Search Results (642)

Chronic allograft dysfunction, driven by interstitial fibrosis and tubular atrophy, remains a major cause of long-term renal allograft loss. Everolimus (EVR), a mammalian target of rapamycin (mTOR) inhibitor, may reduce fibrosis through antifibrotic effects and calcineurin inhibitor minimization. This study aimed to evaluate the impact of EVR-involving immunosuppression on renal allograft fibrosis and to identify predictors of fibrotic progression. A total of 104 living-donor kidney transplant recipients transplanted between 2011 and 2017 were retrospectively analyzed (EVR, n = 61; non-EVR, n = 43). Interstitial fibrosis was quantified in protocol biopsies using digital image analysis. Phosphorylation of the mTOR-signaling proteins p70 ribosomal S6 kinase and eukaryotic translation initiation factor 4E-binding protein 1 was assessed using a semiquantitative immunoreactive score. Multivariable regression analyses identified independent predictors of fibrotic progression. Cytomegalovirus infection was less frequent in the EVR group, whereas acute rejection, graft function, and graft survival were comparable between groups. At 1-year posttransplantation, interstitial fibrosis was significantly lower in the EVR group. EVR significantly suppressed p-4EBP1 phosphorylation and effectively modulated the mTOR-signaling pathway. Multivariable analysis identified the absence of EVR therapy as an independent predictor of accelerated fibrosis. EVR-involving immunosuppression attenuated renal interstitial fibrosis, likely through suppression of mTOR-signaling. Full article

Trehalose is a functional disaccharide widely used in the food, pharmaceutical, and cosmetic industries. It is industrially produced via a dual-enzyme process involving maltoligosaccharide trehalose synthase (MTSase) and maltoligosaccharide trehalose hydrolase (MTHase), with Escherichia coli (E. coli) serving as the expression host. Bacillus subtilis (B. subtilis) is an ideal host for industrial trehalose production due to its generally recognized as safe (GRAS) status and low phage susceptibility. However, engineered B. subtilis strains often exhibit slow growth, low heterologous protein expression, and high fermentation costs, thereby limiting their industrial application. To address these challenges, this study employed a synergistic strategy that combined chassis modification, expression element optimization, and knockout of substrate-competition pathways. First, a tryptophan-independent strain was constructed by reverting the trpC2 mutation to shorten the growth cycle. Next, knockout of flgD, yueB, and integration of E. coli-derived glutamate dehydrogenase (gdhA) significantly enhanced biomass accumulation. Expression of MTSase and MTHase was markedly improved through tandem strong promoters (P_HpaII-P₃₆) and ribosome-binding site (RBS) optimization (RBS1), achieving a 10.87-fold and 4.22-fold increase in enzyme activity, respectively. Finally, disruption of the amyE gene reduced non-specific substrate degradation. Using maltodextrin as substrate, the final trehalose conversion rate reached 76%. This study constructed B. subtilis chassis cells that highly express MTHase and MTSase respectively, laying a foundation for subsequent industrial trehalose production. Full article

