Search Results (4,873)

Background: Bacterial adaptation to environmental and chemical stress involves coordinated, system-level responses collectively described as perturbome. Understanding conserved elements within core perturbomes may reveal strategic vulnerabilities for antimicrobial development. Methods: In this study, we implemented an integrative framework combining functional and comparative genomics, drug–target interactions and molecular docking to prioritize conserved stress-response targets in Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. Results: A total of 147 genes from previously defined core perturbomes were analyzed through interactome reconstruction and functional enrichment. Interactome and functional analyses revealed significant connectivity and functional clustering, primarily associated with molecule biosynthesis, translation, transcriptional regulation, and energy metabolism. Orthology-based comparative genomics identified six conserved orthogroups shared across at least two species, representing key stress-adaptive nodes including fatty acid synthesis initiation, metabolic stress buffering, transcription termination (Rho), ATP synthesis, peptidoglycan remodeling, and UDP-glucose-mediated envelope biosynthesis. Drug–target interaction analyses suggested that these conserved proteins are modulated by enzymatic inhibitors, metabolite analogs, or active-site competitors. Structural and docking analyses focused on a selected protein, FabF (β-ketoacyl-ACP synthase II) and confirmed catalytically coherent binding of cerulenin within the active site, with high concordance between experimentally resolved and AlphaFold-predicted structures, supporting the reliability of structure-based prioritization. Conclusions: Overall, the results demonstrate that bacterial stress responses converge on evolutionarily conserved metabolic and regulatory elements essential for homeostasis and tolerance to perturbations, being the first work integrating core perturbome data from different microorganisms. The proposed perturbome-informed framework provides a rational strategy to identify robust, broad-spectrum antimicrobial targets and highlights opportunities for drug repurposing and future experimental validation. Full article

Background: Age-related macular degeneration (AMD) is the leading cause of irreversible vision loss in older adults. An important challenge is the recognition of its early asymptomatic stages and the monitoring of its progression, which requires reliable biomarkers. Growing evidence indicates that AMD-related biochemical changes are reflected in the proteome of tear fluid (TF). Although TF is a non-invasive and easily collectable diagnostic material, its proteomic analysis is complex and costly and therefore has limited clinical value. Methods: In this pilot single-center retrospective cross-sectional study, we developed a new method for dry AMD screening based on analysis of nano-differential scanning fluorimetry (nanoDSF) tear protein denaturation profiles (TDPs) within 15 min. The TDPs were recorded in representative groups of dry AMD patients (37% early, 48% intermediate, 15% geographic atrophy), and in control groups, including patients with refractive abnormalities (basic control), other retinal degenerative diseases (diabetic retinopathy, peripheral retinal dystrophy), or TF-affecting conditions (dry eye syndrome). High-dimensional TDP data were processed using unsupervised machine learning followed by k-means cluster analysis. Results: The presented pipeline distinguished AMD from the basic control with 74% accuracy and a sensitivity of 0.81 without relying on prior labels. The specificity of AMD detection was confirmed by its effective differentiation from diabetic retinopathy (72%; 0.74), peripheral retinal dystrophy (79%; 0.76) and dry eye disease (76%; 0.81). Classifying the AMD group from the entire population of other patients yielded an accuracy of 71% and a sensitivity of 85%, with a false-negative rate of only 15%. Conclusions: This study is a proof of concept for the nanoDSF-based approach, which can be considered a fast, cost-effective, and convenient tool for population screening for dry AMD, suitable for use in preventive medicine and public health. Full article

Neuroblastoma is characterized by frequent involvement of bone marrow (BM) as a site of cell dissemination and spread. In this study, single-cell RNA sequencing (scRNA-seq) was used to analyze the cellular heterogeneity of a subset of metastatic BM samples collected at initial diagnosis. Comparison of the single-cell data with bulk RNA sequencing further refined the analysis. An enrichment of regulatory T cells relative to a healthy control and activation of the CD24, CD47, and CD200 “don’t eat me” signals were documented. Computational analyses highlighted communication between neuroblastoma and myeloid cells via the amyloid precursor protein (APP) and midkine (MK) signaling networks. Within neuroblastoma cells, mutually exclusive adrenergic and transitory cell states were identified, and ten sub-clusters were denoted. In addition, common and unique tumor cell antigens were investigated. CNTFR and CHRNA3, as high-ranking candidates, were validated, confirming their strong selectivity for neuroblastoma cells. Taken together, these findings support the existence of a significant tumor-dependent modulation of the BM ecosystem, which should be considered when introducing immunotherapy. Furthermore, they highlight the potential to investigate new antigens at the single-cell resolution. Full article

