Search Results (317)

With the increase in Qatar’s population, the generation of plastic waste has grown, resulting in high levels of environmental pollution. Polyhydroxyalkanoates are sustainable bio-alternatives to petrochemical plastics. Despite their market potential, the industrial implementation of PHAs is still limited. This study aimed to develop sustainable processes for PHA accumulation by screening and isolating novel haloarchaeal strains from Qatari extreme environments with the ability to convert carbon sources to PHAs. In total, 24 positive haloarchaeal members, belonging to Natrinema, Haloarcula, and Halostagnicola genera, were identified for the first time in Qatari ecosystems through 16S rRNA and phaC/phaE gene sequence analyses. Among them, the promising PHA-producing archaeon Haloarcula sp. PLQ exhibited the highest production, reaching a PHB concentration of 496 ± 24 mg L⁻¹ and a cell dry weight of 1109.8 ± 58.6 mg L⁻¹, corresponding to a maximum yield of 44.69 wt % ± 2.13 under optimal conditions. Polymer characterization confirmed the production of poly(3-hydroxybutyrate). In addition, the thermal properties analyzed by TGA (Tonset = 250 °C; Td = 270 °C) and DSC (Tm = 169 °C) confirmed a PHB-like film with thermal behavior comparable to standard PHB. Therefore, future pilot-scale studies on the pure culture of a promising strain for PHA production from renewable feedstocks under non-sterile, batch, or continuous fermentation will be conducted. Full article

Aspartic proteases (APs), a class of proteolytic enzymes involved in protein maturation, degradation, and signaling, are known to contribute to fungal virulence and pathogenicity. However, the AP gene family in Talaromyces marneffei (T. marneffei), a dimorphic opportunistic pathogenic fungus, has not yet been functionally analyzed. In this study, we identified 27 AP genes from the T. marneffei genome, and the encoded APs retained conserved domains and exhibited similar motifs and structural properties crucial for catalytic activity. Phylogenetic and collinearity analyses found that TmAPs were most recently homologous to Aspergillus gene families, with both tandem and segmental duplications contributing to their expansion. Expression patterns, combined with RNA-sequencing data, revealed the specialized roles of TmAP1 and TmAP2 in the dimorphic conversion between the yeast and mycelial phases. Protein–protein interaction network analysis uncovered links to cell fusion, mitochondrial function, and programmed cell death. Under abiotic stress conditions, several TmAP genes displayed significant transcriptional changes, implying their involvement in short-term adaptation and stress responses. This study provides the first comprehensive and systematic analysis of the AP gene family in T. marneffei, highlighting their potential biological roles in fungal development, dimorphic conversion, and stress adaptation. Our findings offer valuable insights into further functional characterization of AP genes in T. marneffei and may facilitate the development of novel therapeutic targets and intervention strategies against T. marneffei infection. Full article

Nano-antimony trioxide (Nano-Sb₂O₃) is extensively utilized in industrial production and consumer products, leading to widespread environmental contamination and human exposure. Accumulating evidence has demonstrated that Nano-Sb₂O₃ induces male reproductive toxicity, yet the underlying molecular mechanisms remain poorly understood. In this study, male C57BL/6 mice were exposed to Nano-Sb₂O₃ (2.5, 5.0, and 7.5 mg/kg/day). Exposure to Nano-Sb₂O₃ induced dose-dependent reproductive toxicity, evidenced by dose-dependent reductions in sperm motility (56.70% to 36.10%) and sperm density (15.76 × 10⁶/mL to 2.79 × 10⁶/mL) and a marked elevation in sperm malformation rates (4.56% to 44.36%), as well as severe histopathological alterations, testicular Sb accumulation, and elevated reactive oxygen species (ROS) levels. Transcriptomic analysis revealed significant enrichment of the PPAR and PI3K-Akt signaling pathways and identified SPP1 as one of the most significantly differentially expressed genes. Computational pathway perturbation analyses further yielded hypothesis-generating evidence supporting the potential involvement of PPAR signaling suppression and PI3K-Akt and inflammatory pathway activation following Nano-Sb₂O₃ exposure. Both mRNA and protein levels of SPP1 were significantly upregulated in a dose-dependent manner in mouse testes and TM4 Sertoli cells. In vitro experiments further demonstrated that Nano-Sb₂O₃ increased the expression of pro-inflammatory cytokines IL-1β and IL-6 by up to 5.6-fold and 4.7-fold, respectively, while impairing Sertoli cell viability and wound-healing capacity. Importantly, Spp1 silencing attenuated inflammatory responses and restored the expression of blood–testis barrier (BTB)-associated proteins, including ZO-1, Claudin-11, and N-cadherin. These findings suggest that SPP1 may contribute to Nano-Sb₂O₃-induced inflammatory responses and alterations in BTB-associated proteins, thereby potentially participating in male reproductive injury. Full article

