Search Results (11,766)

Background/Objectives: Lactic acid bacteria have long been recognized as pivotal microorganisms in food fermentation and health promotion. However, their significance has recently grown due to innovative applications in various fields, particularly at the intersection of biotechnology and nanotechnology. This study aimed to provide a comprehensive overview of these emerging applications. Methods: The latest scientific literature was drawn from online databases and thoroughly reviewed. The new nomenclature system based on the post-2020 reclassification was used for reports. Results: The current study highlighted the evolving role of lactic acid bacteria, beyond their traditional use as starter cultures for food fermentation, in newer challenges, including the production of high-value bioactive compounds through bioprocessing under optimal conditions to enhance the yield, underlining the involved genes and pathways. Furthermore, this review addressed the beneficial effects of lactic acid bacteria as probiotics, postbiotics, and paraprobiotics in the treatment of various diseases and disorders, their application in the production of functional foods, and the encapsulation of their bioproducts to produce advanced health-promoting functional ingredients. The potential use of lactic acid bacteria to synthesize metallic nanoparticles, minicells, and carbon dots was also explored, promising significant advancements in nanomedicine. Conclusions: This review could open a new horizon for leveraging the potential of lactic acid bacteria in biotechnology, food science, and nanomedicine. The multilateral perspective offered here would provide a foundation for future research and development to exploit the capabilities of lactic acid bacteria across these innovative fields. Full article

Liver cirrhosis (LC) is a complex pathological condition characterized by extensive transcriptomic reprogramming, yet the regulatory role of non-coding RNAs in disease progression remains poorly understood. This study aimed to systematically investigate long non-coding RNA (lncRNA)-messenger RNA (mRNA) interaction networks in LC through weighted gene co-expression network analysis (WGCNA). Gene expression profiles from datasets GSE197406, GSE107170, and GSE17548 were retrieved from the Gene Expression Omnibus (GEO) database, and differentially expressed lncRNAs and mRNAs were identified. Co-expression modules were constructed using WGCNA. Furthermore, functional enrichment analyses were conducted and drug repurposing opportunities were evaluated. Additionally, lncRNA-mRNA co-expression networks and lncRNA-mRNA-pathway networks were constructed to identify key regulatory relationships. Molecular docking simulations were subsequently performed to validate potential drug–target interactions. The results revealed several co-expression modules significantly associated with LC, particularly the turquoise module (r = 0.81). Genes within this module were enriched in several biological pathways, including the PI3K-Akt signaling pathway, NF-κB signaling pathway, and chemokine signaling pathway. The hub lncRNA in the turquoise module, NONHSAT134945.2, was found to be co-expressed with mRNAs involved in inflammasome-mediated pyroptosis and hepatocyte activation, such as CSF1R, HCK, and CASP1. Based on this hub gene signature, AB-1010, GW768505A, and Dasatinib were identified as potential therapeutic candidates. Molecular docking analysis confirmed that these compounds exhibit high binding affinity to CSF1R and HCK, with all interatomic distances maintained below 3.5 Å. These findings provide new insights into the molecular mechanisms underlying LC and suggest that the NONHSAT134945.2–CSF1R/HCK axis may serve as a valuable target for future translational research and therapeutic development. Full article

Nitrite is a common toxic substance in aquaculture, and microplastics are environmental pollutants capable of adsorbing small molecules/particles. Shrimp rely mainly on the hepatopancreas to accomplish detoxification metabolism. In this study, we investigated the individual and combined effects of nitrite and microplastics on the physiological function of the P. vannamei hepatopancreas. The results demonstrated that both nitrite and microplastics induced morphological damage, with the combined stress exacerbating tissue damage. Oxidative stress biochemical indicators were disrupted, and most enzyme activities and gene expression levels were upregulated to varying degrees in each experimental group. The expression levels of immune genes (cytC, CASP-3, Crus, ALF, and proPO), detoxification metabolism genes (CYP450, EH1, SULT, and UGT), and oxidative-stress-related genes (ROMO1, SOD, GPx, and Trx) exhibited different fluctuations. Nitrite and microplastic stress resulted in altered hepatopancreatic function, mainly involving amino acid biosynthesis and metabolism, ABC transporters, oxidative phosphorylation, and the mTOR pathway. We identified 17 metabolic biomarkers, including 6 lipids (Oleic acid, Prostaglandin G2, Linoleic acid, Palmitic acid, Docosahexaenoic acid, Docosapentaenoic acid), 6 amino acids (L-Leucine, Agmatine, L-Arginine, L-Tyrosine, Ornithine, N-Acetylornithine), and 5 carbohydrates (Glyceric acid, Citric acid, D-Mannose, Sorbitol, Fumaric acid). These findings suggest that nitrite and microplastic stresses cause hepatopancreatic tissue damage and induce oxidative stress, physiological and metabolic dysfunction in the shrimp P. vannamei, thereby impacting its normal physiological functions. Full article

