Glucose deprivation is a major metabolic stress that requires coordinated adaptive responses to maintain cellular homeostasis and survival, yet the role of tripartite motif-containing 24 (TRIM24) in this process remains unclear. To address this question, we generated CRISPR-Cas9-mediated TRIM24-knockout MCF-7 and HEK293 cell lines, performed targeted metabolomic profiling and aspartate assays, used 5-aminoimidazole-4-carboxamide-1-β-D-ribofuranoside (AICAR), aminooxyacetic acid (AOA), aspartate supplementation, and glutamic-oxaloacetic transaminase 2 (GOT2) knockdown to probe AMPK signaling and aspartate metabolism, and examined starvation responses in constitutive Trim24 knockout mice on a C57BL/6 background. Loss of TRIM24 sensitized cells to glucose deprivation. Re-expression of TRIM24 partially restored cell viability under glucose deprivation in both MCF-7 and HEK293 cells. Under glucose-free conditions, TRIM24 deficiency was associated with impaired AMP-activated protein kinase (AMPK) pathway activation, increased intracellular aspartate accumulation, and altered ATP/AMP levels. Pharmacological reactivation of AMPK by AICAR improved the survival of TRIM24-deficient cells under glucose deprivation. Reducing intracellular aspartate by AOA treatment or GOT2 knockdown restored AMPK pathway activation and improved adaptation to glucose deprivation, whereas exogenous aspartate suppressed AMPK signaling and increased ATP/AMP levels. In vivo, starvation of Trim24-deficient mice was associated with reduced AMPK pathway activation and increased aspartate levels. Together, these findings support a model in which TRIM24 contributes to adaptation to glucose deprivation and in which abnormal aspartate accumulation contributes to impaired AMPK pathway activation in TRIM24-deficient cells.

The NAC (NAM, ATAF1/2, and CUC1/2) family of transcription factors (TFs) play critical roles in regulating salt tolerance across diverse plant species. This study identified and characterized 101 NAC TFs in eggplant (Solanum melongena L.), revealing their diverse physicochemical properties, chromosomal distributions, and evolutionary relationships. Based on its salt stress-induced expression pattern and homology to known salt-responsive NAC factors, SmNAC28 was selected as a key candidate for functional investigation of salt tolerance. Expression profiling indicated that SmNAC28 is preferentially expressed in roots and stems, and its transcript levels are modulated by salt stress. Subcellular localization confirmed that SmNAC28 localizes to both the plasma membrane and nucleus, a dynamic distribution regulated by S-palmitoylation. Under normal conditions, SmNAC28 is anchored to the plasma membrane and nucleus via S-palmitoylation; upon salt stress exposure, it undergoes depalmitoylation and translocates to the nucleus. Using a hairy root transformation system in eggplant, we demonstrated that overexpression of SmNAC28 in roots significantly enhanced salt tolerance by mitigating oxidative damage, maintaining ion homeostasis, and promoting osmotic adjustment. Analysis of transcript levels further revealed that SmNAC28 overexpression upregulated ion transporter genes (NHX2, CHXs), signaling genes (CIPKs), and the proline biosynthesis gene (P5CS), which demonstrated that SmNAC28 integrates antioxidant defense, ion homeostasis, and osmotic regulation to confer salt tolerance. This study reveals the response mechanism of SmNAC28 to salt stress of the eggplant transcription factor SmNAC28 under salt stress, and provided a research foundation for salt tolerance breeding.

