Search Results (39)

Although blood–brain barrier (BBB) models are of great value in investigating neurological diseases, the structural complexity and intricate function based on cell–cell interactions of the BBB bring various limitations to the applications of existing models. In this study, a novel BBB micro-organoid model was established by culturing neurovascular unit (NVU) cells on a decellularized squid mantle scaffold (DSMS) film to reconstitute a more authentic and reliable NVU microenvironment for in vitro research. The DSMS applied was obtained from squid mantle scaffolds via decellularization, followed by defatting, and showed good biocompatibility with no cytotoxicity. The DSMS film was finally prepared by lyophilization. The lyophilized film exhibited a void ratio and pore size suitable for the adhesion and growth of endothelial cells (hCMEC/D3) and astrocytes (hACs), which led to the formation of a BBB-like spatial structure. The BBB micro-organoid model exhibited functional barrier properties, including an effective transendothelial electrical resistance (TEER) of approximately 230 Ω/cm², restricted permeability to macromolecules—with apparent permeability coefficients (Papp) of 6.3 × 10⁻⁷ cm/s for 10 kDa and 2.7 × 10⁻⁷ cm/s for 70 kDa FITC–dextran—and expression of tight junctional complex (TJC) proteins such as vascular endothelial cadherin (VE-cad) and Zonula Occludens-1 (ZO-1). Furthermore, low-density lipoprotein receptor-related protein 1 (LRP1), a key receptor stably expressed in these two NVU cell types, was utilized as a critical indicator to assess the integrity of the BBB micro-organ model and its responsiveness to pathophysiological stimuli, particularly under thrombotic conditions. This study not only validates the feasibility of constructing a functionally competent BBB micro-organ model using DSMS films integrated with NVU cells but also provides a promising in vitro platform for subsequent studies on the BBB-related pathological mechanisms and the evaluation of drug permeability across the BBB. Full article

The nutritional value of a diet and its bioavailability in fish depend on three primary capacities: (a) ingestion, (b) digestion, and (c) absorption. Among these, digestive capacity, defined here as the total enzyme activity available to hydrolyze the bonds of dietary macromolecules to obtain hydrolysis products that are ultimately converted into absorbable micromolecular units, establishes the upper limit for the bioaccessibility of nutrients. To clarify usage and measurement, we conducted a systematic SCOPUS survey (January 2020–June 2024; 62 relevant articles). Most studies either omit a clear definition of digestive capacity or conflate it with digestive organ morphology or isolated enzyme activities. We compared indicators and assay conditions (substrate type, pH, temperature, and expression of units), revealing significant inter-study variability. Based on this synthesis, we propose four operational definitions: (a) Extract Theoretical Volume (ETV)—calculated volume of extract, considering both the solvent volume (SV) used for tissue homogenization and the tissue’s water content; (b) digestive capacity (U)—the total catalytic activity present in the digestive tract at the moment of sampling, where 1 U is the amount of enzyme catalyzing the formation of 1 µmol of product per minute under species-specific physiological pH, ionic strength, and temperature, with the total activity expressed as U fish⁻¹, U organ⁻¹, or U g⁻¹ fish or U g⁻¹ organ, enabling direct comparisons across studies; (c) Digestive Processing (DP)—the total number of bonds hydrolyzed during a given digestion time, whether instantaneous or over a defined period; and (d) Digestive Processing Index (DPI, U-min or U-h), which integrates digestive capacity over time. This framework provides a harmonized checklist for assay standardization and advances comparative studies in fish digestive physiology. Full article

The core perturbome is defined as a central response to multiple disturbances, functioning as a complex molecular network to overcome the disruption of homeostasis under stress conditions, thereby promoting tolerance and survival under stress conditions. Based on the biological and clinical relevance of Escherichia coli and Staphylococcus aureus, we characterized their molecular responses to multiple perturbations. Gene expression data from E. coli (8815 target genes—based on a pangenome—across 132 samples) and S. aureus (3312 target genes across 156 samples) were used. Accordingly, this study aimed to identify and describe the functionality of the core perturbome of these two prokaryotic models using a machine learning approach. For this purpose, feature selection and classification algorithms (KNN, RF and SVM) were implemented to identify a subset of genes as core molecular signatures, distinguishing control and perturbation conditions. After verifying effective dimensional reduction (with median accuracies of 82.6% and 85.1% for E. coli and S. aureus, respectively), a model of molecular interactions and functional enrichment analyses was performed to characterize the selected genes. The core perturbome was composed of 55 genes (including nine hubs) for E. coli and 46 (eight hubs) for S. aureus. Well-defined interactomes were predicted for each model, which are jointly associated with enriched pathways, including energy and macromolecule metabolism, DNA/RNA and protein synthesis and degradation, transcription regulation, virulence factors, and other signaling processes. Taken together, these results may support the identification of potential therapeutic targets and biomarkers of stress responses in future studies. Full article