Drug resistance is an important challenge in medical research and clinical practice, posing a serious threat to the effectiveness of current therapeutic strategies. Transcriptomics has played a crucial role in analyzing resistance-related genes and pathways, while the application of machine learning in high-throughput data analysis and prediction has also opened up new avenues in this field. However, existing studies mostly focus on a single drug or specific categories, and their conclusions are limited in applicability across drug categories, while studies on drugs beyond antibacterial and antitumor categories remain limited. In this study, we systematically analyzed the transcriptomic data of resistant cell lines treated with 1738 drugs spanning 82 categories and identified core genes through an integrated analysis of three classical machine learning methods. Using the antibacterial drug salinomycin as an example, we established a resistance prediction model that demonstrated high predictive accuracy, indicating the significant value of the selected core genes in prediction. Meanwhile, some of the core genes identified through the protein–protein interaction (PPI) network overlapped with those derived from machine learning analysis, further supporting the reliability of these core genes. Pathway enrichment analysis of differential genes revealed potential resistance mechanisms. This study provides a new perspective for exploring resistance mechanisms across drug categories and highlights potential directions for resistance intervention strategies and novel drug development. Full article

Waterlily (Nymphaea L.), a globally renowned aquatic ornamental plant, is prized for its aesthetic flowers and intense floral fragrance. However, the molecular mechanisms underlying floral scent biosynthesis in waterlily remain poorly characterized, and integrated analyses of dynamic volatile emission patterns and their associated biosynthetic pathways are lacking. In this study, we combined headspace solid-phase microextraction/gas chromatography–mass spectrometry (HS-SPME/GC-MS) with transcriptome sequencing (RNA-seq) to investigate the composition, emission dynamics, and biosynthesis of volatile organic compounds (VOCs) in the stamens of Nymphaea ‘Paul Stetson’ across three developmental stages. A total of 671 VOCs, classified into 14 categories, were identified. Transcriptome analysis revealed 47,951 differentially expressed genes (DEGs). Integrative omics analysis demonstrated correlated DEGs and differentially accumulated volatiles were significantly enriched in pathways related to phenylpropanoid biosynthesis, terpenoid backbone biosynthesis, diterpenoid biosynthesis, and ubiquinone/other terpenoid-quinone biosynthesis. Five candidate functional genes exhibiting strong positive correlations with VOC accumulation levels were identified, three of which are implicated in terpenoid biosynthesis. These findings provide a theoretical foundation for elucidating aroma composition and biosynthesis in waterlily and offer novel avenues for the genetic improvement of fragrance traits for ornamental, beverage, and cosmetic applications. Full article

This study systematically characterized functional compartmentalization along the intestinal tract of New Zealand rabbits by analyzing mucosal tissue and luminal contents from distinct segments, including the duodenum, jejunum, ileum, cecum, and colon, using RNA-seq and 16S rRNA sequencing. Transcriptomic analysis revealed that differentially expressed genes identified between the small and large intestines were mainly enriched in digestion, absorption, and immune functions. Genes associated with the transport of amino acids, sugars, vitamins, and bile salts showed significantly higher expression in the small intestine, whereas genes related to water absorption, short-chain fatty acids (SCFAs), nucleotides, and metal ion transport were preferentially expressed in the large intestine. From an immunological perspective, genes involved in fungal responses were enriched in the small intestine, while bacterial response pathways and pattern recognition receptor (PRR) signaling genes were upregulated in the large intestine. Microbiota analysis demonstrated significantly greater diversity and abundance in the large intestine compared with the small intestine. Specifically, Proteobacteria and Actinobacteria were enriched in the small intestine, whereas Firmicutes, Verrucomicrobia, and Bacteroidetes dominated the large intestine. Correlation analysis further identified significant associations between gut microbiota composition and host genes involved in nutrient digestion and absorption. Together, these findings provide transcriptome-based evidence for regional specialization of nutrient transport, immune responses, and microbial ecology along the rabbit intestine. Full article

