Search Results (11,845)

Background/Objectives: Signaling mediators of PPARγ influence pathways involved in adipogenesis, lipid storage, inflammation, energy-related processes, and glucose utilization. Recent research indicates that PPARγ coregulators, recruited or released during ligand binding, govern specific gene pathways. It was recently discovered that Gα_q, a heterotrimeric G protein subunit, also signals to PPARγ and may significantly affect adipogenesis and glucose sensitivity. Methods: To explore Gα_q’s role in adipocytes, we generated CRISPR-mediated Gα_q (Gnaq) knockout (Gnaq KO) and scramble control cells from 3T3-L1 preadipocytes. Results: The absence of Gα_q resulted in increased lipid accumulation and elevated serine 273 (but not serine 112) phosphorylation of PPARγ. Gα_q deficiency also decreased mitochondrial abundance and respiration in response to PPARγ ligands such as rosiglitazone, pioglitazone, and troglitazone. RNA sequencing comparing differentiated Gnaq KO and control adipocytes identified over 800 differentially expressed genes, including those associated with enhanced lipid metabolism and reduced inflammation. Corresponding PamGene kinome profiling showed increased serine/threonine kinase activity and decreased phosphotyrosine kinase signaling in Gnaq KO adipocytes. Conclusions: These findings support Gα_q as a regulator of adipocyte function, linking kinase signaling pathways to PPARγ-mediated transcription. This research provides mechanistic insights into targeting Gα_q as a potential treatment for individuals with obesity and metabolic disorders. Full article

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

With the increasing demand for sustainable animal production, the utilization of agricultural and processing by-products as functional feed ingredients has gained growing attention. However, the application of Xiasangju processing residues, a by-product generated during the industrial processing of the traditional Chinese herbal formula Xiasangju, in poultry nutrition remains poorly understood. This study aimed to evaluate the nutritional composition, bioactive components, and potential functional effects of Xiasangju processing by-products as a dietary supplement for late-laying hens. Chemical composition was characterized using LC-MS and conventional nutritional analysis, while potential anti-inflammatory mechanisms were predicted via network pharmacology. A total of 288 Jingfen laying hens (55 weeks old) were randomly assigned to four dietary treatments supplemented with 0, 0.5%, 1.0%, or 1.5% Xiasangju processing by-products for 56 days. Results showed that 11 major active compounds were identified, including relatively high levels of linarin and rosmarinic acid, along with abundant crude protein, fiber, minerals, and amino acids. Dietary supplementation at 1.5% was associated with higher egg production rate, egg weight, and yolk color without obvious adverse effects on organ indices or serum biochemical parameters. This treatment was also associated with lower inflammatory gene expression, including IL-6 and COX-2 in the ileum and NF-κB, IL-6, COX-2, and TNF-α in the cecum. No significant effects were observed on antioxidant status in yolk or liver, or intestinal morphology. Integrated analyses using network pharmacology, molecular docking, and in vitro COX-2 inhibition suggested that anti-inflammatory-related responses may involve COX-2-related pathways, while 16S rRNA sequencing indicated changes in gut microbiota composition. In conclusion, Xiasangju processing by-products may serve as a potential functional feed ingredient for late-laying hens, with 1.5% inclusion showing favorable overall performance under the conditions of this study. These effects may be associated with the combined contribution of residual nutrients and bioactive compounds in the residues. Full article

Background: Early endolysosomal and autophagic defects are among the earliest cellular alterations observed in Alzheimer’s disease (AD). However, the molecular mechanisms linking amyloid precursor protein (APP) metabolism to vesicle trafficking dysfunction remain incompletely understood. The APP-derived fragment C99 has emerged as a potential upstream mediator of intracellular toxicity, but its impact on organelle homeostasis and its modulation by metabolic interventions remain unclear. Methods: To investigate these mechanisms, we expressed human C99 in Drosophila neurons and examined intracellular pathology using ultrastructural analysis, fluorescent reporters of autophagy and mitochondrial turnover, and proteomic interactome mapping. The effects of the ketone body β-hydroxybutyrate (BHB) were evaluated to assess the impact of metabolic intervention. Results: Neuronal C99 expression induced pronounced vesicular abnormalities, impaired autophagic turnover, and disrupted mitochondrial quality control. Transmission electron microscopy revealed extensive accumulation of enlarged vesicular compartments, accompanied by reduced mitochondrial turnover and accumulation of aged mitochondria. BHB treatment restored autophagic cargo clearance, improved mitochondrial turnover, and normalized vesicular ultrastructure. These protective effects required neuronal ketone transport, indicating a neuron-intrinsic metabolic mechanism. Proteomic analysis of the C99-associated interactome revealed that ketone treatment remodels networks enriched for vesicle trafficking and proteostasis pathways. Network prioritization identified the retromer component VPS35 as a candidate regulatory hub. Functional analyses demonstrated that depletion of VPS35 abolished the BHB-dependent restoration of autophagy, mitochondrial turnover, and vesicle morphology. Conclusions: Ketone treatment restores mitochondrial quality control and autophagic homeostasis through a VPS35-dependent mechanism in C99-induced neurodegeneration. These findings provide mechanistic insight into how metabolic interventions may restore intracellular homeostasis in Alzheimer’s disease. Full article

