Search Results (6,399)

To investigate the codon usage bias (CUB) and its influencing factors in the chloroplast genome of Styphnolobium japonicum f. oligophyllum, we sequenced, assembled and annotated the genome using Illumina high-throughput sequencing, and systematically analyzed 52 protein-coding sequences. The chloroplast genome is 158,739 bp with a typical quadripartite structure, containing 129 functional genes. It presents a mean GC₃ content of 28.26% and a mean ENC value of 45.40, indicating weak CUB and low gene expression. Among 31 preferred codons (RSCU > 1), 29 (93.5%) end with A/U. Neutrality plot, ENC-plot and PR2-plot analyses reveal that natural selection is the primary regulator of CUB. A total of 19 optimal codons were identified. These results provide fundamental reference data that may facilitate future genetic engineering efforts in S. japonicum f. oligophyllum. Full article

The stingless bee Geniotrigona thoracica is an ecologically and economically important pollinator in Southeast Asia, yet comprehensive genomic resources for this species remain limited. In this study, we sequenced, assembled, and annotated the complete mitochondrial genome (mitogenome) of G. thoracica to investigate its genomic architecture and phylogenetic position. The circular mitogenome is 16,061 bp in length and comprises the typical set of 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes. The genome exhibits a strong A + T bias, consistent with other hymenopteran mitogenomes, and codon usage patterns reflect this nucleotide composition. Most tRNAs display the canonical cloverleaf secondary structure, although minor structural variations were observed. Comparative analyses revealed several gene rearrangements, including transposition and inversion events, suggesting lineage-specific rearrangements, including transposition of the cox1–trnL–cox2–trnD–atp8–atp6–cox3 block and transposition with inversion of the trnF–nad5–nad4–nad4l–trnP block, relative to the ancestral hymenopteran gene order. Phylogenomic analyses based on concatenated mitochondrial genes strongly supported the monophyly of Meliponini and placed G. thoracica within a well-supported Indo-Malayan clade, closely related to Tetragonula, Heterotrigona, and Lepidotrigona. Furthermore, stingless bees were recovered as more closely related to bumblebees than to honeybees, consistent with previous studies. Overall, this study provides a complete, annotated mitogenomic resource for G. thoracica and contributes to a better understanding of mitochondrial genome evolution, phylogenetic relationships, and biogeographic patterns in stingless bees. Full article

The high-rate biological contactor (HRBC) is an enhanced-primary, biosorption-based, carbon-diversion wastewater treatment process with short hydraulic retention time (HRT), short solids retention time (SRT), low dissolved oxygen (DO), and high food-to-microorganism ratio (F/M). This paper presents modifications to a commercial full-plant wastewater biodegradation model using extracellular polymeric substances (EPS) in waste activated sludge (WAS) to simulate pilot test biosorption data. Bench-scale HRBC tests found that each mg of EPS as COD (COD_EPS) biosorbed 1.02 mg sCOD contained in raw wastewater. The fraction of AS organics identified as EPS in terms of COD was 37% in a conventional AS (CAS), 33% in a trickling filter-solids contact (TF/SC), and 18% in a membrane bioreactor (MBR). The modeling process used stoichiometry equations to convert EPS from its constituent concentrations (carbohydrates, proteins, humic acids, uronic acids) into COD. The conversion did not alter the finding that the normalized total EPS showed a positive relationship with soluble chemical oxygen demand sCOD biosorption with a 0.91 coefficient of determination. The modified commercial biodegradation model gave a maximum error of −12.6% when simulating pilot-scale results, and 80% of all data points were less than ±10% error. The modified model predicted 16% sCOD biosorption by EPS using the design data for a full-scale HRBC facility currently under construction. Full article