DNMT1 variants are linked to complex neurodegenerative syndromes, yet their variant-specific functional and epigenomic consequences remain poorly defined. DNMT1 variants were identified in eight patients using gene-panel or whole-exome sequencing. Functional effects were assessed by site-directed mutagenesis and transient expression in HEK293T cells. Genome-wide methylation profiling of peripheral blood leukocyte DNA was performed using Nanopore sequencing, enabling direct quantification of 5-methylcytosine (5mC). CpG island-level differential methylation and gene set enrichment analysis (GSEA) were conducted. Variants in the replication foci targeting sequence (RFTS) domain (p.Y511H, p.Y540C, p.H569R) exhibited reduced DNMT1 protein expression, decreased enzymatic activity, and cytosolic aggregation. Variants in the C-terminal catalytic domain (p.A1334V and p.P1546S) showed reduced protein expression with relatively mild enzymatic impairment. Patients carrying the p.Y511H variant demonstrated a significant reduction in global 5mC levels compared with controls. Principal component analysis revealed distinct methylomic profiles separating most patients from controls, with marked intra- and inter-familial heterogeneity. CpG island-level analysis identified a single significantly hypomethylated region in p.Y511H carriers, and GSEA revealed differential enrichment of multiple Gene Ontology biological pathways. This study defines domain-dependent functional effects of DNMT1 variants and provides the first nanopore-based methylome analysis, revealing variant-specific and heterogeneous epigenomic alterations. Full article

Background/Objectives: Neuroblastoma cells are phenotypically plastic, transitioning between mesenchymal and adrenergic states. Core functional genes (e.g., YAP1) mark the mesenchymal state, which is linked to unfavorable prognosis. We and others previously demonstrated relapse-specific Hippo-YAP pathway activation in matched primary/relapsed neuroblastomas. Here we explored the role of YAP1 in neuroblastoma aggressiveness and response to therapy. Methods: RT-qPCR and immunoblotting assessed YAP1 expression in neuroblastoma cell lines. RNA-sequencing detected YAP1-dependent gene signatures in Tet-ON SK-N-AS and SH-EP neuroblastoma cell models expressing wildtype YAP1 or constitutively activated YAP1^S127A. Data from cell models were compared with our published YAP1 expression data from neuroblastomas. Efficacy of commonly used chemotherapeutics was comparatively analyzed in the cell models. Results: YAP1 expression showed marked variability across a panel of neuroblastoma cell lines, assessed by mRNA analysis in 10 cell lines and protein analysis in a subset of 9 cell lines. RNA sequencing in constitutively activated YAP1^S127A mutant and wildtype YAP1 models detected 2162 and 1837 significantly differentially expressed genes in the SK-N-AS and SH-EP backgrounds, respectively. Continuously activating YAP1 in SK-N-AS cells upregulated mesenchymal signature genes and mesenchymal-associated transcription factors. Gene expression influenced by YAP1 activity in the cell models significantly overlapped with YAP1-associated genes (e.g., CYR61 and SPRY4) in published tumor data. Functionally, YAP1^S127A expression rendered neuroblastoma cells resistant to chemotherapy. Conclusions: Findings corroborate the idea of a mechanistic role for YAP1 in neuroblastoma adrenergic to mesenchymal reprogramming and therapy resistance. The YAP1-mediated plastic switch towards a mesenchymal expression state in neuroblastoma cells may provide the molecular basis for novel therapeutic avenues. Full article

Sexual size dimorphism (SSD) refers to the phenomenon where males and females of the same species exhibit differences in overall or partial body size, and it is widespread among mammals, birds, reptiles, and fish. Notably, this dimorphism is significantly influenced by the sexually dimorphic secretion of growth hormone (gh), a key pituitary-derived growth regulator. Commonly, the secretion of gh is positively regulated by glucagon family members such as growth hormone-releasing hormone (ghrh) and adenylate cyclase-activating polypeptide 1 (adcyap1). To explore the stimulators for pituitary hormones (especially gh) in the teleost, we performed genome-wide identification and functional characterization of the glucagon family on Chinese tongue sole (Cynoglossus semilaevis) that exhibits typical female-biased sexual size dimorphism. Four members of adcyap1/vasoactive intestinal polypeptide(vip)/ghrh family and ten members of their receptor family were identified. Expression pattern analysis revealed high expression of adenylate cyclase-activating polypeptide 1b (adcyap1b) and its receptors in the brain. Moreover, two alternative splice variants for the adcyap1b gene were discovered, resulting from the skipping of exon 4. Following the acquisition of the two eukaryotic recombinant protein splice variants (ADCYAP1b_tv1 and ADCYAP_tv2) from HEK 293T cells, incubation experiments were conducted using C. semilaevis pituitary cell line. The results demonstrated that both variants promoted the expression of gh, pro-opiomelanocortin (pomc), and corticoliberin (crh), but ADCYAP1b_tv1 had a significantly stronger effect and uniquely stimulated prolactin (prl) and somatolactin (sl). This study demonstrates a functional divergence between the two ADCYAP1b splice variants in teleosts, with ADCYAP1b_tv1 acting as a more potent and versatile pituitary hormone stimulator. Further research on their receptor-binding affinity and downstream signaling pathways would be valuable for exploring the mechanism underlying sexual size dimorphism. Full article