Hemp hurds (HHs), an underutilised lignocellulosic biomass (LB) from agricultural waste, offer potential for bioconversion into high-value bioproducts within a circular bioeconomy. Building on prior work involving magnetic nanoparticle-immobilised cellulase hydrolysis of pretreated HH, this study computationally designed candidate phaCAB expression constructs for cellulolytic hosts toward future polyhdroxybutyrate (PHB) production. The objective was to evaluate, in silico, the feasibility of introducing the phaC1, phaA and phaB1 genes from Cupriavidus necator H16 (C. necator) (assembly GCA_000009285.2; loci H16_A1437–H16_A1439) into the cellulolytic hosts Clostridium thermocellum DSM 1313 (C. thermocellum) and Trichoderma reesei RUT C-30 (T. reesei). Coding sequences were retrieved and translated individually and host-specific expression compatibility was assessed via codon adaptation index, effective number of codons, GC content and rare-codon frequency/clustering. Host-specific architectures were designed: three independent tef1-promoter cassettes with fungal Kozak contexts and cbh1 terminators for T. reesei (TrePHB3 integration construct), and a single groEL-promoter operon with graded ribosome-binding sites for the pIKM1-based C. thermocellum construct (pCtPHB1); Escherichia coli BL21 (DE3) (E. coli)/pET-24a(+) served only as an intermediate assembly platform. Clustal Omega alignment, virtual plasmid assembly and simulated restriction digestion (SnapGene) confirmed preservation of the open reading frames and expected fragment sizes. ProtParam analysis indicated instability indices below 40 and negative GRAVY values for PhaC, PhaA and PhaB, indicating overall hydrophilic character. This computational framework links HH valorisation, cellulolytic Consolidated Bioprocessing (CBP) hosts and PHB pathway design within a conceptual biorefinery, supporting future integrated biomass-valorisation platforms; it is computational only and does not demonstrate transformation, expression, PHB accumulation or biomass conversion, which require experimental validation. Full article

Neglected arboviruses dengue (DENV), Zika (ZIKV), yellow fever (YFV), Japanese encephalitis (JEV), and chikungunya collectively affect hundreds of millions of people annually, yet no specific antiviral drug has been approved for any of them. Alkaloids, nitrogen-containing specialized metabolites produced by diverse plant families, have emerged as a promising source of broad-spectrum antiviral scaffolds. This review compiles and critically analyzes over 100 alkaloid-virus pairs across several RNA virus families, providing a comparative mechanistic analysis. Lycorine, narciclasine, emetine, and berbamine, among others, exhibit potent activity against phylogenetically distant viruses, with the most potent activities reported against flaviviruses (narciclasine: EC₅₀ 0.02 µM against DENV, ZIKV, YFV, and JEV; pancratistatine: 0.0063 µM against ZIKV). Structure-activity analysis of multiple alkaloid classes identifies key pharmacophoric features, including the phenanthridine nucleus (lycorine derivatives) and the bis-benzylisoquinoline scaffold (tetrandrine, berbamine), as determinants of antiviral potency, selectivity, and broad-spectrum activity. Genetic resistance data in West Nile virus challenge the widely accepted model of lycorine as a direct nucleoside inhibitor, instead pointing toward the involvement of the membrane-associated NS4A-2K-NS4B replication complex, though direct validation remains limited for other flaviviruses. Converging structural, biochemical, and transcriptomic evidence suggests that ribosome-mediated translational stress may represent an additional host-directed antiviral mechanism for isoquinoline-type alkaloids, though the causal chain from ribosome binding to activation of the integrated stress response and to antiviral effect has not been established. The present analysis highlights that in vivo validation remains limited to a few alkaloid-virus pairs. Unbiased target deconvolution and formal testing of the ribosome/integrated stress response hypothesis stand out as essential research priorities. Full article

Diffuse intrinsic pontine glioma (DIPG) is a rare and fatal pediatric brainstem malignancy for which effective treatment options are lacking. Cerebrospinal fluid (CSF) analysis can reveal intrinsic alterations and characteristic metabolic profiles of the tumor microenvironment. In this study, the proteome and metabolome of CSF from DIPG patients were comprehensively analyzed to identify potential biomarkers and the pathways involved. Functional annotation and pathway enrichment analyses were performed using the GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases. Bioinformatics methods were used to comprehensively analyze the proteomic and metabolomic results to identify key differentially expressed proteins, metabolites, and potential signaling pathways involved in DIPG. In total, 885 DEPs (differentially expressed proteins) were identified in cerebrospinal fluid from DIPG patients, of which 54 were upregulated and 831 were downregulated, primarily originating from the cytoplasm and cell membrane. Among the top 20 upregulated proteins, URB1 (nucleolar pre-ribosomal-associated protein 1) had the greatest statistical significance, while the remaining proteins were mostly immunoglobulin fragments. GO enrichment analysis revealed that the downregulated proteins were enriched primarily in cellular processes, metabolic processes, and binding functions. KEGG analysis revealed that upregulated proteins were significantly enriched in complement and coagulation cascades, whereas downregulated proteins were primarily associated with endocytosis and certain microbial infections. A total of 1372 metabolites were identified, of which 40 were differentially expressed: 24 were upregulated, and 16 were downregulated. Pathway analyses of the differentially expressed metabolites revealed that they were primarily related to purine metabolism and tyrosine metabolism. The multiomics analysis revealed that purine metabolism is particularly important in DIPG. Full article