There have been reports of an association between the gut microbiota and the development of chronic liver disease, fibrosis, and carcinogenesis; however, it is not yet possible to reach a definite conclusion. In this cross-sectional study, we examined the association between the presence or absence of hepatocellular carcinoma (HCC) and the gut microbiota in patients with chronic hepatitis B virus (HBV) infection. The study subjects consisted of 62 consecutive HBV patients admitted to our hospital who provided informed consent to participate in the study. We performed 16S rRNA analysis using DNA extracted from fecal pellets. The sequencing depth per sample was 80,000 to 90,000 reads. We calculated the proportion of each bacterial genus so that the total for each sample added up to 100%. The male-to-female ratio was 49/13, the median age was 67 years, and 46 of the patients had HCC. Twenty microbial phyla spanning 41 classes, 79 orders, 163 families, and 431 genera were identified. Receiver operating characteristic (ROC) analysis was performed on the identified bacterial taxa, from the level of phylum down to genus, to assess their ability to distinguish between patients with and without HCC. Several bacteria with an area under the curve (AUC) > 0.65 were identified as follows: TM7 phylum TM7-3 class (AUC = 0.700); Firmicutes phylum Clostridiales class Lachnobacterium genus, Dialister genus, Ruminococcus genus, and Roseburia genus (AUC = 0.670, 0.668, 0.667, and 0.660, respectively); and Firmicutes phylum Erysipelotrichi class (AUC = 0.656). Combining three of these taxa resulted in high discriminative power (p = 0.000585) with a sensitivity and specificity of 0.761 and 0.750, respectively. A similar trend was observed in the subgroup analysis based on liver reserve capacity. Even after adjusting for factors related to liver reserve capacity in the multivariate analysis, an association between these bacterial genera and HCC was confirmed. Our results suggest that gut microbiota may be associated with the prevalence of HCC in HBV patients. Full article

Across all kingdoms of life, ribosomes are indispensable molecular machines that translate genetic information into the proteome of living cells. The fundamental catalytic centers of the ribosome, constructed primarily from ribosomal RNA (rRNA), exhibit remarkable conservation between the major domains of life. The ribosome’s A-site deciphers the mRNA’s triplet code, while the P-site synthesizes the growing protein chain and the E-site provides exit for deacylated tRNA; a distinct tunnel facilitates nascent polypeptide export. While the conservation of ribosomal proteins is less pronounced between bacteria and eukaryotes, striking homology exists from simple eukaryotes to humans. Ribosomal proteins were traditionally viewed mainly as scaffolding agents, steering rRNA folding during ribosome biogenesis and maintaining structural stability during translation. However, since the early 2000s, advances in structural and functional ribosome analysis have ushered in a more nuanced paradigm: ribosomes are no longer considered uniform machines. Instead, an array of rRNA and ribosomal protein modifications generates a spectrum of ribosome populations capable of specialized translation. RiboScreen^TM technology leverages this regulatory potential of individual ribosomal proteins, enabling deliberate modulation of target protein output and representing a promising tool for correcting dysregulated protein expression involved in rare and common diseases. This review will first introduce relevant aspects of ribosome biology and then showcase the tools of this new technology. Finally, we report examples for the delivery of small molecules to target ribosomal proteins for tailored restoration of protein production levels in rare and prevalent diseases. Full article