Background: The ACE Y215C mutation is a common, functionally damaging missense variant (~1.5% allele frequency) associated with reduced plasma ACE levels and increased Alzheimer’s disease (AD) risk. In CHO and HEK cell models, this mutation caused a ~3–6-fold decrease in ACE surface expression, soluble ACE levels, and ACE enzymatic activity compared to those of wild-type ACE. Methods: Circulating ACE levels and activity were measured in EDTA plasma obtained from 84 carriers of the ACE Y215C mutation using a set of mAbs to the ACE. The mAbs 5B3/1G12 binding ratio was revealed as a sensitive marker for the circulating Y215C ACE mutant. Whole-exome and whole-genome sequencing (WES/WGS) were performed to identify genetic variants potentially modifying circulating ACE levels. In parallel, published sequencing and proteomic data from 35,559 Icelanders participants were analyzed to identify genes influencing ACE shedding. Sequence comparison was performed between carriers with elevated and reduced ACE concentrations to identify the potential protective variants that may compensate for decreased ACE levels due to the Y215C mutation itself. Results: Most carriers of the Y215C ACE mutation demonstrated significantly decreased ACE levels (median is 62% of control ACE levels). However, substantial inter-individual variability was observed in plasma ACE activity among carriers. Comparative sequencing analysis revealed 9648 variants unique to individuals with elevated ACE, mapping to 5779 protein-coding genes and enriched for pathways related to intracellular and transmembrane transport. Conclusions: The presence of the damaging ACE mutation Y215C does not invariably result in low plasma ACE or, likely, elevated AD risk. Therefore, combined blood ACE phenotyping and whole-exome sequencing are recommended to more accurately assess ACE-related AD susceptibility in mutation carriers. Full article

Fabry disease is an X-linked lysosomal storage disorder caused by mutations in the GLA gene, leading to α-galactosidase A deficiency, accumulation of globotriaosylceramide (Gb3), and progressive multiorgan involvement. Increasing evidence indicates that oxidative stress plays a central role in disease pathogenesis. This review aims to synthesize current knowledge on the molecular mechanisms underlying oxidative stress, the relevance of oxidative damage biomarkers, and potential therapeutic implications. A comprehensive literature search was conducted in PubMed/MEDLINE, Scopus, Web of Science, and Google Scholar using terms related to Fabry disease, Gb3 metabolism, mitochondrial and endothelial dysfunction, inflammatory signaling, and oxidative stress markers. Clinical, experimental, and translational studies were included. Available data demonstrate that Gb3 accumulation disrupts mitochondrial function and activates NADPH oxidase, NF-κB, and MAPK signaling pathways, resulting in excessive production of reactive oxygen species. These processes contribute to cellular injury, particularly within the cardiovascular, renal, and nervous systems. Biomarkers such as malondialdehyde, 8-hydroxy-2′-deoxyguanosine, glutathione redox status, and antioxidant enzyme activities appear useful for assessing oxidative burden and monitoring therapeutic responses. Overall, current evidence underscores the pivotal role of oxidative stress in the progression of Fabry disease and highlights the need for further research into targeted antioxidant and disease-modifying therapeutic strategies. Full article

There is increasing evidence that exposure to environmental toxicants may impact fertility, especially during critical windows of reproductive axis development. Hypothalamic gonadotropin-releasing hormone (GnRH) neurons, essential for puberty onset and fertility, originate from the olfactory placode and migrate toward the hypothalamus during development, making them particularly vulnerable to environmental insults. Cadmium (Cd), a widespread heavy metal, is well known for its gonadotoxicity, but its impact on human hypothalamic neuron development remains unclear. Using human fetal GnRH neuroblasts (FNCB4) we investigated the effects of Cd exposure on their morpho-functional and developmental features. Cd induced oxidative stress and COX2 mRNA upregulation, indicative of inflammatory pathway activation, which was accompanied by reduced cell migration and downregulation of motility-related genes. These effects were associated with F-actin disassembly and altered expression of adhesion molecules. Electrophysiological analyses showed that Cd altered membrane potential, increased capacitance and permeability, and disrupted gap junctional communication, as also confirmed by connexin-43 delocalization. Moreover, Cd significantly reduced the expression of specific GnRH neuronal markers, suggesting impaired functional maturation. Overall, our findings provide the first evidence that Cd may interfere with mechanisms crucially involved in human GnRH neuron development, adding new mechanistic insights into the comprehension of how early-life exposure to Cd may contribute to fertility concerns. Full article