The ATP-binding cassette transport protein Pdr5p is known to play a role in multidrug resistance in Saccharomyces cerevisiae by effluxing structurally diverse xenobiotics; yet the physicochemical determinants of substrate recognition remain poorly defined. To address this, density functional theory (DFT) calculations at the B3LYP-D3BJ/def2-SVP level were combined with machine learning to derive a predictive model of substrate recognition using a curated dataset of 66 compounds spanning 9 functional categories. A hybrid support vector machine (SVM) classifier achieved 96.3% accuracy (95% CI: 81.0–99.9%, Clopper–Pearson exact) in discriminating substrates from non-substrates under leave-one-out cross-validation. Feature importance analysis identified lipophilicity (LogP, F-score = 37.5) as the dominant descriptor, suggesting that membrane partitioning constitutes the initial recognition step. The HOMO–LUMO gap contributed secondarily (F-score = 12.4). Substrates were further distinguished by high frontier orbital focalization, with frontier orbital spread of 1.8–2.6%, compared to 4.18–7.22% for non-substrates. Notably, a model trained exclusively on Pdr5p data achieved 87% prediction accuracy when applied without retraining to the human P-glycoprotein (ABCB1) dataset, suggesting conserved physicochemical principles of substrate recognition across evolutionarily distant ABC transporters. These findings provide a quantum chemical framework for understanding and potentially predicting MDR transporter substrate specificity. Full article

Adult bone marrow-derived mesenchymal stem cells (BMSCs) are multipotent progenitors capable of differentiating into diverse cell lineages, including osteogenic, chondrogenic, adipogenic, and neuronal lineages. In BMSCs, intracellular glutathione (GSH) is a critical determinant of stemness maintenance and differentiation outcomes. However, how intracellular GSH homeostasis is regulated during BMSC-to-neuron differentiation remains unclear. In neurons, GSH synthesis critically depends on cysteine uptake mediated by the excitatory amino acid carrier 1 (EAAC1). Here, we investigated the expression, subcellular localization, and functional contribution of EAAC1 and its regulatory protein, glutamate transporter-associated protein 3-18 (GTRAP3-18) in mouse BMSCs and neuron-like BMSCs generated by Notch intracellular domain-based induction (NICD-3F BMSCs). BMSCs exhibited higher intracellular GSH levels than NICD-3F BMSCs, despite comparable levels of EAAC1 protein. In contrast, EAAC1-dependent cysteine uptake and plasma membrane localization of EAAC1 were markedly reduced in BMSCs, indicating differentiation-dependent regulation of EAAC1 trafficking. Treatment with the xCT inhibitor erastin reduced intracellular GSH levels in both BMSCs and NICD-3F BMSCs. GTRAP3-18 expression was high in BMSCs and significantly reduced in NICD-3F BMSCs. Notably, GTRAP3-18 knockout decreased intracellular GSH levels in BMSCs without altering total EAAC1 protein or intracellular cysteine levels, whereas in NICD-3F BMSCs, both GSH and EAAC1 protein levels were increased. These findings demonstrate lineage-dependent divergence in GSH regulatory mechanisms and reveal previously unrecognized functions of GTRAP3-18 in redox control during stem–to–neuron differentiation. Full article

Skeletal muscle differentiation relies on transient DNA strand breaks (DSBs), yet excessive DNA damage remains harmful to myogenic progression. The RNA-binding protein Zfp36l1 is expressed in skeletal muscle and contributes to muscle regeneration; nevertheless, its role in preserving genome stability during myogenic differentiation has not been defined. Here, we investigated the role and mechanism of Zfp36l1 in regulating DNA damage using C2C12 myoblast cells, combining loss- and gain-of-function assays, RNA-seq, and rescue experiments. The results revealed that Zfp36l1 expression is strongly induced during early myogenic differentiation, coinciding with the onset of physiological DSBs. Functional assays revealed that silencing Zfp36l1 aggravates DSB accumulation, reinforces G0/G1 cell cycle arrest, and promotes apoptosis, whereas Zfp36l1 overexpression attenuates these abnormalities. Transcriptomic profiling shows that Zfp36l1 knockdown impairs homologous recombination (HR)-mediated DNA repair by downregulating core repair factors, including Rad51 and Brca1. Gene set enrichment analysis further confirms significant suppression of the HR-dependent DSB repair pathway. Mechanistically, Zfp36l1 regulates HR repair by suppressing p21 expression, thereby relieving inhibition of E2F1-mediated Rad51 transcription. Co-silencing p21 restores Rad51 expression and reduces DNA damage in Zfp36l1-knockdown cells. Collectively, these findings identify Zfp36l1 as an essential safeguard of genome stability during myogenic differentiation by balancing DNA damage levels through the p21-E2F1-Rad51 signaling axis, and provide new insights into the regulatory basis of muscle development and genomic instability-associated muscle diseases. Full article