The homeodomain-leucine zipper (HD-Zip) transcription factor family is conserved in land plants and is critical for regulating growth, development, and stress responses. Flax (Linum usitatissimum L.) is an economically valuable dual-purpose crop valued for its high nutrition and notable drought tolerance; however, its HD-Zip gene family has not been systematically characterized. In this study, a comprehensive genome-wide analysis was performed to identify and characterize the HD-Zip family in flax. A total of 34 LuHD-Zip genes were identified, which were unevenly distributed across 15 chromosomes and exhibited substantial variation in physicochemical properties. The encoded proteins ranged from 200 to 372 amino acids in length, with molecular weights of 22.7–40.3 kDa and theoretical isoelectric points (pI) of 4.49–9.46. All LuHD-Zip proteins were predicted to be hydrophilic and localized to the nucleus. Phylogenetic analysis divided these proteins into two major subfamilies (Group 1 and Group 2), a classification strongly supported by conserved gene structures and motif compositions, implying potential functional redundancy within each group. Gene duplication analysis revealed that segmental duplication events (29 pairs) were the primary drivers of family expansion. Comparative syntenic analysis further indicated that the LuHD-Zip gene family has remained relatively conserved throughout evolution. Promoter cis-element analysis identified multiple regulatory elements associated with hormone signaling and abiotic stress responses, suggesting complex transcriptional control in response to environmental stimuli. Expression profiling via quantitative real-time PCR (qRT-PCR) demonstrated that LuHD-Zip genes exhibit tissue-specific expression patterns and are differentially regulated by various phytohormone treatments and abiotic stresses. This study provides the first genome-wide characterization of the HD-Zip gene family in flax, offering valuable insights into its evolution and potential functions. These findings establish a solid foundation for future functional investigations of the LuHD-Zip gene family.

Inflammatory joint diseases, including osteoarthritis, are multifactorial disorders in which dysregulated innate immune signaling and non-coding RNA (ncRNA)-mediated regulation of gene expression play essential roles. MicroRNA-155 (miR-155), its host gene MIR155HG, and Toll-like receptor 4 (TLR4) form a tightly linked inflammatory signaling axis, yet their combined genetic variability in chronic joint inflammation remains insufficiently characterized. The aim of this study was to investigate genetic variants in MIR155HG exon 3, mature miR-155, and TLR4 exon 3 and assess their potential synergistic role in chronic inflammatory joint disease. A case–control study was conducted with 100 cases (50 osteoarthritis patients and 50 matched healthy controls). Genomic DNA was analysed using polymerase chain reaction (PCR) and Sanger sequencing. Variant alleles and genotypes were identified, and their allele frequencies and genotypes were calculated using Mutation Surveyor. Detected variants were compared with public databases, and in silico tools were used to estimate the structural impact of TLR4 missense mutations. Sixteen heterozygous variants were identified in MIR155HG exon 3, most of them novel and population-specific. Interestingly, the highest variant frequencies for MIR155HG exon 3 were observed at positions 12448G>GC and 12481T>TA (both 64.3%), followed by 12442T>TC (57.1%). Additionally, two novel variants were detected in the miR-155 gene (chr21:29,694,314 G>A and chr21:29,646,351 T>C), each present at an allele frequency of 7.1% and absent from current external variant databases. Moreover, two rare TLR4 exon-3 variants were identified; a synonymous variant, c.147C>A (Pro49Pro; rs375037549), and a missense mutation, c.148G>A (Asp50Asn; rs776561489). Notably, in silico analyses and molecular dynamic simulations indicated that the Asp50Asn (D50N) substitution destabilizes the TLR4 protein. Conclusion: Concurrent variants in MIR155HG, miR-155, and TLR4 suggest a convergent regulatory molecular axis that may contribute to disease susceptibility and inflammatory progression.