Insulin is an anabolic hormone involved in the regulation of several processes, such as the storage of glucose into glycogen, decrease of glucose output, stimulation of glucose transport into cells, etc. The hormone binds to its receptor, thereby activating an intracellular signaling cascade. Once activated, the insulin receptor (INSR) phosphorylates multiple intracellular substrates, which initiate the downstream signaling pathway. The nature of insulin signaling pathways may vary depending on the organ or tissue. In the central nervous system (CNS), INSRs are expressed in all cell types. This observation may suggest that insulin signaling is involved in important and diverse processes. It regulates glucose metabolism, supports cognitive functions, enhances the outgrowth of neurons, as well as plays a role in the modulation of release and uptake of catecholamine, among other roles. Importantly, insulin can freely cross the blood–brain barrier (BBB) from the circulation and is also synthesized locally within the brain. Insulin resistance (IR) impairs insulin signaling, which may accelerate brain aging, affect plasticity, and potentially contribute to neurodegeneration. Dysregulation of insulin signaling has been implicated in several diseases, including diabetes mellitus, metabolic syndrome, certain cancers, and neurodegenerative diseases, such as Alzheimer’s disease. There are two principal insulin signaling pathways: the PI3K/AKT pathway, primarily associated with metabolic effects, and the MAPK pathway, which is involved in cell growth, survival, and gene expression. Our review describes the role of insulin in the human brain, as well as the disturbances in insulin signaling resulting from brain insulin resistance, with a particular focus on its association with Alzheimer’s disease. Full article

Background/Objectives: In severe peripheral artery disease (PAD) with limb ischemia, hypercholesterolemia (HC) is associated with impaired neovascularization. Extracellular vesicles (EVs) are present within ischemic muscles, and they contain microRNAs (miRs) involved in several biological functions, including angiogenesis and neovascularization. Methods: We used a mouse model of PAD and compared the response to hindlimb ischemia in hypercholesterolemic ApoE^−/− vs. normocholesterolemic mice. Next-generation sequencing (NGS) was used to perform full miR expression profiling in ischemic skeletal muscles and in EVs of varying sizes—large EVs (lEVs) and small EVs (sEVs)—within these muscles. Results: We identified several miRs with potential pro-angiogenic effects (angiomiRs) that are reduced by HC in lEVs (Let-7b-5p, miR-151-3p, Let-7c-5p) or sEVs (miR-21a-5p, miR-196b-5p, miR-340-5p). As proof of principle, we showed that the overexpression of Let-7b-5p in lEVs, or miR-21a-5p in sEVs, can significantly increase the angiogenic capacity of these EVs in vitro. HC also impaired the enrichment of specific angiomiRs in lEVs (miR-100-5p), sEVs (miR-142a-3p), or in both lEVs and sEVs (miR-146b-5p). In silico approaches, including the prediction of miR targets, pathway unions, and gene unions, identified the resulting predictive effects of HC-modulated miRs in EVs on processes with key roles in the modulation of angiogenesis and neovascularization, such as the regulation of the actin cytoskeleton and focal adhesion and the HIF-1, MAPK, AMPK, and PI3K-Akt signaling pathways. Conclusions: Our results constitute an important first step towards the identification of specific miRs that could be targeted to improve EV angiogenic function in hypercholesterolemic conditions and reduce tissue ischemia in patients with severe PAD. Full article

This study aimed to screen candidate genes related to body size traits in Dongfeng sika deer bucks by genome-wide association analysis. A total of 266 adult Dongfeng sika deer underwent 20× whole-genome resequencing. Genome-wide association analysis (GWAS) was performed using a mixed linear model (MLM), and gene annotation was conducted on SNP loci. GO and KEGG enrichment analyses were subsequently conducted to identify biological functions and pathways associated with body size regulation. The GWAS results screened 774 SNP sites significantly associated with body size. Functional enrichment analysis further identified that four genes—CDH4, TSHR, SLC23A2, and RIMS1—were potentially associated with body size traits. This study provides a reference basis for subsequent functional exploration of candidate genes. Full article