I metabolic stability over EK1. Conclusions: Polyarginine conjugation enhances the membrane-binding affinity and antiviral efficacy of posaconazole. Posa-R8 represents a promising lead for developing next-generation SARS-CoV-2 fusion inhibitors. Full article

Adsorption therapies in hemodialysis have emerged as an innovative approach for removing protein-bound uremic toxins (PBUTs). The present work focuses on the enhancement of the adsorption capacity of hemodialysis membranes through the incorporation of Metal–Organic Frameworks (MOFs). The removal capacity of PBUT p-cresyl sulfate by cellulose acetate (CA)/silica (SiO₂)/MOF mixed matrix membranes was investigated with two types of MOFs, UiO-66 which synthesis and characterization has been previously reported, and UiO-66-NH₂. The UiO-66-NH₂ MOFs were synthesized and characterized by infrared spectroscopy, X-ray diffraction, nitrogen adsorption–desorption equilibrium at −196 °C, and thermogravimetry analysis. Both mixed matrix membranes were synthesized by coupling the phase inversion technique with the sol–gel method and with casting solutions incorporating the MOF dispersions. The two membrane types of MOFs were characterized in terms of hydraulic permeability, molecular weight cut-off, and rejection coefficients to pCS and bovine serum albumin (BSA). The mixed matrix membranes CA/SiO₂/UiO-66-NH₂ exhibited lower permeability and molecular weight cut-off when compared to the CA/SiO₂/UiO-66 ones. In permeation tests simulating a hemodialysis session with a feed solution of 100 ppm pCS and 35 g/L BSA, it is shown the improved performance of MOFs membranes as the rejection coefficients of free pCS is 0.2% for the CA22/SiO₂/UiO-66 membrane with 1.5% of MOF and 2.6% for the CA22/SiO₂/UiO-66-NH₂ membrane with 2% of MOF. The capacity of these MOF membranes in removing pCS bound to BSA was addressed through the development of a new methodology to quantify the pCS free and bound to BSA. The CA22/SiO₂/UiO-66 membrane with 1.5% of MOF has a removal capacity of 99.8% and the CA22/SiO₂/UiO-66-NH₂ membrane with 2% of MOF 95.9%. Based on these results, it is concluded that the mixed matrix membranes CA22/SiO₂/UiO-66 and CA22/SiO₂/UiO-66-NH₂ are promising candidates for PBUTs removal in hemodialysis. Full article

Sickle cell disease (SCD) is an autosomal recessive hemoglobin disorder that is mainly characterized by the presence of hemoglobin S (HbS; point mutation [Glu6Val] in the beta-globin gene). Under deoxygenated conditions, HbS polymerizes and serves as the primary trigger of oxidative stress in red blood cells (RBCs), promoting polymerization of Band 3, a major membrane scaffold protein that links the lipid bilayer to the spectrin–ankyrin cytoskeletal network. Phosphorylation at key residues within the cytosolic domain of Band 3 induces conformational changes that weaken ankyrin binding and enhance lateral mobility and clustering of Band 3. These effects are mediated through a coordinated network of erythrocyte tyrosine kinases, primarily spleen tyrosine kinase (SYK) and sarcoma (Src) family kinases, which act sequentially to modify distinct tyrosine residues. Structural features of these kinases, including tandem SH2 domains in SYK and conserved SH2–SH3–kinase domain architecture of Src family members, enable precise recognition of phosphotyrosine motifs and propagation of phosphorylation cascades. Sequence alignment and structural superimposition of SH2 domains across studied kinases demonstrate a highly conserved fold that is critical for phosphotyrosine recognition, suggesting potential overlap in substrate engagement. Therapeutically, targeting these kinases has shown considerable promise, as tyrosine kinase inhibitors (TKIs) reduce Band 3 phosphorylation, restore RBC deformability, and decrease hemolysis and vaso-occlusive interactions in vitro. Thus, in this narrative review, we focus on the regulation of Band 3 by the above-mentioned tyrosine kinases, as well as the therapeutic potential of TKIs in SCD. Full article