(1) Objective. To conduct a comparative bioinformatics analysis of the transcriptomic profiles of peri-implantitis and periodontitis to identify common and specific molecular signatures underlying their pathogenesis, as well as molecular parallels with atherosclerosis. (2) Methods: We used datasets from the Gene Expression Omnibus (GEO) database: dataset GSE223924 (30 gingival tissue samples from patients with peri-implantitis, periodontitis, and healthy subjects) and GSE100927 (atherosclerotic and control tissue; n = 104). Differentially expressed genes (DEGs) were identified based on the criteria: |logFC| > 1 and FDR < 0.05. To quantitatively assess the relative abundance of immune cells, we used the xCell deconvolution algorithm. (3) Results: In the peri-implantitis group, 3669 DEGs with upregulated expression and 3106 with downregulated expression were identified; in the periodontitis group, 1968 and 1250 DEGs, respectively. Functional analysis of the upregulated DEGs revealed activation of inflammatory processes, cell adhesion, and angiogenesis in both diseases. Key differences lay in the activation of adaptive immune mechanisms in peri-implantitis (enrichment of the “graft rejection” and “T-cell receptor signaling”) and innate immunity in periodontitis (enrichment of the “lipopolysaccharide response” and “Toll-like receptors (TLR) signaling” pathways). Analysis of downregulated DEGs revealed more profound disruptions in cytoskeletal organization and epithelial differentiation in periodontitis, as well as suppression of xenobiotic and lipid metabolism in both diseases. xCell deconvolution confirmed a significant increase in B cells, neutrophils, monocytes, M1 macrophages, and dendritic cells in peri-implantitis, and also revealed a trend toward an increase in these cells in periodontitis (p > 0.05), which is consistent with the activation of TLR signaling. In periodontitis, a significant increase in M2 macrophages and a decrease in Th1 cells were observed. Comparison with atherosclerosis revealed 272 common DEGs with peri-implantitis and 173 common DEGs with periodontitis. Functional analysis of the common genes confirmed their role in leukocyte transendothelial migration, cytokine production, and the “Lipids and Atherosclerosis” pathway. (4) Conclusions: Functional analysis and immune deconvolution consistently demonstrate that peri-implantitis is characterized by statistically significant activation of both adaptive and innate immunity, whereas in periodontitis, the activation of innate immunity manifests primarily at the level of signaling pathways. The significant overlap found between the transcriptional profiles of both diseases and atherosclerosis may indicate the presence of common pathogenetic links.

A new strategy to reduce the morbidity and mortality associated with invasive Streptococcus agalactiae (Streptococcus group B, GBS) diseases encompasses the development of vaccines. Candidate vaccines at different stages of clinical trials have been developed on capsular polysaccharides or protein antigens. We studied 328 GBS isolates identified using routine microbiological tests, latex-agglutination, and PCRs. The samples were categorised into two main groups: vaginal (69.2%) and extra-vaginal (30.8%). The molecular serotyping and target gene factors were determined using singleplex or multiplex PCRs. The most common serotypes identified were Ia (24.7%), V (22.0%), and III (18.9%). Serotypes I–V constituted a total of 89.0%. The non-typeable were 9.8%. The frequency of genes included in the recombinant GBS-NN (rib + bca) and GBS-NN2 (epsilon + alp2/3) vaccines were 54.3% and 40.8%. We noted a significant prevalence in the distribution of serotypes II, III, and non-typeable in GBS-NN, whereas serotypes Ia and IV were predominant in GBS-NN2. The serotype prevalence identified in our research was consistent with the data from our region and confirmed the predominance of the six main serotypes included in the hexavalent conjugated vaccine. We highlighted the importance of the combined administration of both protein vaccines, ensuring optimal vaccine coverage.

Alzheimer’s disease is a progressive neurodegenerative disorder marked by declining cognitive function. While early-stage treatment focuses on acetylcholinesterase (AChE) inhibition, butyrylcholinesterase (BChE) activity increases as the disease progresses, contributing to cholinergic deficits and neuroinflammation. This shift in enzyme dominance presents a compelling rationale for developing BChE-specific inhibitors as a potential therapeutic avenue. This study explores small, three-membered rings, scaffolds offering potential for interaction with the enzyme’s active site, as building blocks for novel BChE inhibitors. Employing a computational approach based on quantum–chemical multiligand simultaneous molecular docking, we virtually fitted these compounds into the BChE active site to predict binding affinity and key interactions. Our calculations extend beyond simple shape matching by incorporating accurate electronic properties, leading to more reliable predictions of binding strength and stability. The goal was not immediate identification of potent inhibitors, but a systematic assessment of how these rings interact with BChE. This foundational knowledge will inform the design and synthesis of larger, more complex molecules with enhanced binding affinity and selectivity, ultimately aiming to develop compounds to inhibit BChE activity and potentially slow Alzheimer’s progression.