We previously showed that TCEA1 deficiency in myeloid cells promotes proliferation, impairs differentiation and inhibits apoptosis, but its role and underlying mechanism in acute myeloid leukemia (AML) are unknown. Here, in NB-4 cells, an M3 subtype of AML, TCEA1 overexpression suppressed proliferation (p < 0.001), induced S-phase arrest (from 35.35% to 19.47%, p < 0.001), increased apoptosis (from 10.37% to 23.5%, p < 0.001), and promoted differentiation. Mechanistically, TCEA1 overexpression upregulated C/EBPε and IRF8 at the mRNA and protein levels; conversely, TCEA1 knockdown downregulated both. Rescue experiments in TCEA1 knockdown 32Dcl3 cells showed that ectopic C/EBPε or IRF8 reversed the uncontrolled proliferation, blocked apoptosis, and impaired differentiation. In xenograft mouse models, TCEA1 overexpression reduced leukemic infiltration in the bone marrow, spleen, and liver; extended overall survival; and elevated C/EBPε and IRF8 expression in vivo. Analysis of public APL datasets revealed that high TCEA1 expression is associated with a favorable prognosis (HR = 0.43, 95% CI: 0.2–0.93, logrank p = 0.028). Collectively, our findings demonstrate that TCEA1 suppresses proliferation, promotes apoptosis and differentiation, and attenuates disease progression by upregulating C/EBPε and IRF8, positioning this regulatory mechanism as a potential therapeutic target and prognostic biomarker for this disease. Full article

Background: Osteoarthritis (OA) is a heterogeneous joint disease characterized by cartilage degeneration. The interplay between extracellular matrix (ECM) remodeling, endoplasmic reticulum (ER) stress, and inflammatory signaling in OA pathogenesis remains incompletely understood. This study aimed to identify robust diagnostic biomarkers and explore the mechanistic convergence of key genes in OA cartilage through an integrated transcriptomic framework. Methods: Three independent cartilage transcriptomic datasets (GSE285234, GSE287861, GSE289464) were integrated after ComBat batch correction. Differentially expressed genes (DEGs) were identified using limma, followed by ORA and GSEA for functional enrichment. LASSO logistic regression identified hub genes for a diagnostic model and nomogram, validated by leave-one-out cross-validation (LOOCV). Consensus clustering stratified OA samples into molecular subtypes. Single-cell RNA-sequencing (scRNA-seq) data (GSE169454, GSE220243) were used to validate cell-type-specific expression. Virtual gene knockout (scTenifoldKnk) and pathway analysis inferred downstream functional consequences. Results: Fifty-eight DEGs (predominantly downregulated) were enriched in ECM and ER protein processing pathways. Six hub genes (EIF2S1, GANAB, STT3A, XBP1, MGP, PMP22) showed robust selection stability. The diagnostic model achieved a LOOCV AUC of 0.769, a well-calibrated nomogram, and superior net benefit. Unsupervised clustering revealed two OA subtypes with divergent unfolded protein response (UPR) and TGF-β pathway activities. scRNA-seq confirmed hub gene expression in chondrocytes and other joint microenvironment cells. Notably, virtual knockout of five hub genes convergently perturbed IL-17, NF-κB, and chemokine signaling pathways. Conclusions: This study identified and validated a six-gene signature reflecting ECM-ER-inflammatory crosstalk in OA cartilage. The convergent perturbation of inflammatory pathways by functionally distinct hub genes reveals a mechanistic core that may serve as a diagnostic panel and a platform for targeted therapeutic investigation in OA. Full article