The misuse of antibiotics is causing widespread antibiotic resistance, creating an urgent need for new treatment options such as nanoparticle-based therapies. This study aimed to compare silver nanoparticles (AgNPs) produced via green synthesis methods with those made through traditional chemical processes. Furthermore, the study investigated and contrasted the bacterial responses to these two types of AgNPs over a 21-day period of selection pressure using experimental evolution techniques. Analysis using scanning electron microscopy and transmission electron microscopy revealed a consistent, uniform morphology among the AgNPs produced via chemical methods. In contrast, AgNPs synthesized through green methods displayed an irregular morphology. Despite these morphological differences, all nanoparticles from both synthesis approaches were under 100 nm in diameter. These findings were further supported by the absorption spectrum data, which showed a maximum absorption peak between the 400 and 500 nm wavelength range. E. coli exposed to green synthesized AgNPs for 21 days adapted to their presence, exhibiting both enhanced resistance to the green synthesized AgNPs themselves and the development of cross-resistance to ionic silver, a pattern not observed in chemically synthesized AgNP-selected populations. Populations selected using chemical synthesized AgNPs did not develop increased resistance to either chemically or green synthesized AgNPs; however, they showed a slight increase in resistance to ionic silver. Genomics analysis identified polymorphism in genes in a green synthesized AgNP-resistant line including but not limited to the multidrug efflux transporter system (EmrAB), DUF4756 family protein (D1792_RS05680), putative zinc-binding protein YnfU/cold shock-like protein (ynfU/cspB) and imcF-related family protein (D1792_RS10035). Bacterial resistance to chemical AgNPs involves specific polymorphisms in key bacterial components like the RNA polymerase sigma factor (RpoE) and the EmrAB efflux pump. Collectively, the method used to synthesize the AgNPs influences their antibacterial efficacy and the likelihood of bacteria developing resistance. Understanding this interaction is vital for developing effective and resistance-controlled applications of AgNPs across medicine, environmental science, and industry. Full article

This research analyzed metabolomic and proteomic differences between participants with gingivitis (>20 bleeding sites) and generally healthy participants (≤3 bleeding sites) at baseline and 4 weeks post stannous fluoride (SnF₂) dentifrice treatment. Sixty-two metabolites were different (p < 0.05) between groups at baseline. Forty cytokines were analyzed using immunoassays and a group of proinflammatory cytokines (IL-1α, IL-1β, TNF-α, SAA, ICAM-1, VCAM-1) was elevated in participants with gingivitis (p < 0.1) versus healthy gingiva at baseline, with C-reactive protein (p < 0.05) being significantly elevated. Proteomic analysis carried out in baseline oral lavage revealed four of the top hits (p < 0.0004) were central-metabolism-related: aldolase A, triosephosphate isomerase, lactate dehydrogenase, and malate dehydrogenase. Enzymatic assays confirmed the proteomic finding that malate dehydrogenase and triosephosphate isomerase activities were elevated in gingivitis samples; SnF₂ dentifrice treatment reduced their activity. Collectively, 20 proteins with the lowest p-values in oral lavage appeared to be indicative of periodontal health, potentially forming the basis to cluster samples into healthy and unhealthy groups. A TLR-ATP biosensor model was established and demonstrated that microbial virulence factors induced the observed changes in oral lavage. Combined findings suggest gingivitis involves upregulation of host cell bioenergetic processes involving enzymatic activity in the glycolysis and citric acid cycle pathways. Full article