Cadmium exposure results in the impairment of pancreatic β-cells. The FTO protein, the product of the Fto gene, is a key regulator of diverse pathophysiological processes, including oxidative damage and cell death. However, it remains unclear whether Fto gene knockout affects cadmium-induced pancreatic β-cell damage, and the precise mechanisms involved are yet to be elucidated. Under conditions of cadmium exposure, Fto gene knockout was found to alleviate pancreatic β-cell damage significantly. Specifically, Fto gene knockout counteracted cadmium-induced cytotoxicity—manifested as reduced cell viability, increased apoptosis, and heightened lactate dehydrogenase (LDH) release—while simultaneously suppressing DNA damage and preserving cellular membrane integrity. On a molecular level, Fto gene knockout markedly mitigated cadmium-induced oxidative stress. This was achieved by curbing excessive reactive oxygen species (ROS) accumulation, lowering malondialdehyde (MDA) generation, and reducing 8-hydroxy-2′-deoxyguanosine (8-OHdG) levels, alongside restoring superoxide dismutase (SOD) activity. Furthermore, ER-Tracker Red staining revealed that cadmium treatment induced clustered aggregation of the endoplasmic reticulum (ER) and increased fluorescence intensity, suggesting the activation of endoplasmic reticulum stress (ERS). Conversely, Fto knockout ameliorated ER morphological abnormalities, thereby effectively antagonizing the excessive activation of ERS. In summary, our study elucidates the impact and underlying molecular mechanisms of the Fto gene in cadmium-induced toxicity in pancreatic β-cells from the perspectives of oxidative damage, ERS, and apoptosis. These findings identify the Fto gene as a potential molecular target for mitigating cadmium-induced toxicity in pancreatic β-cells, thereby providing a new theoretical basis for the prevention and treatment of cadmium-induced pancreatic β-cell injury.

Plant functional genomics and comparative genomics have emerged as transformative disciplines in modern plant biology, providing unprecedented insights into gene function, regulatory networks, and evolutionary trajectories across diverse species [...]

Peptide deformylase (PDF) belongs to a conserved enzyme family critical for N-terminal methionine excision (NME), an essential protein maturation process in prokaryotes and eukaryotic organelles (chloroplasts, mitochondria). To explore the potential functions of OsPDFs in Oryza sativa, this study employed bioinformatics approaches and experimental validation to systematically identify and analyze the OsPDF gene family. Three OsPDF genes (OsPDF1A, OsPDF1B, OsPDF1B2) were identified in rice. These genes are exclusively distributed on chromosome 1. The biophysical properties of these proteins showed that OsPDF1A and OsPDF1B are alkaline proteins, while OsPDF1B2 is acidic, and all are hydrophilic with moderate thermostability potential. Synteny analysis revealed closer evolutionary relationships between Oryza sativa and the monocot Triticum aestivum than with dicots, reflecting conserved PDF function in gramineous plants. Analysis of cis-acting elements in the 2000 bp upstream region of OsPDF gene promoters revealed numerous elements associated with abiotic stress response and hormone regulation. Furthermore, quantitative real-time PCR (qRT-PCR) data supported these findings, indicating that OsPDF1A and OsPDF1B were upregulated under low-temperature stress, and all three OsPDF genes were transcriptionally activated by heat, salt and UV-B stresses, indicating their active involvement in rice growth, development, and abiotic stress tolerance. In summary, OsPDFs exhibit significant functions in rice’s stress adaptation, growth, and development. This study not only enhances our understanding of the OsPDF gene family’s genomic, evolutionary, and functional characteristics, but also provides new perspectives and foundational data for further exploring their regulatory mechanisms in protein maturation and abiotic stress responses, as well as their potential applications in rice stress tolerance breeding.