4-Ethylguaiacol (4-EG) is a volatile phenolic compound associated with smoky, woody, and spicy aroma notes in fermented foods and beverages, including Baijiu. In this study, a 4-EG-producing strain, designated JN11, was obtained by screening isolates from Baijiu pit mud and identified as Bacillus coagulans based on morphological, physiological, biochemical, and 16S rRNA analyses. In sorghum juice medium, strain JN11 produced 271.6 ± 2.7 μg/L 4-EG. To investigate the upstream decarboxylation step involved in volatile phenol formation, the phenolic acid decarboxylase gene, BcPAD, was cloned and heterologously expressed in Escherichia coli BL21(DE3). The BcPAD gene comprises 504 bp and encodes a 167-amino-acid protein. Recombinant BcPAD exhibited maximal activity at pH 6.0 and 50 °C and retained more than 60% residual activity after 5 h at 30–40 °C. Fe³⁺ increased enzyme activity to 115.36% of the control, whereas Zn²⁺ markedly inhibited enzyme activity and SDS completely inactivated the enzyme. BcPAD showed the highest activity toward p-coumaric acid, with a specific activity of 460.6 ± 18.3 U/mg and a catalytic efficiency (Kcat/Km) of 12.1 ± 1.4 mM⁻¹·s⁻¹, while lower activities were observed toward caffeic acid and ferulic acid, and no activity was detected toward sinapic acid. Homology modeling and molecular docking suggested that the superior catalytic performance toward p-coumaric acid may be related to favorable hydrogen-bonding interactions and substrate orientation within the active site. Although 4-EG production was observed during fermentation by strain JN11, BcPAD was biochemically characterized as a phenolic acid decarboxylase likely responsible for the upstream formation of vinyl derivatives in the proposed pathway. These findings improve our understanding of phenolic acid decarboxylases from B. coagulans and provide a basis for further investigation of the roles of strain JN11 and BcPAD in volatile phenol formation during Baijiu production. Full article

Background: Natto, a well-known fermented soybean product beneficial for bone health, remains unclear in its mechanism. Methods: This study investigated its effect on secondary osteoporosis (OP) in mice. Results: Natto significantly inhibited weight loss, bone quality deterioration, and bone morphological damage, and regulated OPG/RANKL pathway protein expression (p < 0.05) in OP mice. Analysis of 16S rRNA revealed that natto increased gut microbiota α-diversity and the abundance of Sutterella, Roseburia, and Coprococcus, while reducing harmful bacteria such as Streptococcus, Shigella, and Helicobacter. These microbial changes positively correlated with body weight, bone size, and serum osteogenic metabolism in OP mice. Serum metabolomics showed differential metabolites of the natto group enriched in PPAR signaling and primary bile acid biosynthesis. Verification by mRNA and ELISA indicated that the upregulated liver and circulating PPARα by natto may regulate downstream bile acid pathways, linking gut microbiota to multi-organ metabolic functions. Conclusions: In summary, natto may act on gut microbiota to alleviate bone loss via the “gut microbiota–bile acid–OPG/RANKL” network, targeting multiple organs including gut, liver, and bone. This provides a theoretical basis for natto dietary intervention in osteoporosis prevention through the gut–bone axis. Full article

Background/Objective: Highly palatable foods are pleasurable and motivational stimuli that activate the brain’s reward system and can induce overeating in the absence of physiological needs. This study investigated how different access patterns to a cafeteria diet influence food intake, body weight-related parameters, and metabolic and neurobehavioral outcomes. Methods: At postnatal day 31, forty male Wistar rats were assigned to a standard diet or a cafeteria diet with continuous, predictable intermittent, or unpredictable intermittent access. After 10 weeks, the open-field and sucrose-preference tests assessed exploratory and anxiety-like behaviors and reward-related responses, respectively. Body composition, serum biochemical parameters, neurotransmitter content, and mRNA and protein levels were analyzed in reward-related brain regions. Results: Intermittent access increased food intake on cafeteria days compared with continuous access, with unpredictable access yielding the highest intake. Continuous-access rats exhibited higher final body weight and fat accumulation than chow-fed Control rats. Despite similar body weight, both intermittent-access groups had higher visceral adiposity, obesity indices, and adverse metabolic outcomes than the Control group. All cafeteria-fed rats displayed anxiety-like behavior, and all groups preferred sucrose except the continuous-access group. Molecular analyses revealed region-specific differences in gene expression related to neuroplasticity, stress response, and epigenetic regulation that varied with access pattern and predictability. Conclusions: Our results suggest that, beyond diet composition, the pattern and predictability of food access are key determinants of feeding behavior. Intermittent access increases the motivational value of the cafeteria diet, promoting overeating and driving reward- and stress-related neuroadaptations with potential metabolic and mental health implications. Full article