Background: Pathogenic germline BRCA1 and BRCA2 variants cause most hereditary breast and ovarian cancers. Widespread genetic testing has revealed thousands of variants with unknown effects on disease risk, known as variants of uncertain significance (VUS). BRCA VUS, the majority of which are missense, complicate genetic test interpretation and clinical decision-making. This study aimed to evaluate BRCA1 VUS pathogenicity with enhanced accuracy through computational, functional and structural methods. Methods: We characterized the structural distribution of BRCA1 variants. In silico tools scored known consequence variants within a specific region of BRCA1. The Molecular Feature Selection Tool (MolecularFeaST; Renwick Lab at Queen’s University; Kingston, ON, Canada) performed feature selection of the most discriminative tools. MATLAB (MATLAB R2024a; Mathworks; Natick, MA, USA) Classification Learner Application trained supervised machine learning models using combinations of the most accurate tools; the best model assigned pathogenicity prediction scores to VUS. Select VUS were functionally assessed through phosphopeptide binding pull-down assays and structurally analyzed on PyMOL (v2.4.1; Schrödinger Inc.; New York, NY, USA). Results: The RING and BRCT domains were identified as hotspots for missense pathogenic variants and VUS; BRCT was selected as the focus of the computational classifier. Nine in silico tools (CADD hg19, MetaRNN, ClinPred, VEST4, BayesDel AD, EVE, Eigen PC, gMVP and PolyPhen2) defined the BRCT-specific missense variant classifier. Twenty-two VUS (R1699P, F1704S, W1837L, W1712G, F1734S, V1804A, I1674V, V1804L, V1804I, I1807V, T1675S, I1764L, N1774I, E1698K, Q1848K, P1749S, A1669T, N1774H, L1839V, T1658I, L1705I, V1654L) demonstrated varying phosphopeptide binding ability and protein levels relative to the wildtype. Computational structural modeling contextualized VUS phosphopeptide interactions and structural implications. Conclusions: We provide in silico and functional evidence for the classification of BRCA1 BRCT VUS and highlight the utility of domain-specific computational approaches for characterizing missense variants in multi-domain genes. Full article

Respiratory syncytial virus (RSV) is considered the leading causative agent of acute lower respiratory infections in infants and young children worldwide, which makes it a major contributor to pediatric morbidity and mortality. Infants are especially susceptible to severe disease in early life, which underlines the urgent need for developing effective immunization strategies against this virus. However, the development of vaccines against RSV has long been associated with significant challenges. For example, initial attempts, especially those involving formalin-inactivated RSV, resulted in vaccine-enhanced respiratory disease upon subsequent infection, which set a significant safety obstacle for future vaccine candidates. Other challenges facing vaccine development against RSV include the short-lived immunity induced by natural infection, lack of clear correlates of immunity, and immune naivety in infants. Recent breakthroughs in structural virology and immunology have provided insights into protective immunity against RSV, especially regarding neutralizing antibodies that recognize the virus in its prefusion conformation of the viral F protein. Among promising vaccine candidates, intranasal live-attenuated vaccines have emerged as especially promising for infant immunization, especially considering their close mimicry of natural infection that can elicit systemic as well as mucosal immunity in the respiratory tract. A newly emerging approach for live-attenuated virus vaccine development is codon-pair deoptimization (CPD), which is based on synthetic recoding that reduces viral replicative capacity while maintaining intact protein sequences and structure. The preclinical results of CPD-based RSV candidates have provided evidence of such vaccines’ ability to elicit robust immunity while maintaining favorable safety profiles. This review addresses the major challenges associated with the development of effective RSV vaccines for infant immunization, with particular emphasis on lessons learned from previous vaccine failures and recent advances in RSV vaccine development, particularly CPD-based attenuation strategies. Full article