Exercise-induced regulation of cortical GPCR pathways in diabetic obesity remains unclear. This study aimed to investigate exercise-associated GPCR-related transcriptomic pathway changes in the cerebral cortex of diabetic-obese rats. Cerebral cortical samples from male Zucker Fatty Diabetes Mellitus (ZFDM) rats subjected to a 12-week swimming program were examined using RNA sequencing, functional enrichment, GSOAP clustering, and STRING-based protein–protein interaction (PPI) analysis. Exercise training reduced fasting glucose and body weight. RNA sequencing identified 817 exercise-responsive transcripts (403 upregulated and 414 downregulated; p < 0.05), including 48 associated with GPCR signaling. Results showed that these 48 genes mapped to three major GPCR-related networks: cAMP signaling, with increased Adcyap1r1, Gipr, Tshr, and Vipr2 and decreased Vip, Chrm1, Gabbr2, and Sst; calcium signaling, with increased Ntsr1 and Trhr and decreased Chrm1; and neuroactive ligand–receptor interaction, with increased Trh, Trhr, and Crh and decreased Opr-related transcripts. These findings provide hypothesis-generating evidence for interpreting cortical GPCR-related transcriptomic pathway associations in diabetic-obese conditions. Full article

Ventricular remodeling occurring in heart failure (HF) involves structural disarray of the sarcolemma T-tubule (TT)–sarcoplasmic reticulum (SR) dyad junctions, thereby disrupting the close apposition of L-type Ca²⁺ channels (Ca_V1.2) with ryanodine receptors (RyR2) that trigger SR Ca²⁺ release and myofilament contraction. In a rat ischemic heart failure model expressing low thyroid hormone (TH) function, we used 3D stochastic optical reconstruction microscopy (STORM) to image RyR2 clusters with Ca_V1.2 channels, and the associated protein junctophilin-2 (Jph2). We tested whether treatment with T3, the biologically active form of TH, throughout progression of the disease would preserve T-tubule structure and dyadic ion channel organization. Confocal microscopy of isolated cardiomyocytes (CMs) stained with ANEPPS membrane dye showed significantly decreased TT density in diseased CMs while T3 treatment attenuated TT disorganization. 3D STORM images of dyadic ion channels labeled with fluorescent-tagged antibodies to RyR-Dylight550, Jph-CF647 and Ca_V1.2/IgG-Dylight488 were captured. A density-based algorithm defined RyR2 clusters, and a 400 nm spherical 3D volume of interest around each RyR2 cluster’s centroid determined the number of Ca_V1.2 and Jph2 localizations associated with each RyR2 cluster. Analysis revealed significant reduction in RyR2 cluster size and number with reduced co-localized Jph2 in failing CMs. T3 treatment increased RyR2 cluster numbers and cluster volumes albeit non-significantly, with increased co-clustering of Jph2. The number of Ca_V1.2 co-localized with RyR2 clusters trended lower in the failing CMs. These results support maintaining TH homeostasis in optimizing the nanoscale organization of Ca²⁺ ion channels in triggering Ca²⁺ release and myofibrillar contraction in patients with heart disease. Full article