The escalation of antimicrobial resistance (AMR) represents a serious global threat to public health, with AMR-associated mortality estimated to increase by 70% by 2050. As pathogens evolve through enzymatic inactivation, target modification, efflux-mediated clearance, biofilm formation, and broader genetic adaptation, conventional therapies are increasingly compromised, while the antibiotic development pipeline remains critically constrained by high discovery and development costs, weak commercial incentives, and the escalating complexity of resistance mechanisms. This review comprehensively synthesizes advanced pharmacological and biotechnological innovations designed to circumvent these entrenched resistance mechanisms. We highlight the development of novel therapeutic classes, particularly lariocidin, which disrupts bacterial protein synthesis via a previously unexploited ribosomal-binding site. Moreover, we critically evaluate molecular interventions, emphasizing CRISPR/Cas-based gene silencing and genome editing as precise tools to neutralize specific resistance determinants, such as the mecA gene in methicillin-resistant Staphylococcus aureus (MRSA). Concurrently, we explore the integration of engineered nanoparticles to revitalize existing antimicrobials by overcoming biofilm barriers, improving drug solubility, and enabling targeted delivery. Collectively, mastering the evolving AMR landscape requires a multidimensional framework that seamlessly integrates these novel molecular targets with advanced rapid diagnostics and robust international governance. Full article

Antimicrobial resistance in Neisseria gonorrhoeae is a global concern. Spectinomycin is unusual in that resistance can emerge rapidly during localized outbreaks yet often disappears from clinical populations after drug withdrawal, suggesting an associated growth cost. To investigate evolutionary routes to spectinomycin resistance, we performed in vitro selection on two N. gonorrhoeae strains and two commensal Neisseria species. Derived cell lines were characterized by minimum inhibitory concentration (MIC) determination, whole-genome sequencing, growth-kinetics analysis, and molecular modelling of the RpsE (ribosomal protein S5) interface with the ribosome. All high-level resistant isolates (MIC > 2048 mg/L) acquired substitutions or deletions in loop 2 of RpsE. Modelling showed that these mutations perturb the conserved network of stabilizing contacts between RpsE residues Lys25 (Lys23 in E. coli numbering) and Lys28 (Lys26), as well as helix 34 nucleotides G922, A923, and C1069 of 16S rRNA, potentially altering the architecture of the spectinomycin-binding site. These mutations were associated with high-level resistance but reduced growth rates, with the resulting growth costs depending on the specific pattern of contact rearrangements. Convergent evolution towards loop 2 mutations supports the existence of a constrained mutational pathway to high-level spectinomycin resistance in the strains and species examined here. This constraint may help explain the rapid decline of resistant variants in the absence of drug pressure and underscores the importance of genomic surveillance. Full article