Optimizing nutrient management is critical for enhancing crop productivity and grain nutritional quality in reclaimed soils, where poor soil fertility and salinity often limit barley cultivation. In that context, this study evaluated the effects of NPK fertilization on barley grain metabolism in reclaimed soil, using four barley cultivars (Betaone, Heuknuri, Nurichal, and Sogang) under fertilized (F) and non-fertilized (NF) conditions. Chemical fertilization (N–P₂O₅–K₂O = 88–72–36 kg ha⁻¹) increased crude protein (CP) concentrations in Heuknuri and Sogang by over 30%, while reducing the soluble sugar content by 15–24%. In contrast, starch content remained relatively stable across all cultivars. Gas chromatography–mass spectrometry (GC–MS) profiling revealed that fertilization caused only modest changes in grain primary metabolism, including increased fatty acids (oleate, linoleate), alongside consistent accumulation of amino acids related to nitrogen assimilation (asparate, asparagine, glutarate, proline). Two-way ANOVA and principal component analysis (PCA) revealed that the cultivar identity, rather than fertilization, was the dominant factor shaping metabolic variation, affecting 23 of 28 detected metabolites. Notably, Betaone and Heuknuri exhibited higher overall metabolite accumulation and stable metabolic profiles across treatments, suggesting better physiological adaptation to nutrient-deficiency stress. These results indicate that NPK fertilization under reclaimed soil conditions promotes nitrogen assimilation more than carbon storage, and grain metabolic changes are largely cultivar-dependent. However, the underlying regulatory mechanisms controlling carbon–nitrogen allocation and lipid metabolism under fertilization were not fully investigated and require further multi-omics and long-term field studies. Full article

Background/Objectives: Chronic myeloid leukemia (CML) is primarily associated with the BCR:ABL1 fusion protein. Although tyrosine kinase inhibitors (TKIs) have markedly enhanced treatment outcomes, the development of agents with improved therapeutic characteristics remains necessary. The present work focused on the synthesis of a new series of thiazolone derivatives (F1-11) and the assessment of their anti-CML activity through inhibition of ABL tyrosine kinase (TK). Methods: The designed compounds were prepared through a multistep synthetic pathway involving the formation of a new chalcone intermediate (A), synthesis of a new pyrazoline carbothioamide intermediate (B), and cyclization with different aldehydes to produce the target new thiazolone derivatives (F1-11). Cytotoxic effects were investigated against K562 CML cells using the MTT assay. The lead compound was additionally evaluated in HL-60 AML cells and normal PBMCs. Apoptotic induction was analyzed using Annexin V/ethidium homodimer staining, whereas ABL TK inhibitory activity was measured through the ADP-Glo assay. Molecular docking studies were conducted to explore ligand interactions within the ATP-binding domain of ABL TK. Results: Among the synthesized molecules, F-4 demonstrated the strongest activity against K562 cells with an IC₅₀ value of 6.85 µM, close to that observed for imatinib (IC₅₀ = 5.20 µM). The compound showed reduced cytotoxicity toward HL-60 cells (IC₅₀ = 33.44 µM) and exhibited favorable selectivity toward PBMCs (SI = 13). Apoptosis studies revealed 51% early apoptotic cells and 43% late apoptotic cells following treatment. In the kinase assay, F-4 inhibited ABL TK activity by 39% at 10 µM and by 70% at 100 µM. Docking simulations suggested interactions with residues His361 and Asp381 in addition to nearby hydrophobic amino acids, although the interaction network was less extensive than that of imatinib. Conclusions: The findings identify F-4 as a promising new thiazolone-derived scaffold with selective anti-CML activity and notable ABL TK inhibitory potential. Additional structural optimization may further enhance its binding characteristics and therapeutic efficacy. Full article