The fine regulation of antioxidant systems and intracellular production of reactive oxygen species (ROS) is responsible for cellular redox balance. The main organelles responsible for ROS production are mitochondria, and they complete this process through the electron transport chain. These potentially harmful molecules are buffered by enzymatic and non-enzymatic antioxidant systems. Oxidative stress is determined by an imbalance between the production and clearance of ROS in favor of the accumulation of these detrimental species, which generate cellular damage by interacting with macromolecules. In neurodegenerative diseases, oxidative stress has been demonstrated to be a crucial component, both causal and consequential to the disease itself. On the other hand, neurodegeneration disrupts neuromuscular junctions, leading to reduced muscle use and subsequent atrophy. Additionally, systemic inflammation and metabolic dysfunction associated with neurodegenerative diseases exacerbate muscle degeneration. Thus, sarcopenia and atrophy are common consequences of neurodegeneration and play a significant role in these disorders. Regarding this, ROS have been defined as promoting sarcopenia, stimulating the expression of genes typical of this condition. Overall, this review aims to contribute to filling the gap in the literature regarding the consequences at the muscular level of the relationship between oxidative stress and neurodegenerative diseases. Full article

Seed shattering (SS) functions are a survival mechanism in plants, enabling them to withstand adverse environmental conditions and ensure reproduction. However, this trait limits seed yield. Psathyrostachys juncea, a perennial forage grass with many favorable traits, is constrained by SS, limiting its broader application. To investigate the mechanisms underlying SS, second-generation Illumina sequencing and third-generation PacBio sequencing were conducted on abscission zone tissues of P. juncea at 7, 14, 21, and 28 days after heading. GO enrichment analysis identified several significant biological processes, including the “cell wall macromolecule catabolic process”, “cell wall polysaccharide catabolic process”, “hemicellulose catabolic process”, and “xylan catabolic process”, all involved in cell wall degradation. KEGG enrichment analysis showed that differentially expressed genes were predominantly enriched in pathways related to “starch and sucrose metabolism”, “fructose and mannose metabolism”, “phenylpropanoid biosynthesis”, “pentose and glucuronate interconversions”, and “galactose metabolism”, each linked to both the synthesis and degradation of the cell wall. Further analysis of the “starch and sucrose metabolism” pathway revealed genes encoding fructokinase, hexokinase, β-glucosidase, sucrose phosphate synthase, sucrose synthase, and endoglucanase, all of which affected cellulose content. Reduced cellulose content can alter cell wall structure, leading to SS. These findings provide new insights into the regulation of SS in P. juncea and offer valuable references for other species within the Poaceae family. Full article

Glucose-dependent insulinotropic polypeptide (GIP) of the incretin group has been shown to exert pleiotropic actions. There is growing evidence that advanced glycation end products (AGEs), senescent macromolecules formed at an accelerated rate under chronic hyperglycemic conditions, play a role in the pathogenesis of atherosclerotic cardiovascular disease in diabetes. However, whether and how GIP could inhibit the AGE-induced foam cell formation of macrophages, an initial step of atherosclerosis remains to be elucidated. In this study, we address these issues. We found that AGEs increased oxidized low-density-lipoprotein uptake into reactive oxygen species (ROS) generation and Cdk5 and CD36 gene expressions in human U937 macrophages, all of which were significantly blocked by [D-Ala²]GIP(1–42) or an inhibitor of NADPH oxidase activity. An inhibitor of AMP-activated protein kinase (AMPK) attenuated all of the beneficial effects of [D-Ala²]GIP(1–42) on AGE-exposed U937 macrophages, whereas an activator of AMPK mimicked the effects of [D-Ala²]GIP(1–42) on foam cell formation, ROS generation, and Cdk5 and CD36 gene expressions in macrophages. The present study suggests that [D-Ala²]GIP(1–42) could inhibit the AGE-RAGE-induced, NADPH oxidase-derived oxidative stress generation in U937 macrophages via AMPK activation and subsequently suppress macrophage foam cell formation by reducing the Cdk5-CD36 pathway. Full article