Inflammatory bowel disease (IBD) is associated with microbial dysbiosis, yet subtype-specific alterations in the tongue-coating microbiome remain insufficiently characterized. In this cross-sectional study, tongue-coating samples from 158 participants (94 healthy controls [HC], 19 ulcerative colitis [UC] patients, and 45 Crohn’s disease [CD] patients) were analyzed by 16S rRNA gene amplicon sequencing. We compared alpha and beta diversity, taxonomic composition, differential taxa, exploratory random-forest feature rankings, and SPIEC-EASI co-occurrence networks. Species richness did not differ significantly among groups, whereas Shannon and Simpson indices were lower in UC than in HC and CD. Bray–Curtis and Jaccard ordinations showed significant but partially overlapping community differences among the three groups. UC was characterized by enrichment of Proteobacteria, Neisseria, and Porphyromonass (p < 0.001), whereas CD showed higher relative abundances of Prevotella, Veillonella, Leptotrichia, and TM7x. Random forest and LEfSe analyses yielded concordant candidate discriminative taxa, but no independent validation cohort was available. Network analysis suggested group-specific co-occurrence patterns, with results interpreted as statistical associations rather than direct microbial interactions. These findings support the presence of subtype-associated tongue-coating dysbiosis in IBD and identify candidate taxa for future validation. Full article

Copper supplements are prominent antibiotic alternatives in livestock production, but their excessive use poses environmental risks, necessitating safer substitutes. Potassium diformate (KDF), an organic acid salt, has shown potential as a feed additive, yet its effectiveness in copper-unsupplemented diets remains unclear. This study compared the effects of copper glycinate (Cu_Gly) and KDF on weaned piglets fed a copper-unsupplemented basal diet. Forty-five Meishan piglets were allocated to a control group (basal diet), a Cu_Gly group (basal diet + 60 mg/kg Cu_Gly), or a KDF group (basal diet + 10 g/kg KDF). The KDF group exhibited a lower feed conversion ratio (FCR) than the control group. Although no significant differences in average daily gain were observed, KDF supplementation significantly enhanced immune function by increasing plasma IgG and decreasing IgM, IL-6, and IL-1 levels compared to the control. 16S rRNA sequencing analysis revealed that the Control group was enriched with pathogenic genera (Staphylococcus, Escherichia-Shigella, Brevibacterium) in the ileum and cecum. Cu_Gly supplementation enriched Bacillus, Longispora, and Terrisporobacterin the ileum, while KDF increased the abundance of beneficial taxa (TM7, Nesterenkoniain the ileum; Lachnospiraceae_UCG-007 in the cecum). Correlation analysis showed that the abundances of Escherichia-Shigella and Staphylococcus were negatively correlated with IgG but positively correlated with IgM and IL-6. Cecal Lachnospiraceae_UCG-007 (enriched in the KDF group) was negatively correlated with IL-1. In summary, KDF improved feed efficiency and demonstrates superior immunomodulatory effects compared to Cu_Gly. The enrichment of bacteria linked to metal resistance in the Cu_Gly group suggested a potential drawback not associated with KDF. Therefore, KDF represented a viable and sustainable alternative to copper supplements, offering a combination of improved gut health, enhanced immunity, and a reduced environmental risk profile. Full article

Tenebrio molitor (Coleoptera: Tenebrionidae) is a suitable candidate for use as a biomass resource, recognized for its large-scale breeding and the high nutritional value of its protein content. Feeding obese Zucker rats the cuticle of T. molitor enhances fatty liver metabolism through the mediation of gut microorganisms. Cuticular proteins are demonstrated to be pivotal in the formation of the insect cuticle throughout the developmental stage. The endocuticle structural glycoprotein (Abd) belongs to the RR-1 subclass, a major group of structural cuticular proteins characterized by the conserved Rebers–Riddiford (RR) motif. Nevertheless, there remains a paucity of research into the molecular properties and functions of SgAbd (endocuticle structural glycoprotein) in Coleoptera. In this study, we successfully identified and described the gene TmAbd5 in T. molitor. The coding sequence of TmAbd5 is 306 bp, corresponding to a 101-aa protein. The functional domain predicted that TmAbd5 consists of a signal peptide and a chitin-binding domain 4 (ChtBD4). Motif prediction analysis indicated that TmAbd5 belongs to the CPR (cuticular proteins with Rebers–Riddiford consensus) family with the RR-1 motif. Expression analysis revealed that TmAbd5 is upregulated in the integument, particularly during the first three days of development in the 13th instar stage. Although the RNAi-mediated silencing of TmAbd5 did not cause apparent phenotypic abnormalities and the insects successfully molted into pupae, histological examination revealed a substantial thickening of the endocuticle at 72 h post-pupation, along with a notable increase in lamellar spacing and a disrupted pore canal. In summary, TmAbd5 contributes to the formation and structural organization of the endocuticle, which provides a theoretical basis for the screening of target genes for cuticle development and for the effective utilization of cuticle resources in T. molitor. Full article