Deep dermatophytosis is a rare, life-threatening fungal infection characterised by the invasion of dermatophytes beyond the superficial layers of keratinised tissue into the dermis and subcutaneous tissues. The present review aimed to identify the current knowledge on the role of Caspase Recruitment Domain-containing protein 9 (CARD9) deficiency in the pathogenesis, clinical spectrum, diagnosis, and management of deep dermatophytosis. For innate immune activation, CARD9 acts as an adaptor molecule. Basically, CARD9 helps mediate the connection between the fungal pattern recognition receptor (Dectin-1) and the NF-κB and MAPK signalling pathways, and it mediates cytokine production, thereby activating phagocytic activities. Thereby, any change or mutation in the CARD9 gene may disrupt these pathways, leading to dysfunctional neutrophils and impaired Th17-mediated antifungal immunity. Clinically, patients with CARD9 deficiency are immunocompetent but susceptible to recurrent and/or severe fungal infections [Candida, dermatophytes (Trichophyton spp.), and phaeohyphomycetes]. Deep dermatophytosis in these patients is usually chronic, treatment-resistant, and characterized by erythematous papules, nodules, plaques, ulcers, or necrotic lesions, most of which occur on the lower limbs. It usually occurs in adulthood and is more common in males. There have been instances of geographic clustering of CARD9 deficiency in Asia, North Africa, and the Middle East. Early recognition and genetic diagnosis of CARD9 mutations in patients with recurrent or atypical deep dermatophytosis. Although antifungal therapy is essential, hematopoietic stem cell transplantation can be a definitive treatment for selected patients with CARD9 deficiency. Thus, CARD9 deficiency is a critical factor in the better management of patients but remains an underrecognized cause of severe, treatment-resistant deep dermatophytosis, and early genetic diagnosis is essential for guiding targeted management and improving patient outcomes. This review emphasises the importance of CARD9 in antifungal immunity and underscores the need for greater clinical awareness and the incorporation of genetic evaluation into the management of deep dermatophytosis. Full article

Chilling injury is a major problem limiting the postharvest storage and marketability of mango fruit at low temperature. The present study investigated the individual and combined effects of sodium nitroprusside (SNP), L-arginine (Arg) and salicylic acid (SA) on chilling tolerance, regulation of oxidative stress and the postharvest quality of ‘Keitt’ mango fruit stored at 5 ± 1 °C for 28 days followed by 4 days of shelf life at 23 °C. Fruits were pre-treated with 1 mM SNP, 1 mM Arg, 2 mM SA or their binary combinations before storage. The chilling injury, membrane damage, lipid peroxidation, protein oxidation and fruit softening were greatly enhanced by cold storage in untreated fruits. In contrast, all the treatments significantly ameliorated these deteriorative changes, and the combined treatments were superiorly effective. Among these, SNP + Arg was the most effective treatment, which reduced the chilling injury index from 4.05 in control fruits to 1.00 after shelf life, completely inhibiting the incidence of decay and reducing electrolyte leakage and malondialdehyde accumulation by 47.4 and 48.2%, respectively. The same treatment also maintained higher firmness, titratable acidity, visual appearance and ascorbic acid content than untreated fruits. The enhanced chilling tolerance was accompanied by increased antioxidant defense, as SNP + Arg significantly stimulated the activities of superoxide dismutase, catalase and peroxidase, but suppressed the activity of pectin methylesterase. Multivariate analyses, such as PCA, clustered heatmap and integrated stress index, demonstrated a strong negative relationship between oxidative stress markers and antioxidant metabolism. The results showed that combined SNP and Arg treatments enhanced chilling tolerance through increasing antioxidant capacity, preserving membrane integrity, and retarding ripening-related metabolism, which provides an effective way to maintain the postharvest quality of cold-stored mango fruit. Full article

Paraleyrodes minei is an invasive alien species in China, representing a new record for Yunnan Province and a new sugarcane pest. The mitochondrial genome of P. minei was sequenced using the Illumina NovaSeq 6000 sequencing platform. The genome sequence was assembled and annotated, and its structural characteristics and nucleotide composition were analyzed. A phylogenetic tree of 18 species in the family Aleyrodidae was constructed using maximum likelihood (ML) and Bayesian inference (BI) methods to analyze the phylogenetic relationship of P. minei within the family Aleyrodidae. The results indicated that the mitochondrial genome of P. minei was 18,774 bp in length and contained 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 1 non-coding control region. The A+T content of the mitochondrial genome of P. minei was 80.93%, indicating a marked A+T preference. ATN was used as the start codon for the PCGs, and TAA, TAG, TA, and T were used as the stop codons. In the secondary structure of tRNA, the TΨC arm was missing in trnA, trnC, and trnG, and the DHU arm was missing in trnS1 and trnS2, with G-U base mismatches present. The phylogenetic tree revealed that the 18 species of 10 genera in the two subfamilies of the family Aleyrodidae clustered into two major branches: the subfamilies Aleyrodinae and Aleurodicinae. All 10 genera were monophyletic groups; among them, the genus Paraleyrodes and the genus Aleurodicus formed a sister relationship, and both belonged to the subfamily Aleurodicinae. This study represents the first successful sequencing of the mitochondrial genome of P. minei, as well as the first mitochondrial genome of the genus Paraleyrodes, laying the foundation for the control of P. minei and the analysis of phylogenetic relationships among various genera of the family Aleyrodidae. Full article