Alzheimer’s disease (AD) is characterized by Tau hyperphosphorylation, β-amyloid (Aβ) accumulation, and progressive neuronal loss. Gastrodia elata (G. elata), a traditional Chinese medicine with well-established neuroprotective properties, was investigated. Two G. elata-derived miRNAs, Gas-miR04-3p and Gas-miR19-5p, were identified as regulators of JNK3. By means of Western blot, RT-qPCR, and assessments of antioxidant indices, it was demonstrated that Gas-miR04-3p and Gas-miR19-5p can suppress JNK3 expression, reduce Tau phosphorylation at Ser202 and Ser396, enhance antioxidant capacity, and attenuate apoptosis in AD-related cellular and molecular pathology models. These miRNAs were also detectable in murine brain tissues following oral administration of total RNA extracted from G. elata. Their administration was associated with decreased JNK3 activation, alleviated Tau hyperphosphorylation, and improved expression of apoptosis-related proteins in AD mouse models. These results suggest that G. elata miRNAs may exert neuroprotective effects through regulation of JNK3 signaling, thereby attenuating Tau-related pathological changes and neuronal injury in AD-related models. Full article

Silver pomfret (Pampus argenteus), a highly valued marine fish, faces challenges in aquaculture due to its sensitivity to environmental conditions. Recirculating aquaculture system (RAS) is likely to become a primary indoor cultivation method for silver pomfret in the future, so studying hydrodynamic characteristics at varying flow rates in silver pomfret RAS is crucial and has far-reaching implications for both aquaculture practices and economic returns. This study investigated the effects of water flow rates (low: 400 L/h, moderate: 600 L/h, high: 800 L/h) on the growth performance, nutritional metabolism, and gut microbiota of silver pomfret over an 8-week period. Transcriptome and 16S rRNA sequencing revealed that the moderate-flow-rate group exhibited superior growth performance, with enhanced expression of genes related to protein synthesis (HYOU1, PDIA6, ITGA11) and redox regulation (GLUL, DUSP1, GST). Additionally, the moderate flow rate promoted gut microbial diversity and stability, with higher abundances of fermentation- and chemoheterotrophy-related functions, suggesting improved nutrient metabolism. In contrast, high flow rates induced anaerobic metabolism, leading to lactate accumulation and reduced growth. These findings demonstrate that a moderate flow rate of 600 L/h optimizes silver pomfret aquaculture by enhancing growth, metabolic efficiency, and microbial health, providing a foundation for sustainable large-scale farming practices. Full article

Maize plant height and stalk mechanical strength are critical traits that influence planting density, yield, and lodging resistance. Although numerous dwarf mutants have been characterized in maize, most cannot be directly utilized in breeding programs due to associated developmental and reproductive deficiencies. In a previous study, we demonstrated that ZmNAC17 regulates mesocotyl elongation by mediating auxin and reactive oxygen species (ROS) biosynthetic pathways. Here, we characterize the role of ZmNAC17 in maize stalk development using both zmnac17 mutants and ZmNAC17-overexpressing (OE) lines. Plant height, stalk diameter, and internode length were reduced in both the zmnac17-1 EMS mutant and the zmnac17-3 CRISPR mutant. Internode cell length and cell area were decreased, whereas cell number was increased in zmnac17-1. Cellulose and lignin contents were elevated in zmnac17-1. Stalk bending force was diminished in zmnac17-3 but enhanced in the OE lines. The ratio of syringyl to guaiacyl (S/G), a key lignin monomer composition, was increased in zmnac17-3 while reduced in the OE lines. ZmNAC17 functions as a transcription factor, with its downstream targets implicated in phytohormone biosynthesis, phytohormone signaling, and lignin biosynthesis. CUT&Tag binding profile, EMSA, and dual-luciferase reporter assay demonstrate that ZmNAC17 promotes the expression of caffeoyl-CoA O-methyltransferase (CCoAOMT). IP-MS, Co-IP, and GST pull-down assays reveal that ZmNAC17 interacts with Beta glucosidase aggregating factor1 (BGAF1). Collectively, our findings indicate that ZmNAC17 regulates maize stalk development through transcriptional activation and protein–protein interactions, thereby providing new genetic resources for modifying plant architecture and mechanical strength in maize. Full article