Background/Objectives: The Indian star tortoise (Geochelone elegans) is a protected species for which physiological and molecular health indicators remain poorly characterized. This study aimed to monitor and analyze plasma proteome profiles and biochemical parameters in captive adult Indian star tortoises and to identify potential diagnostic biomarkers. Methods: Plasma samples from nine clinically healthy adult Indian star tortoises (four males and five females) maintained in captivity were subjected to biochemical profiling and proteomic analysis. Sex-related differences in biochemical parameters were evaluated, and differentially expressed proteins were mapped to Homo sapiens Reactome pathways to identify significantly enriched biological processes. Results: Plasma biochemical profiling established baseline reference values, indicating stable hepatic and metabolic function in captive tortoises. Creatinine and urea concentrations were significantly higher in females than in males (p < 0.05), suggesting sex-related differences in protein metabolism or renal function. No significant sex-related differences were observed in hepatic enzymes (ALP, ALT, AST, and GGT), muscle-associated enzymes (CK and LDH), glucose, cholesterol, triglycerides, total proteins, albumin, or electrolyte concentrations (Na, K, Ca, Mg, Cl, P, and Fe). Proteomic analysis identified 12 differentially expressed proteins, including nine upregulated and three downregulated proteins. Functional pathway analysis revealed 90 significantly enriched Reactome pathways (FDR < 0.05). Upregulated proteins were primarily associated with cytoskeletal organization (KRT75, KRT5, and KRT17), lipid transport and remodeling (APOB), coagulation (F10), extracellular transport (TTR), immune response (WFDC3), transmembrane signaling (KCP), and gamete interaction (ZAN). Downregulated proteins (C7, SERPING1, and PZP) were linked to complement activation and acute-phase response pathways. Conclusions: Captive Indian star tortoises exhibited increased cytoskeletal remodeling and coagulation activity together with reduced complement activation. These findings provide novel insights into the plasma proteome of this species and identify candidate biomarkers that may support future health assessment, physiological monitoring, and diagnostic applications in Indian star tortoises. Full article

Choline-based ionic liquids (ILs) have emerged as promising candidates for application in multifaceted avenues, including electrochemistry, biomaterials, and environmental remediation technologies. However, their regulatory effects on the growth of agricultural plants have rarely been discussed. In this study, 14 choline–fatty acid ILs ([Chl][FA] ILs) containing different FA anions were synthesized, and their effects on the maize growth were investigated. Hydroponic experiments revealed that low concentrations (20 mg/L) of dicarboxylic acid-based [Chl][FA] ILs (e.g., choline pentane diacid [Chl][Pent]) significantly promoted maize root and shoot biomass, whereas higher concentrations inhibited it. Specifically, [Chl][Pent] enhanced chlorophyll content without altering Fv/F₀, upregulated nitrate reductase (NR) and glutamine synthetase (GS) activities, and stimulated the expression of key nitrogen metabolism (NR and GS) and photosynthetic (Rubisco) genes. Pathway analyses of differentially expressed genes indicated that [Chl][Pent] was associated with the upregulation of nitrogen and glycerophospholipid metabolism. [Chl][Pent] increased the average grain yield by 6.88% over two years compared to CK. Field application of [Chl][Pent] increased grain yield and protein accumulation relative to both control and choline chloride treatments. Overall, these findings demonstrate the potential of dicarboxylic acid-based [Chl][FA] ionic liquids as eco-friendly biostimulants for enhancing crop growth, yield, and quality. Full article

Semaphorins are a large family of proteins originally identified for their roles in axon guidance during neural development. Recent findings have established the importance of semaphorins members in modulating diverse immune responses of T cells in vitro and in vivo. Class 3 semaphorins, typified by Sema3A, signal through Neuropilin-1 and Plexin-A receptors in an activation-dependent manner, suppressing effector proliferation while promoting regulatory T cell stability and shaping cytokine profiles in autoimmunity and cancer. Sema3E and Sema3F similarly fine-tune host defense and inflammation by directing Th1/Th17 responses or restraining aberrant chemotaxis. Class 4 members, such as Sema4A and Sema4D, engage Plexin-B1, Plexin-D1, and CD72 to deliver both “forward” co-stimulatory and “reverse” signals: they amplify CD4⁺ and CD8⁺ effector functions, support T helper-B cell crosstalk, and influence tumor immunity via receptor shedding and bidirectional signaling. Finally, although less well defined, class 7 Sema7A operates indirectly—through APCs and Tregs—to regulate inflammatory recall responses and Th1/Th17 driven pathology. Together, these semaphorin-mediated pathways underscore a complex, context-dependent network that balances protective immunity against immunopathology, offering novel therapeutic targets in autoimmunity, infection, and cancer. Full article