Clinical genomics has traditionally focused on protein-coding variation, yet many pathogenic mechanisms arise through alterations in RNA processing, stability, localisation, translation, and surveillance. Prior reviews have addressed individual RNA layers, splicing, non-coding RNAs, RNA therapeutics, or RNA diagnostics in isolation. This review presents an integrated, mechanism-matched framework linking RNA-level disease mechanisms to diagnostic reasoning and therapeutic selection across all major RNA layers, offering a practical resource for clinical geneticists and translational researchers. I examine how splicing defects, pseudoexon inclusion, polyadenylation disruption, RNA editing loss, untranslated-region variants, premature termination codons, stop-loss variants, RNA-binding protein dysfunction, non-coding RNA dysregulation, altered codon usage, ribosome stalling, and surveillance pathway failure, including nonsense-mediated decay, nonstop decay, and no-go decay, each create distinct and mechanistically addressable disease states. A central argument of this review is that treatment selection must be mechanism-matched rather than gene- or variant-class-based: splice defects may require antisense oligonucleotide (ASO)-mediated correction or small-molecule splice modulation; toxic transcripts may require ASO- or siRNA-mediated silencing; haploinsufficiency may require mRNA replacement or transcript rescue; premature termination codons are candidates for readthrough only when transcript and protein context are favourable. I further argue that RNA sequencing, long-read transcriptomics, allele-specific expression analysis, and functional assays are essential for both diagnosis and therapeutic stratification. The framework described here moves clinical variant interpretation beyond descriptive classification toward mechanism-based, RNA-centric precision medicine. Full article

Tropical maize often exhibits photoperiod sensitivity, which limits its adaptation to temperate regions. Understanding its proteomic dynamics under long-day conditions is therefore crucial for germplasm improvement. This study employed a Tandem Mass Tag (TMT)-based proteomic approach to investigate stage-specific protein expression patterns in the tropical maize inbred line QR273 under long-day conditions (16 h light/8 h dark). Seeds were cultivated in climate chambers, and leaves were collected at the four-leaf (P4) and nine-leaf (P9) stages. A total of 2881 differentially expressed proteins (DEPs) were quantified between the P4 and P9 stages, among which only 7 were upregulated and 2874 were downregulated at the P9 stage. Gene Ontology (GO) enrichment analysis revealed that these DEPs were significantly enriched in processes related to proteolysis, membrane components, and ATP binding. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed the enrichment of DEPs in amino acid biosynthesis, secondary metabolite biosynthesis, and aminoacyl-tRNA biosynthesis pathways. Protein–protein interaction (PPI) network analysis identified 60S ribosomal protein L12, adenosine 5′-phosphosulfate reductase, and RuvB helicase as core hub proteins. Based on functional annotation of representative DEPs, the DEPs were classified into four categories: 9 proteins related to storage material protection, 14 proteins related to protein modification, 12 proteins related to photosynthesis, and 25 proteins with other biological functions. Comparative analysis demonstrated a decrease in storage material protection, protein modification, and photosynthetic capacity at the P9 stage relative to the P4 stage. These findings provide insights into the proteomic dynamics underlying tropical maize development under long-day conditions and offer a theoretical basis for genetic improvement of tropical maize germplasm. Notably, inferences regarding nutrient reallocation based on DEP downregulation are derived solely from proteomic data and require further experimental validation. Full article

In vitro maturation (IVM) is a critical step affecting the efficiency of bovine in vitro embryo production; however, oxidative stress during in vitro culture can impair oocyte quality and subsequent developmental competence. This study investigated the effects of cysteine supplementation on bovine oocyte IVM, redox homeostasis, mitochondrial status, and transcriptomic changes. Bovine cumulus-oocyte complexes were cultured in IVM medium supplemented with 0, 25, 50, 75, 100, or 125 μM cysteine, and 75 μM was identified as the optimal concentration. Compared with the control group, 75 μM cysteine increased the first polar body extrusion rate from approximately 78% to 81% and improved the fertilization/cleavage rate from approximately 74% to 82%. It also significantly increased the proportions of 2-cell, 4-cell, and 8-cell embryos, whereas morula and blastocyst rates were not significantly affected. At the cellular level, 75 μM cysteine significantly reduced ROS levels and increased GSH content, as indicated by changes in relative fluorescence intensity. JC-1 staining showed that the JC-1 monomer signal decreased from approximately 16.0 to 13.5, whereas the JC-1 aggregate signal increased from approximately 13.2 to 14.8, indicating improved mitochondrial membrane potential status. In addition, lipid droplet fluorescence intensity increased from approximately 11.8 to 13.4, mitochondrial fluorescence intensity increased from approximately 6.0 to 7.0, and cytoskeletal fluorescence intensity showed no significant difference between groups. Smart-seq2 transcriptomic analysis identified 1935 differentially expressed genes, including 1778 upregulated and 157 downregulated genes, which were mainly enriched in translation, ribosomal structural components, RNA binding, oxidative phosphorylation, and metabolism-related pathways. qRT-PCR further confirmed the upregulation of key genes, including NDUFS2, VDAC3, ANXA2, MTHFD1L, and SCD. Overall, 75 μM cysteine improves bovine oocyte IVM quality by enhancing antioxidant capacity, improving mitochondrial membrane potential, increasing lipid-derived energy substrate storage, and regulating genes related to energy metabolism and developmental competence. Full article