Background/Objective: Leishmaniasis is a neglected tropical disease caused by species of the genus Leishmania, with a broad clinical spectrum that can overlap with other infectious and non-infectious conditions. Accurate species identification is critical for appropriate treatment and prognosis; however, parasitological methods are limited by suboptimal sensitivity, specificity, and inability to reliably differentiate species. This study aimed to develop and validate a real-time PCR assay based on melting-curve analysis (Leish-qPCR) for the detection of Leishmania spp. and the differentiation of Leishmania (Leishmania) amazonensis and Leishmania (Viannia) braziliensis. Methods and Results: Genus-specific primers were designed based on the kDNA (kinetoplast DNA) minicircle consensus sequences of Leishmania species, while species-specific primers targeted the internal transcribed spacer 2 (ITS2) consensus regions of the ribosomal RNA locus of L. (L.) amazonensis and L. (V.) braziliensis. Analytical performance was evaluated in silico and in vitro using a panel of protozoa, fungi, and bacteria, exhibiting 100% specificity with no cross-amplification. The limit of detection was one copy per reaction for all targets using positive controls. Clinical validation was performed using skin biopsy specimens from patients with granulomatous lesions. The optimized Leish-qPCR assay, performed in separate reaction tubes within the same run, demonstrated reliable analytical specificity and sensitivity, with distinct and reproducible melting temperature (Tm) peaks across plasmid controls, parasite DNA, and clinical samples. Comparative analysis with histopathological examination demonstrated moderate agreement between the methods, supporting the applicability of the assay for sensitive detection and species-level discrimination of Leishmania spp. in clinical samples. Conclusions: The Leish-qPCR assay presented high sensitivity, specificity, and diagnostic accuracy, representing a promising tool for routine diagnosis of leishmaniasis and for the differentiation of L. (L.) amazonensis and L. (V.) braziliensis in clinical samples. Full article

Primary open-angle glaucoma (POAG) is a leading cause of irreversible blindness driven by elevated intraocular pressure from compromised aqueous outflow. While genome-wide association studies have identified numerous risk loci, specific candidate proteins and their cellular mechanisms remain elusive. We employed a multi-omics framework integrating UK Biobank plasma proteomics (N = 53,022) and large-scale POAG GWAS summary statistics. We performed a Proteome-Wide Association Study, Mendelian Randomization, and Bayesian colocalization to infer causality. Identified candidates were mapped to human and mouse ocular scRNA-seq atlases to characterize cell-type specificity, followed by druggability assessments. We prioritized five putative causal proteins, with SEL1L and TFPI demonstrating the strongest evidence. Cross-species scRNA-seq revealed that SEL1L and SERPINF1 are robustly expressed in the trabecular meshwork (TM), particularly the juxtacanalicular tissue, implicating them in outflow resistance. Conversely, TFPI and SLC9A3R2 localize to Schlemm’s canal endothelium, suggesting a role in modulating barrier function. Pathway analyses highlighted endoplasmic reticulum protein processing and coagulation cascades. This study maps putative causal POAG proteins to conventional outflow pathway cells, highlighting SEL1L as a novel target for TM homeostasis and TFPI for drug repurposing, thereby providing data-driven hypotheses to facilitate precision glaucoma therapeutics. Full article