Renal-resident macrophages (RMs) are essential regulators of kidney homeostasis and repair, yet the mechanisms governing RM niche regeneration after acute depletion remain poorly defined. To overcome these limitations, we have developed an inducible human CD59- intermedilysin (hCD59-ILY) ablation system, enabling rapid, specific, and reversible depletion of targeted macrophage populations, and subsequent replenishment of RMs, followed by longitudinal scRNA-seq analysis of kidneys at baseline and days 1, 3, and 7 post-ablation. RM ablation triggered a rapid and sustained upregulation of Cx3cl1, predominantly in proximal tubular epithelial cells (PTC1/PTC2), establishing a persistent chemotactic niche signal that coincided with macrophage repopulation. Regenerating RMs transitioned from inflammatory/stress-associated states toward metabolically active and proliferative phenotypes enriched in glycolysis, oxidative phosphorylation, MYC, and cell-cycle programs, with attenuation of canonical inflammatory pathways. Cell–cell communication analysis revealed an early burst of intercellular signaling at day 1, followed by progressive normalization, with fibronectin (Fn1), osteopontin (Spp1), chemokine (Ccl), and amyloid precursor protein (App) axes emerging as key mediators of niche restoration. Transcriptional network analysis identified a conserved regulatory module (Tfe3, Mitf, Hif1a, Myc, Gabpa, Rcor1) coordinating macrophage differentiation and regenerative programming, linking metabolic adaptation to lineage reconstitution. Sub-clustering revealed five dynamically shifting RM subsets with distinct inflammatory, remodeling, proliferative, and surveillance states, reflecting a hierarchical regeneration process. Functional validation using clodronate-mediated depletion in Secreted Phosphoprotein 1 (Spp1) (Opn)-deficient mice demonstrated impaired macrophage repopulation, establishing osteopontin as a critical regulator of RM regeneration. Together, these data define a coordinated epithelial–immune circuit in which Cx3cl1-driven chemotaxis, Spp1-dependent signaling, and a core transcriptional network orchestrate macrophage niche reconstitution and kidney repair following acute immune cell ablation. Full article

Background and Objectives: Temporomandibular disorders (TMDs) encompass a broad spectrum of functional and structural abnormalities of the temporomandibular joint (TMJ). Conventional diagnostic tools, although essential, often fail to capture the underlying biochemical mechanisms driving disease progression. Synovial fluid (SF), by virtue of its direct proximity to intra-articular tissues, represents an accessible biological matrix for identifying molecular signatures of inflammation, cartilage degradation, lubrication failure, oxidative stress, and angiogenic activation. The objective of this review is to synthesize current evidence on SF proteomics in TMD and evaluate its potential translational value in precision medicine. Materials and Methods: A narrative review of the literature was conducted on PubMed to identify human studies focused on SF proteomic and biochemical biomarkers in TMD. Eligible studies included original research articles assessing SF composition in relation to specific TMJ pathologies, diagnostic categories, or clinical phenotypes. Extracted data included study design, sample characteristics, analytic methodology, biomarkers investigated, and key findings. Google Gemini (Google LLC, Mountain View, CA, USA) was used as an AI-assisted tool to support language editing and manuscript writing during the preparation of this article. The use of this tool was limited to linguistic refinement; all scientific content, data interpretation, and conclusions were formulated and verified by the authors. Results: Across the analyzed studies, TMD phenotypes—particularly disc displacement with or without reduction (DDwR, DDwoR) and osteoarthritis (OA)—were characterized by consistent alterations in cytokines (IL-1β, IL-6, IL-8, TNF-α), extracellular matrix (ECM) components (aggrecan, glycosaminoglycans (GAGs), decorin, MMP-2, MMP-9), lubrication molecules (lubricin/PRG4), oxidative stress mediators (myeloperoxidase (MPO), nitric oxide (NO), glutathione peroxidase (GPX)), adipokines (chemerin, resistin, adiponectin), and angiogenic factors (vascular endothelial growth factor (VEGF), fibroblast growth factor-2 (FGF-2)). Recent liquid chromatography–tandem mass spectrometry (LC–MS/MS) analyses further revealed phenotype-specific protein clusters and pathways related to inflammation, ferroptosis, hypoxia signaling, and proteoglycan metabolism. Conclusions: Current evidence suggests that SF proteomics and multi-analyte biomarker profiling offer a promising, hypothesis-generating approach for understanding the biological mechanisms underlying TMD. The integration of proteomic, metabolic, and inflammatory markers holds future potential for diagnostic panel development; however, prospective clinical validation is still required before SF-based molecular profiling can be implemented as a precision medicine tool in TMJ disorders. Full article