Pulsed electric field (PEF) is an up-to-date non-thermal processing technology with a wide range of applications in the food industry. The inactivation effect of PEF on Escherichia coli was different under different conditions. The E. coli inactivated number was 1.13 ± 0.01 lg CFU/mL when PEF was treated for 60 min and treated with 0.24 kV/cm. The treatment times were found to be positively correlated with the inactivation effect of PEF, and the number of E. coli was reduced by 3.09 ± 0.01 lg CFU/mL after 100 min of treatment. The inactivation assays showed that E. coli was inactivated at electrical intensity (0.24 kV/cm) within 100 min, providing an effective inactivating outcome for Gram-negative bacteria. The purpose of this work was to investigate the cellular level (morphological destruction, intracellular macromolecule damage, intracellular enzyme inactivation) as well as the molecular level via transcriptome analysis. Field Emission Scanning Electron Microscopy (TFESEM) and Transmission Electron Microscope (TEM) results demonstrated that cell permeability was disrupted after PEF treatment. Entocytes, including proteins and DNA, were markedly reduced after PEF treatment. In addition, the activities of Pyruvate Kinase (PK), Succinate Dehydrogenase (SDH), and Adenosine Triphosphatase (ATPase) were inhibited remarkably for PEF-treated samples. Transcriptome sequencing results showed that differentially expressed genes (DEGs) related to the biosynthesis of the cell membrane, DNA replication and repair, energy metabolism, and mobility were significantly affected. In conclusion, membrane damage, energy metabolism disruption, and other pathways are important mechanisms of PEF’s inhibitory effect on E. coli. Full article

Dupuytren’s disease (DD) is a prevalent fibroproliferative disorder of the hand, shaped by genetic, epigenetic, and environmental influences. The extracellular matrix (ECM) is a complex assembly of diverse macromolecules. Alterations in the ECM’s content, structure and organization can impact both normal physiological functions and pathological conditions. This study explored the content and organization of glycosaminoglycans, proteoglycans, and collagen in the ECM of patients at various stages of DD, assessing their potential as prognostic indicators. This research reveals, for the first time, relevant changes in the complexity of chondroitin/dermatan sulfate structures, specifically an increase of disaccharides containing iduronic acid residues covalently linked to either N-acetylgalactosamine 6-O-sulfated or N-acetylgalactosamine 4-O-sulfated, correlating with the disease’s severity. Additionally, we noted an increase in versican expression, a high molecular weight proteoglycan, across stages I to IV, while decorin, a small leucine-rich proteoglycan, significantly diminishes as DD progresses, both confirmed by mRNA analysis and protein detection via confocal microscopy. Coherent anti-Stokes Raman scattering (CARS) microscopy further demonstrated that collagen fibril architecture in DD varies importantly with disease stages. Moreover, the urinary excretion of both hyaluronic and sulfated glycosaminoglycans markedly decreased among DD patients.Our findings indicate that specific proteoglycans with galactosaminoglycan chains and collagen arrangements could serve as biomarkers for DD progression. The reduction in glycosaminoglycan excretion suggests a systemic manifestation of the disease. Full article

The eukaryotic microalga Nannochloropsis oceanica represents a promising bioresource for the production of biofuels and pharmaceuticals. Urea, a crucial nutrient for the photosynthetic N. oceanica, stimulates the accumulation of substances such as lipids, which influence growth and physiology. However, the specific mechanisms by which N. oceanica responds and adapts to urea addition remain unknown. High-throughput mRNA sequencing and differential gene expression analysis under control and urea-added conditions revealed significant metabolic changes. This involved the differential expression of 2104 genes, with 1354 being upregulated and 750 downregulated, resulting in the reprogramming of crucial pathways such as carbon and nitrogen metabolism, photosynthesis, and lipid metabolism. The results specifically showed that genes associated with photosynthesis in N. oceanica were significantly downregulated, particularly those related to light-harvesting proteins. Interestingly, urea absorption and transport may depend not only on specialized transport channels such as urease but also on alternative transport channels such as the ABC transporter family and the CLC protein family. In addition, urea caused specific changes in carbon and lipid metabolism. Genes associated with the Calvin cycle and carbon concentration mechanisms were significantly upregulated. In lipid metabolism, the expression of genes associated with lipases and polyunsaturated fatty acid synthesis was highly activated. Furthermore, the expression of several genes involved in the tricarboxylic acid cycle and folate metabolism was enhanced, making important contributions to energy supply and the synthesis and modification of genes and macromolecules. Our observations indicate that N. oceanica actively and dynamically regulates the redistribution of carbon and nitrogen after urea addition, providing references for further research on the effects of urea on N. oceanica. Full article