Acinetobacter baumannii is a significant pathogen of hospital-acquired infections, and its multidrug resistance (MDR) and extended drug resistance (XDR) have become increasingly severe, posing a global public health challenge. This article provides a narrative review of the major resistance mechanisms of Acinetobacter baumannii, including β-lactamase production, efflux pump overexpression, target site modification, reduced membrane permeability, and biofilm formation. Additionally, it summarizes the current main drugs and their target sites for treating MDR Acinetobacter baumannii infections, with a focus on the mechanism of action, antibacterial activity, and clinical research progress of the novel fully synthetic fluorocycline antibiotic—eravacycline. Eravacycline inhibits protein synthesis by high-affinity binding to the bacterial ribosomal 30S subunit and demonstrates activity against multidrug-resistant Acinetobacter baumannii (excluding Pseudomonas aeruginosa), providing a potential novel therapeutic option for MDR/XDR Acinetobacter baumannii infections. Finally, the article outlines future research directions and treatment strategies. Due to the narrative nature of this review, no systematic methodology (e.g., PRISMA) was applied, and the available clinical evidence, particularly for CRAB infections, remains limited. Full article

Ribosome-inactivating proteins are a class of toxins that target eukaryotic ribosomes, inhibit protein synthesis, and ultimately induce cell death. Several of these toxins pose significant clinical and public health threats. Among these, ricin, derived from the castor bean plant (Ricinus communis), is a highly potent biotoxin with recognized bioterrorism potential. Other ribosome-inactivating proteins, including Shiga toxin produced by pathogenic Shigella and Escherichia coli, as well as mucoricin from Mucorales fungi, contribute to disease severity and can lead to life-threatening complications. Despite these risks, no approved therapeutics are currently available. The development of effective inhibitors depends on robust and well-defined strategies to identify and validate small molecules that disrupt toxin–ribosome interactions. Efforts to target the catalytic active site have met with limited success, largely due to its broad, shallow, and highly polar architecture, which is not conducive to high-affinity binding by drug-like molecules. In contrast, the ribosome-binding interface represents a more tractable target, as it is essential for toxin recruitment and offers more structurally defined and druggable features. Inhibitors targeting this interface can also exert allosteric effects by disrupting long-range conformational coupling between the ribosome-binding region and the active site, thereby attenuating catalytic activity without directly engaging the catalytic pocket. In this review, we compile and evaluate biophysical and biochemical assays for the discovery and characterization of small-molecule inhibitors that target toxin–ribosome interactions. We examine in vitro binding approaches, including surface plasmon resonance-based fragment screening and fluorescence anisotropy assays for ranking inhibitory activity. We further review biochemical and molecular assays that assess ribosome protection from toxin-mediated depurination, along with complementary cell-based assays that evaluate functional rescue in cellular systems. Collectively, this review consolidates current screening methodologies and highlights opportunities to refine assay strategies, thereby supporting the advancement of targeted therapeutics. Full article