Background: Systemic sclerosis (SSc)-associated interstitial lung disease (SSc-ILD) is the leading cause of morbidity and mortality in patients with SSc, with an unmet need for validated, minimally invasive biomarkers for early detection. Extracellular vesicles (EVs) present underexplored pathogenic players and potential biomarker sources in SSc-ILD. We performed a proteomic shotgun study aiming to identify disease-specific protein signatures and potential biomarker candidates. Methods: The study included 30 SSc patients divided into SSc-ILD and SSc w/o ILD groups and 20 matched controls. Plasma-derived EV-enriched fractions were analysed using liquid chromatography–mass spectrometry. Bioinformatic analysis, including differentially expressed proteins (DEPs), functional enrichment, protein–protein interaction network and Markov Cluster (MCL) analysis was performed. Results: Analysis of DEPs showed 14 significantly upregulated and 1 downregulated protein when comparing the SSc-ILD to the SSc w/o ILD group, 222 upregulated and 257 downregulated proteins between the SSc-ILD and control group, as well as 362 upregulated and 492 downregulated proteins between the SSc w/o ILD and control group. Functional enrichment analysis and MCL analysis pointed to disease-specific processes of extracellular matrix (ECM) and immune dysregulation, which largely overlapped between SSc-ILD and SSc w/o ILD groups. Among identified DEPs, SP-B, Cav-1 and Siglec-5 emerged as potential candidate biomarkers for SSc-ILD. Conclusions: Proteomic analysis of plasma-derived EV-enriched fractions shows potential EV involvement in pathogenic SSc processes, mainly related to ECM and immune dysregulation, as well as potential candidate biomarkers for SSc-ILD. Further studies are required to validate these results and assess biomarker potential and translational applicability of identified proteins. Full article

Indigenous goat populations are valuable genetic resources for livestock production in arid and semi-arid environments, yet many remain insufficiently characterized at the phenotypic and genomic levels. This study investigated phenotypic variation and genome-wide associations in two local Ardi goat lines in Bahrain: Ardi Bahraini and Ardi Mu’atar, the latter being distinguished by a characteristic facial marking pattern. A total of 280 goats were phenotypically characterized for qualitative traits and body measurements, and 76 animals were genotyped using the Illumina Caprine 60K single nucleotide polymorphism (SNP) BeadChip. After quality control, 49,716 autosomal SNPs were retained for genome-wide association analysis. Phenotypic analysis showed that the two lines differed significantly in body weight, body length, hip height, face width, tail length, ear width, and tail circumference, while discriminant analysis identified tail length, ear width, tail circumference, and facial patterns differentiating the lines. Principal component analysis (PCA) showed partial genomic clustering of the two lines, and genome-wide significant and suggestive SNPs based on Bonferroni and false discovery rate (FDR) thresholds on chromosomes 6, 13, 14, and 29. The strongest association was observed for rs268277393 on chromosome 13, located near DOK5 (Docking Protein 5) and TRNAC-GCA (transfer RNA cysteine, anticodon GCA), and was associated with the Ardi Mu’atar facial pattern. Additional candidate regions were located near genes with possible roles in pigmentation, development, or morphological variation. These findings provide preliminary genomic evidence supporting the phenotypic distinctiveness of Ardi Mu’atar goats and identify candidate markers that may contribute to future conservation and breeding programs. Further validation in larger populations and functional studies will be required to confirm the biological role of these candidate regions. Full article