The extracellular matrix (ECM) is a complex three-dimensional network of macromolecules that provides structural support for the cells and plays a significant role in tissue homeostasis and repair. Growing evidence indicates that dysregulation of ECM remodeling contributes to various pathological conditions in the body, including age-associated diseases. In this work, gene expression data of normal human tissues obtained from the Genotype-Tissue Expression project, as well as data from MatrisomeDB 2.0, the ECM-protein knowledge database, are used to estimate the age-dependent matrisome transcriptome dynamics in the blood, heart, brain, liver, kidneys, lungs, and muscle. Differential gene expression (DE) analysis revealed dozens of matrisome genes encoding both structural elements of the ECM and ECM-associated proteins, which had a tissue-specific expression profile with age. Among common DE genes that changed expression with age in at least three tissues, COL18A1, MFAP1, IGFBP7, AEBP1, LTBP2, LTBP4, LG14, EFEMP1, PRELP, BGN, FAM20B, CTSC, CTSS, and CLEC2B were observed. The findings of the study also reveal that there are sex-specific alterations during aging in the matrisome gene expression. Taken together, the results obtained in this work may help in understanding the role of the ECM in tissue aging and might prove valuable for the future development of the field of ECM research in general. Full article

Respiratory viruses are the causative agents responsible for seasonal epidemics and occasional pandemic outbreaks and are a leading cause of death worldwide. Type I interferon (IFNα/β) signaling in the lung epithelial cells plays a major role in the innate immunity to respiratory viruses. Gene signatures are a set of differentially expressed genes in a particular disease or condition and are used to diagnose, monitor, and predict disease progression. These signatures can be used to identify regulatory modules and gene regulatory networks (GRNs) in mammalian signal transduction pathways. Considerable progress has been made in the identification of type I interferon-regulated gene signatures in the host response to respiratory viruses, including antiviral, immunomodulatory, apoptosis, and transcription factor signatures. Respiratory virus infections and host defenses require a dramatic change in the metabolic flux of macromolecules involved in nucleotide, lipid, and protein metabolism. The profiling of IFN-stimulated metabolic genes induced in the host response to several respiratory viruses led to the identification of a common gene signature in human lung epithelial cells and in the lungs of mouse models of respiratory virus infection. The regulation of the metabolic gene signature was correlated with the induction of IFN-beta (IFN-β) and IFN-inducible transcription factors at the RNA level in lung epithelial cells. Furthermore, the gene signature was also detected in response to bacterial lipopolysaccharide-induced acute lung injury. A protein interaction network analysis revealed that metabolic enzymes interact with IFN-regulated transcription factors and members of the unfolded protein response (UPR) to form a module and potentially regulate type I interferon signaling, constituting a feedback loop. In addition, components of the metabolic gene expression signature were differentially regulated in the lung tissues of COVID-19 patients compared with healthy controls. These results suggest that the metabolic gene signature is a potential therapeutic target for the treatment of respiratory virus infections and inflammatory diseases. Full article