The scaffold protein RACK1 (Receptor for Activated C Kinase 1) integrates signaling and translation, acting as a core component of the 40S ribosomal subunit. It binds activated Protein Kinase C (PKC) isoforms and membrane receptors. We used an auxin-inducible degron (AID2) system in human HAP1 cells to selectively deplete the free (cytoplasmic) pool of RACK1. The engineered RACK1–mAID–mClover3 fusion was rapidly degraded in the cytoplasm upon addition of 5-phenyl-indole-3-acetic acid (5-Ph-IAA), while the ribosome-bound pool remained detectable in ribosomal fractions, indicating that ribosome association makes RACK1 relatively less accessible to AID2-mediated proteolysis. Upon activation of PKCβII with phorbol-12-myristate-13-acetate (PMA), imaging at defined time points revealed closely matched kinetics of PKCβII membrane recruitment and membrane-proximal enrichment of ribosome-bound RACK1, peaking at ~10 min. Our data support a model in which activated PKCβII engages ribosome-bound RACK1 at membrane-proximal sites, consistent with a diffusion–capture mechanism in which PKCβII first accumulates at the membrane and then captures ribosome-bound RACK1, thereby recruiting the translational machinery to sites of signal input for membrane-proximal translation. These findings provide new insights into the spatial organization of translation. Full article

An eight-week feeding trial was conducted to investigate methionine and lysine supplementation on the growth performance, body composition, antioxidant index and protein synthesis-related gene expression of the FFCR No. 2 strain common carp (Cyprinus carpio). The experiment included five groups: the CON group (basal diet), CM group (supplemented with 0.6% crystalline methionine), CML group (supplemented with 0.6% crystalline methionine and 0.3% crystalline lysine), HM group (supplemented with 0.6% coated methionine), and HML group (supplemented with 0.6% coated methionine and 0.3% coated lysine). The results showed that the WG (weight gain), SGR (specific growth rate) and CF (condition factor) of the HML group were significantly increased (p < 0.05), and the activities of amylase, lipase, and protease in the intestine of those belonging to the HML group were significantly higher than those in the CON group (p < 0.05). The whole-body crude lipid, SOD (superoxide dismutase), GOT (glutamic oxaloacetic transaminase) activity, and BUN (urea nitrogen) levels in serum were reduced significantly in the HM and HML groups than in the CON group (p < 0.05). Additionally, in the HML group the gene expression levels of IGF-1 (insulin-like growth factor-1), IGFBP (insulin-like growth factor binding protein), 4EBP1(recombinant eukaryotic translation initiation factor 4E binding protein 1), and S6K1 (ribosomal protein s6 kinase 1) in the muscle were significantly higher than those in the CON group. In summary, supplementing coated methionine and lysine improved amino acid utilization, enhanced growth performance, and upregulated the expression of genes associated with growth and protein synthesis. Full article

As a devastating disease worldwide, rice bacterial leaf blight—caused by Xanthomonas oryzae pv. oryzae (Xoo)—leads to substantial reductions in grain yield. The increasing resistance to conventional bactericides necessitates the development of novel and sustainable control agents. This study evaluated 58 novel alkyl sulfonamide compounds against Xoo. In the turbidimetric assay at 100 mg/L, several compounds showed potent antibacterial activity. Among them, SYAUP-116 and SYAUP-212 exhibited in vitro inhibition comparable to that of streptomycin sulfate at the same concentration. Furthermore, in EC₅₀ determination assays, both compounds yielded lower EC₅₀ values than zinc thiazole. Among the 58 compounds tested, SYAUP-491 exhibited an in vitro EC₅₀ of 6.96 mg/L and achieved 74.1% in vivo therapeutic efficacy at 200 mg/L, representing the most promising lead for further characterization. Molecular docking, based on prior proteomic data, indicates potential stable binding to ribosomal proteins (50S L33/L34 and 30S S5), with the strongest interaction observed for L33 (binding free energy: −5.73 kcal/mol). This suggests a putative mechanism involving ribosome targeting and protein synthesis inhibition, which may be facilitated by hydrophobic interactions and halogen bonds derived from its trifluoromethyl and sulfonamide groups. SYAUP-491 demonstrates significant potential as a novel bactericide for rice bacterial leaf blight, warranting further research on structure-activity optimization, target validation, and field performance. Full article