Leydig cells (LCs) represent a somatic testicular population responsible for testosterone synthesis, a hormone essential for spermatogenesis and male fertility. The obesity condition impairs LC steroidogenic activity, contributing to testicular oxidative stress and male reproductive dysfunctions. Using a high-fat-diet (HFD) murine model, we investigated the regulatory role of the nuclear factor of activated T cells 5 (NFAT5s) in the obesity-induced LC damage and the resulting alterations in intergenerationally inherited sperm circRNA cargo. Our findings reveal a significant upregulation of both circNFAT5 and NFAT5 protein levels in HFD testis. This molecular signature correlated with decreased antioxidant defense system, increased LC apoptosis, and impaired steroidogenesis. In vitro experiments, performed in TM3 cells, confirmed that NFAT5 nuclear shuttling drives proapoptotic gene activation, while NFAT5 silencing promotes LC survival. The analysis of HFD progeny (F1H) revealed a full recovery of testis oxidative status and LC apoptosis, linked with the recovery of NFAT5 expression. However, a steroidogenic deficiency persisted in F1H offspring. Notably, HFD and F1H epididymides exhibited NFAT5 overexpression concomitantly with impaired sperm morphology, motility, viability, and altered sperm circRNA profiles alongside a deregulated 4-hydroxy-2-nonenal (4HNE) profile, a marker of sperm oxidative stress. Lastly, an enhanced FUS-related amplification of circRNA perturbations was highlighted in F1H spermatozoa. Collectively, our findings reveal a dual functional role of NFAT5 as a testicular regulator of LC fate and an epididymal sentinel of metabolic stress, in turn linking paternal obesity to the persistent transmission of sperm epigenetic anomalies across the offspring. Full article

This study aimed to identify candidate molecular pathways mediating dopaminergic dysfunction induced by PFAS mixture exposure, with a focus on the TM/5-HT signaling axis and calcium-linked lipid metabolites, and to explore potential gut-brain axis involvement. Adult mice were exposed to a PFAS mixture. Behavioral tests assessed spatial memory, spontaneous activity, and motor coordination. Histopathological and ultrastructural analyses examined neuronal atrophy, mitochondrial damage, α-synuclein (α-syn), and tyrosine hydroxylase (TH). Transcriptomics, metabolomics, and gut microbiota profiling (16S rRNA sequencing) were performed, followed by integrated multi-omics and correlation analyses. PFAS exposure was associated with PD-relevant motor and cognitive impairments, including impaired spatial memory, reduced spontaneous activity, and motor coordination deficits. Neuronal atrophy, mitochondrial structural damage, upregulation of α-syn, and downregulation of TH were observed. Transcriptomics identified 315 differentially expressed genes (DEGs) enriched in ciliary movement, neuroactive ligand-receptor interactions, and serotonergic synapses. Metabolomics identified 130 differentially abundant metabolites involved in arachidonic acid metabolism and serotonergic synapses. Integrated analysis highlighted correlative changes in the TM/5-HT signaling pathway. Phosphatidylinositol PI(16:0/20:2(11Z,14Z)) showed a strong positive correlation with Dbh gene expression, suggesting a candidate association between Dbh expression and phosphatidylinositol alterations. Gut microbiota analysis revealed compositional alterations (e.g., Muribaculaceae, Ileibacterium) and predicted functional shifts (e.g., tryptophan metabolism–related modules) were observed; these findings are exploratory. This study identifies multi-omics signatures associated with PFAS mixture-induced dopaminergic dysfunction in mice. The TM/5-HT pathway emerges as a candidate molecular axis requiring further investigation. Gut microbiota alterations suggest a potential peripheral component, but causality and gut-brain axis involvement remain hypothetical and need direct experimental validation. Full article

Soil salinization is a source of major abiotic stress that severely limits the production of alfalfa (Medicago sativa L.), a globally critical forage legume for sustainable livestock production. Its complex autotetraploid genome and self-incompatibility greatly hinder salt tolerance genetic improvement, while the post-transcriptional regulatory mechanism of alfalfa salt stress response remains largely uncharacterized. This study aimed to narrow the gap between genome-wide genetic signals and causal regulatory mechanisms and identify core post-transcriptional regulators of alfalfa salt tolerance via a multi-layered integrative analysis pipeline. We performed a genome-wide association study (GWAS) using 220 globally collected alfalfa accessions, combined with public transcriptome integration, co-expression network analysis, 3′ untranslated region (3′UTR) motif discovery, and AlphaFold2-based protein-RNA docking simulation. We identified 20 significant salt tolerance-associated loci and prioritized the CCCH-type zinc-finger RNA-binding protein (RBP) MsCCCH20 as the core candidate regulator. We further screened 35 high-confidence target genes of MsCCCH20, detected conserved AU/AG-rich 3′UTR motifs, and provided structural predictions consistent with potential sequence-specific interactions (ipTM 0.70–0.79). Our findings establish a robust framework linking genetic association signals to post-transcriptional regulatory networks and provide high-confidence candidate genes and functional markers for the molecular breeding of salt-tolerant alfalfa. Full article