The soluble urokinase plasminogen activator receptor (suPAR) has been implicated in a wide range of pathological conditions including primary nephrotic syndromes and acute kidney injuries. suPAR can trigger transduction cascades in podocytes by outside-in activation of αVβ3-integrin, but there is evidence that the functional cell surface response element is actually a complex of different types of receptors, which may also include the receptor for advanced glycation end-products (RAGE) and formyl peptide receptors (FPRs). Here we observed that ROS accumulation and Src activation could be evoked by continuous 24 h exposure to either suPAR or the FPR agonist fMLF. Responses to suPAR and fMLF were completely blocked by either the FPR antagonist WRW4 or by the αV-integrin inhibitor cilengitide. Moreover, endogenous podocyte mouse Fpr1 co-immunoprecipitates with β3-integrin, suggesting that these receptors occur as a complex on the cell surface. suPAR- and fMLF-evoked activation of Src and ROS differed in time course. Thus, robust pertussis toxin (PTX)-sensitive responses were evoked by 60 min exposures to fMLF but not to suPAR. By contrast, responses to 24 h exposures to either suPAR or fMLF were PTX-resistant and were instead abolished by knockdown of β-arrestin-1 (BAR1). FPRs, integrins, and RAGE (along with various Toll-like receptors) can all function as pattern-recognition receptors that respond to “danger signals” associated with infections and tissue injury. The fact that podocytes express such a wide array of pattern-recognition receptors suggests that the glomerular filter is designed to change its function under certain conditions, possibly to facilitate clearance of toxic macromolecules. Full article

A significant number of discoveries in past two decades have established the importance of long-distance signaling in controlling plant growth, development, and biotic and abiotic stress responses. Numerous mobile signals, such as mRNAs, proteins, including RNA-binding proteins, small RNAs, sugars, and phytohormones, are shown to regulate various agronomic traits such as flowering, fruit, seed development, and tuberization. Potato is a classic model tuber crop, and several mobile signals are known to govern tuber development. However, it is unknown if these mobile signals have any synergistic effects on potato crop improvement. Here, we employed a simple innovative strategy to test the cumulative effects of a key mobile RNA, StBEL5, and its RNA-binding proteins, StPTB1, and -6 on tuber productivity of two potato cultivars, Solanum tuberosum cv. Désirée and subspecies andigena, using a multi-gene stacking approach. In this approach, the coding sequences of StBEL5 and StPTB1/6 are driven by their respective native promoters to efficiently achieve targeted expression in phloem for monitoring tuber productivity. We demonstrate that this strategy resulted in earliness for tuberization and enhanced tuber productivity by 2–4 folds under growth chamber, greenhouse, and field conditions. This multi-gene stacking approach could be adopted to other crops, whose agronomic traits are governed by mobile macromolecules, expanding the possibilities to develop crops with improved traits and enhanced yields. Full article

Bisphenol A (BPA) is an environmental toxin widely used in the production of polycarbonate plastics. A correlation exists between BPA tissue contamination and the occurrence of pathological conditions, including cancer. First-passage detoxification of high BPA amounts in the liver promotes hepatotoxicity and morphological alterations of this organ, but there is a lack of knowledge about the molecular mechanisms underlying these phenomena. This prompted us to investigate changes in the liver transcriptomics of 3-month-old female mice exposed to BPA (50 mg/kg) in drinking water for 3 months. Five female mice served as controls. The animals were euthanized, the livers were collected, and RNA was extracted to perform RNA-seq analysis. The multistep transcriptomic bioinformatics revealed 120 differentially expressed genes (DEGs) in the BPA-exposed samples. Gene Ontology (GO) annotations indicated that DEGs have been assigned to many biological processes, including “macromolecule modification” and “protein metabolic process”. Several of the revealed DEGs have been linked to the pathogenesis of severe metabolic liver disorders and malignant tumors, in particular hepatocellular carcinoma. Data from this study suggest that BPA has a significant impact on gene expression in the liver, which is predictive of the carcinogenic potential of this compound in this organ. Full article

Oxidative stress is a physiological condition that arises when there is an imbalance between the production of reactive oxygen species (ROS) and the ability of cells to neutralize them. ROS can damage cellular macromolecules, including lipids, proteins, and DNA, leading to cellular senescence and physiological aging. The nuclear lamina (NL) is a meshwork of intermediate filaments that provides structural support to the nucleus and plays crucial roles in various nuclear functions, such as DNA replication and transcription. Emerging evidence suggests that oxidative stress disrupts the integrity and function of the NL, leading to dysregulation of gene expression, DNA damage, and cellular senescence. This review highlights the current understanding of the interplay between oxidative stress and the NL, along with its implications for human health. Specifically, elucidation of the mechanisms underlying the interplay between oxidative stress and the NL is essential for the development of effective treatments for laminopathies and age-related diseases. Full article