Search Results (8,094)

The WUSCHEL-related homeobox (WOX) gene family plays crucial roles in plant growth, development, and stress responses. In this study, a comprehensive genome-wide analysis of WOX genes was conducted in three Populus species, P. euphratica, P. pruinosa, and P. deltoides. A total of 16, 16, and 21 WOX genes were identified, respectively, and classified into three clades (ancient, intermediate, and WUS/modern) based on phylogenetic relationships. Structural analyses revealed highly conserved homeodomain motifs and similar exon–intron organizations, indicating strong evolutionary conservation. Furthermore, synteny analyses demonstrated that whole-genome duplication or segmental duplication events were the primary drivers of WOX gene family expansion, with most duplicated gene pairs undergoing purifying selection. Promoter analysis identified abundant cis-acting elements related to light responsiveness, hormone signaling, and stress responses. Notably, transcriptomic profiling during seed germination under drought and salt stress revealed distinct interspecific expression patterns and temporal dynamics between the two desert poplars. Specifically, members such as PeWox11 and PpWox2 were significantly induced, suggesting their potential involvement in abiotic stress adaptation. These findings provide comprehensive insights into the evolutionary conservation and divergence of WOX genes in Populus, establishing a theoretical foundation for the molecular breeding of stress-tolerant woody plants. Full article

Selective inhibition of MEK isoforms remains a central challenge in MAPK-targeted drug discovery, largely due to the structural similarity between MEK1 and MEK2. While MEK1 has been extensively characterized, the structural basis of MEK2-specific ligand recognition is not fully understood. Here, we present crystal structures of human MEK2 in complex with the noncompetitive inhibitor U0126 and the allosteric inhibitor refametinib at resolutions of 3.15 Å and 3.30 Å, respectively. Despite a conserved kinase fold, MEK2 exhibits isoform-specific features within the N-lobe β-sheet. Additional differences are observed in the relative orientation of the helix C and activation segment, and the helix F-supported regulatory spine. Structural differences are reflected in micromolar binding affinities for U0126 (K_d = 9.8 μM) and refametinib (K_d = 7.4 μM). Notably, a single N-lobe substitution (Thr87 in MEK2 versus Phe83 in MEK1) selectively enhanced U0126 binding. The MEK2 T87F mutant exhibited an approximately twofold increase in affinity, while refametinib binding remained largely unchanged. SEC–MALS analysis demonstrated that MEK2 predominantly exists as a monomer in solution, contrasting with the reported homodimeric behavior of MEK1. Molecular dynamics simulations supported these findings by revealing isoform-specific differences in oligomeric state-dependent flexibility and inhibitor-induced dynamics. Collectively, our findings define the structural basis underlying the differential inhibitor recognition of MEK2 and MEK1, providing mechanistic insight into isoform-selective MEK-targeted drug design. Full article

Glycosaminoglycans (GAGs) are the carbohydrate portion of proteoglycans (PGS), a family of complex biomacromolecules ubiquitously found in the extracellular matrix and on cell surfaces that play critical roles in a plethora of physiological and pathological processes. In the present work, chondroitin sulfate (CS) and dermatan sulfate (DS) were extracted and purified from the head (GCB) and skin (GDB) of blue runner fish (Caranx crysos) to explore their structural features and biological properties. GCB and GDB were purified by ion-exchange chromatography with yields of 0.82% and 0.61%, respectively. Chemical and structural analysis showed that GCB and GDD demonstrated quite similar sulfation degrees (4.45% and 4.24%, respectively). The molecular weight values obtained for GCB and GDB as estimated by high-performance size exclusion chromatography coupled with a triple detector array (HP-SEC-TDA) were 48.9 and 28.54 KDa, respectively. Structural features were elucidated using FT-IR and 2D NMR spectroscopy. GCB was mainly identified as chondroitin sulfate, containing 82% GlcA and minor proportions of IdoA and IdoA2S (scoring 18% dermatan-like structures). In contrast, GDB was predominantly dermatan sulfate, with a higher unsulfated IdoA content (54%) and a lower GlcA percentage (17%). In vitro anticoagulant activity, evaluated using APTT and PT assays, demonstrated that both GAGs exhibit significant anticoagulant potential. In addition, both fractions exhibited no antiplatelet activity, suggesting that the isolated glycosaminoglycans selectively target the coagulation cascade without affecting platelet aggregation. Furthermore, hemolytic assays confirmed that neither GCB nor GDB showed any hemolytic activity at the tested concentrations. Cytotoxicity assessment in HEK293 and HUVEK cell lines further confirmed the absence of detectable toxicity even at high concentration. Overall, these marine-derived GAGs present promising therapeutic potential as a source of anticoagulant drugs. Full article