Respiratory syncytial virus (RSV), a member of the genus Orthopneumovirus, is an etiological agent in infant lower respiratory tract infections (LRTIs) producing substantial global morbidity. Here, secretoglobin (Scgb1a1)-derived progenitors play a primary role in triggering innate, inflammatory, and cell state transitions in response to RSV LRTIs. Whether RSV activation of innate signaling in this epithelial sentinel population leads to chronic airway disease is unknown. To understand the role of innate signaling in Scgb1a1-derived progenitors, a model of RSV post-viral disease (PVLD) was developed and studied in the presence or absence of RelA conditional knockout (CKO). Single-cell RNA sequencing (scRNA-seq) studies showed that RSV-PVLD induced a transition of atypical, differentiation-intermediate, alveolar type 2 (aAT2) cells characterized by tumor protein 63 (TRP63), aquaporin 3 (AQP3), and Itgβ4 expression, as well as changes in PDGFRβ mesenchyme. A single-cell trajectory analysis and lineage-tracing experiments using Scgb1a1 CreER^TM X mTmG mice demonstrated that the Scgb1a1+ populations were precursors to the aAT2 population. Mechanistically, we found that the formation of the aAT2 population was prevented by RelA CKO. A differential gene expression analysis revealed that RSV-PVLD coordinately upregulates nuclear receptor subfamily 1 group D (Nr1d1/2), clock and basic helix-loop-helix ARNT-like 1 (Bmal) genes both in the aAT2 cell and in its Pdgfrα+ mesenchymal niche in a RelA-dependent manner. A systematic analysis of intercellular epithelial–mesenchymal communication in the scRNA-seq data showed that the clock-dysregulated epithelial–mesenchymal niche produces aberrant ANGPTL4 expression. ANGPTL4 upregulation was confirmed by the measurement of both its mRNA and protein. Moreover, ANGPTL4 is biologically active in the BALF of RSV-PVLD mice, inhibiting lipoprotein lipase activity. We conclude that RSV-PVLD is mediated, at least in part, by RelA signaling in Scgb1a1-derived epithelial progenitors, dysregulating ANGPTL4 signaling in an epithelial–mesenchymal niche, resulting in persistence of atypical alveolar epithelial cells with dysregulated of clock gene expression. Full article

Japanese encephalitis virus (JEV) is an important flavivirus that causes zoonotic and arboviral diseases. Infection with JEV not only induces acute central nervous system (CNS) infectious diseases but also leads to reproductive disorders. Currently, research on the pathogenic mechanism of JEV has mainly focused on CNS inflammation caused by infection, while studies on the pathogenic mechanism of JEV targeting the reproductive system are relatively scarce. This study used TM3 cells as a model to investigate the regulatory role of the CD4 molecule in JEV infection, the STAT1 signaling pathway, and inflammatory factors. Firstly, we found that CD4 knockdown significantly inhibited JEV replication in TM3 cells. Further virus adsorption and internalization experiments confirmed that CD4 knockdown specifically impaired the early stages of JEV invasion into cells. Additionally, CD4 knockdown also drastically attenuated JEV infection-induced STAT1 phosphorylation (p-STAT1) and the production of downstream inflammatory factors. To distinguish whether CD4 affects p-STAT1 through an indirect effect of reduced viral load or its direct involvement in signal transduction, we performed experiments using RO8191, a specific agonist of the STAT1 signaling pathway. The results showed that RO8191 treatment increased the expression levels of p-STAT1 protein and inflammatory factor mRNA in both normal cells and CD4 knockdown cells, but the recovery amplitude in the CD4 knockdown group was significantly lower. In contrast, CD4 complementation significantly elevated the expression levels of p-STAT1 protein and inflammatory factor mRNA. In conclusion, this study demonstrates that the CD4 molecule positively regulates JEV proliferation in TM3 cells, while also modulating STAT1—a key factor in the STAT signaling pathway—and downstream inflammatory cytokines. Notably, this regulatory effect operates independently of viral replication. These findings provide a theoretical foundation for further elucidation of JEV pathogenic mechanisms and offer a scientific basis for the prevention and control of JEV. Full article