L-carnitine plays a central role in mitochondrial fatty acid transport and cellular energy regulation; effects on the biochemical phenotype of brain cancer cells remain insufficiently characterized. Here, we applied confocal Raman spectroscopy and imaging to investigate the biochemical alterations induced by L-carnitine supplementation—administered as its tartrate salt—in human astrocytoma cells. Raman spectral analysis revealed distinct changes in lipid-, protein-, nucleic acid-, and cytochrome-associated vibrational features following 24 h of treatment, suggesting alterations in mitochondrial activity and cellular energy-related processes. Principal component analysis identified PC1 (93.87%) as representing the intrinsic biochemical composition of the cells, whereas PC2 (1.19%) and PC3 (0.59%) captured subtle yet consistent variations in lipid organization, protein conformation, and redox-sensitive vibrational features associated with L-carnitine exposure. Pearson correlation analysis of Raman cluster spectra indicated biochemical differences across cellular compartments, with the most pronounced changes observed in lipid droplets, supporting modifications in lipid-associated cellular processes. These findings demonstrate that Raman imaging provides a sensitive, label-free platform for resolving L-carnitine-induced biochemical heterogeneity at the single-cell level. Overall, this study highlights vibrational spectroscopy as a powerful tool for characterizing cellular responses to metabolic modulators and provides insight into the biochemical impact of exogenous L-carnitine in brain cancer cells. Full article

Large-scale production of Bacillus thuringiensis, one of the most widely used biopesticides, is often limited by the high cost of conventional culture media. In this study, fermented cassava paste water (EFM), ripe mango pulp juice (CM), and cashew apple juice (JPC) were evaluated as alternative substrates for the liquid fermentation of B. thuringiensis var. kurstaki HD-1. Physicochemical analyses revealed acidic pH values and classified the substrates into two clusters: CM with high C/N ratios, organic matter, total sugars, and proteins, and EFM and JPC with lower C/N ratios and nutrient levels. Fermentation results indicated that JPC supported the highest biomass production (8.29 × 10¹³ CFU mL⁻¹), exceeding that in the standard Tryptone Soy Broth (TSB) medium. However, CM promoted the highest sporulation rate (1.46 × 10¹³ CFU mL⁻¹) and the greatest bioactive lipopeptides—iturins (102.2 mg L⁻¹) and surfactins (554.7 mg L⁻¹)—surpassing TSB. The antifungal activity of crude fermented CM, EFM, and TSB was evaluated against Sclerotium rolfsii. All samples significantly inhibited mycelial growth of the pathogen with no significant differences among substrates or concentrations tested. This study highlights the potential of B. thuringiensis-fermented agrowaste as a cost-effective, environmentally friendly biocontrol tool for Sclerotium rolfsii. Full article

Polygalacturonase (PG) is a key enzyme in cell wall metabolism and fruit ripening. Atemoya (Annona cherimola Mill. × A. squamosa L.) is a high-value tropical fruit that undergoes rapid postharvest softening at room temperature. However, the role of the atemoya PG gene family in this process remains unknown. This study determined that storing atemoya at 28 °C significantly reduced fruit firmness and the total pectin content but increased water-soluble pectin (WSP) and PG activity compared to storage at 15 °C. Genome-wide identification of the AaPG gene family in atemoya revealed that 40 AaPG genes were unevenly distributed across seven chromosomes. Nineteen genes were located within six tandem duplication clusters. AaPG proteins exhibited clade-specific differences: Clades B-E contained the polysaccharide lyase family 6 (PL-6) superfamily domain, while Clade A harbored the Aspergillus niger polygalacturonase 1 (Pgu1) domain and lacked several conserved motifs. Expression profiling and reverse transcription quantitative polymerase chain reaction (RT-qPCR) showed that AaPG19, AaPG21, AaPG23 and AaPG24 were specifically induced at 28 °C. Subcellular localization confirmed that these four proteins were located on the plasma membrane. These findings provide insights into the evolution and temperature-dependent regulation of the AaPG family, identifying candidate genes responsible for the rapid softening of atemoya fruit. Full article