This study aimed to investigate the molecular basis of high-level tetracycline resistance to tetracycline antibiotics in Aeromonas hydrophila isolated from fish farming. Comparative genomic analysis of the tetracycline-sensitive strain NJ-35 and the tetracycline-resistant strain AH823 revealed that the tetracycline repressor gene tetR in AH823 had undergone base mutations, resulting in premature translational termination. The tetR gene in NJ-35 was inhibited using a plasmid-based antisense RNA strategy, and the knockdown efficiency was confirmed by RT-qPCR. The resulting tetR antisense RNA-expressing strain, AHtetR-as, exhibited significantly increased resistance to tetracycline antibiotics (minocycline, tetracycline, and doxycycline), but did not affect biofilm formation or hemolysis. Moreover, tetR knockdown in NJ-35 was associated with increased efflux activity and reduced intracellular doxycycline accumulation. Transcriptomic analysis revealed that genes encoding the 30S ribosomal subunit proteins showed a differential expression pattern, with rpsO upregulated and rpsD and rpsP downregulated. These findings suggest that tetR contributes to tetracycline resistance in A. hydrophila and is associated with broad transcriptional changes related to cellular transport and ribosomal function. Full article

As part of efforts to identify genes associated with Trichomonas vaginalis resistance to 5-nitroimidazole drugs, thirty cryopreserved T. vaginalis isolates were revived and grown using Diamond’s TYM medium. Minimum lethal concentrations (MLCs) for metronidazole (MTZ), tinidazole (TDZ), and secnidazole (SEC) were determined using a drug susceptibility assay. Transcriptome profiling was performed for 15 MTZ-sensitive (MTZ-S, MLC < 50 µg/mL) and 15 MTZ-resistant (MTZ-R, MLC ≥ 50 µg/mL) isolates using next-generation RNA sequencing. Bioinformatics analyses identified differentially expressed genes (DEGs). Among the MTZ-R isolates, six exhibited low MLCs of 50 µg/mL, five had intermediate MLCs between 100 and 200 µg/mL, and four had high MLCs ≥ 400 µg/mL. Differential gene expression analysis identified 28, 140, and 73 significantly altered genes in low-, intermediate-, and high-level MTZ resistance groups, respectively, with predominantly upregulated expression patterns. The SEC-resistant (SEC-R) isolates exhibited 136 differentially expressed genes, whereas the TDZ-resistant (TDZ-R) isolates showed minimal transcriptional changes. Focused analyses of iron transport pathways revealed reduced expression of ZIP-family iron import genes, particularly TvZIP4 (TVAG_273550), the strongest predictor of resistance in elastic-net modeling (AUC = 0.795). Resistant isolates also demonstrated coordinated upregulation of iron–sulfur cluster assembly and hydrogenosomal protein-import pathways. Weighted gene co-expression network analysis (WGCNA) identified multiple resistance-associated transcriptional modules correlated with MTZ and SEC MLCs. A comparative transcriptomic–proteomic analysis revealed concordant upregulation of iron–sulfur cluster machinery but discordant regulation of hydrogenosomal cargo proteins, likely supporting a post-transcriptional restriction model. These findings provide a broader mechanistic framework for understanding 5-nitroimidazole resistance in T. vaginalis and identifying candidate biomarkers and pathways that may support future therapeutic and diagnostic development. Full article

Brassica napus reproductive development and abiotic stress tolerance are critical for yield and quality, and characterizing key transcription factor families is vital for molecular breeding. Here, based on the B. napus cv. Darmor-bzh V5 reference genome, we systematically identified and analyzed the BnaS1fa gene family, uncovering 12 members. Their encoded proteins are mostly small, alkaline, stable, and hydrophilic, with a few having ultra-long structures. Phylogenetic analysis clustered them into three subfamilies; conserved motif and gene structure analyses revealed high overall family conservation with partial member differentiation. Promoter cis-acting element analysis showed enrichment in light, hormone, and stress-responsive elements. Chromosomal localization and intraspecific collinearity analyses indicated the family mainly derived from homologous fragment retention in A and C subgenomes. Transcriptome data demonstrated high BnaS1fa expression in late seed and silique development, with prominent heat stress responses. RT-qPCR, subcellular localization and transcriptional activity assays confirmed BnaS1fa9 and BnaS1fa10 as nuclear-localized transcription factors with heat stress-induced expression. This study elucidates BnaS1fa molecular characteristics and its potential roles in reproductive development and heat stress response, providing candidate genes for B. napus stress-resistant molecular breeding. Further functional validation of these key genes will facilitate the dissection of their precise regulatory mechanisms governing heat stress tolerance and reproductive growth, which can be ultimately applied to advance the genetic improvement of rapeseed stress resistance and yield performance. Full article