Histone deacetylases (HDACs) are important epigenetic regulatory enzymes contributing to cancer proliferation, which could be critical targets in cancer therapy. The structural similarities of the existing HDAC inhibitors have resulted in an increase in the drug resistance. In this study, coumarin was employed as the core scaffold for structural derivatisation to develop a novel class of HDAC inhibitors based on computer-aided design (CADD). Their anti-tumor activity was evaluated against esophageal squamous cell lines. The results showed that most compounds exhibited potent anti-proliferative activity against KYSE70 and KYSE150. Among them, compound 4s and 4p exhibited the most potent activity with IC₅₀ values of 3.44 μM and 3.39 μM against KYSE70. To validate the target of the synthesized compounds, transcriptome sequencing was performed and the results revealed that a total of 487 genes were differentially expressed, including 190 up-regulated and 297 down-regulated genes. Among these, 79 genes were associated with the HDAC regulatory network, accounting for 16.2% of the differentially expressed genes. Molecular docking demonstrated that compound 4s could effectively enter the active site of HDAC, engaging with the cap group, zinc-binding group, and linker region. This multiple interaction network provides a structural basis for the potent inhibitory activity of compound 4s. In conclusion, a series of novel HDAC inhibitors with a coumarin scaffold were discovered, and their mode of action was revealed. This provides a valuable guide for the development of novel HDAC-targeting therapeutics. Full article

The hormonal vitamin D metabolite, 1,25-dihydroxyvitamin D (1,25D), produced primarily in the kidney, acts in numerous end-organs via the nuclear vitamin D receptor (VDR) to trigger molecular events that orchestrate bone mineral homeostasis, immune responsiveness, and aspects of behavior. Tyrosine hydroxylase (TH) encodes a neuronally expressed enzyme that catalyzes the initial, rate-limiting step in the production of several catecholamine neurotransmitters and hormones, including dopamine, norepinephrine, and epinephrine. Herein we report that TH mRNA is significantly induced (2.5-fold) and NURR1 mRNA is induced 9.3-fold by 10 nM 1,25D in differentiated human SH-SY5Y neuroblastoma cells. Similar results were observed in human U87 glioblastoma cells (TH, 2.6-fold; NURR1, 3.6-fold). Comparative analysis of TH gene promoter-proximal sequences from human, mouse, and rat identifies candidate NURR1-responsive elements (NBREs) at the following positions: −35, −855, −1470, and −2343 bp in the human gene; −34 and −961 bp in the mouse gene; and −34, −350, and −873 bp in the rat gene, consistent with NURR1 acting as a recurring regulatory factor at TH promoters across mammalian species. Furthermore, by interrogating VDR ChIP-seq/cistrome datasets, we identified candidate vitamin D-responsive elements (VDREs) at the human NURR1 locus that provide a plausible genomic framework for direct regulation of NURR1 by 1,25D/VDR. We propose that 1,25D-liganded VDR acts as a primary inducer of NURR1, which in turn secondarily activates expression of the TH gene, thereby defining a transcriptional route through which 1,25D/VDR signaling may influence TH-linked dopaminergic gene programs. Retinoid X receptor (RXR) may facilitate both NURR1-dependent and -independent potentiation of TH transcription because the rexinoid, bexarotene, significantly enhances TH mRNA in human U87 cells, either alone (2.0-fold) or in combination with 1,25D (4.1-fold). In addition, bexarotene and its novel analogs, A41 and A55, induce NURR1 mRNA expression in U87 cells by 2.8-, 3.1-, and 4.8-fold, respectively, with A55 outperforming the parent compound at matched concentration. Because Parkinson’s disease is characterized by the selective degeneration of dopaminergic neurons and impaired NURR1-dependent transcriptional programs, our findings identify a 1,25D/VDR–NURR1–RXR transcriptional axis as a previously underappreciated regulatory framework for studying TH gene expression and dopaminergic gene regulation in Parkinson’s disease-relevant neural contexts. Full article

Porcine epidemic diarrhea virus (PEDV) continues to undergo genetic evolution and remains a major etiological agent of enteric disease in swine, causing significant economic losses worldwide. This study investigated the molecular epidemiology and genetic characteristics of PEDV circulating in Chongqing, China, between 2022 and 2024. A total of 296 diarrheic piglet samples collected from nine regions were screened using RT-qPCR, of which 48.31% (143/296) tested positive for PEDV. A subset of positive samples was subjected to S gene amplification and sequencing, yielding 15 complete sequences. Phylogenetic analysis revealed that all sequenced strains clustered within the G2c lineage and showed high nucleotide similarity (93.37–94.09%) to the classical CV777 strain. Recombination analysis indicated potential recombination events among field strains involving S-INDEL and G2b-like parental lineages, although these findings are based on a limited number of sequences. Sequence analysis identified multiple amino acid substitutions within the COE antigenic region, while other neutralizing epitopes (SS2, SS6, and 2C10) remained largely conserved. In addition, variation in predicted N-glycosylation sites was observed among some strains. Structural modelling suggested that these changes may influence spike protein conformation and antigenic properties; however, these interpretations are based on in silico analysis and require experimental validation. Overall, the findings indicate ongoing genetic evolution of PEDV in Chongqing and suggest circulation of G2c-associated variants in diarrheic piglets. However, given the limited and non-random nature of sequencing, these results may not fully represent the broader viral population. Continued large-scale molecular surveillance and functional studies are needed to better understand PEDV evolution and to support the development of improved control strategies and vaccines. Full article

Gonyaulax polygramma is a bloom-forming dinoflagellate that can be difficult to identify accurately during routine harmful algal bloom (HAB) monitoring, particularly when morphologically similar Gonyaulax species occur together in field samples. To improve species discrimination and quantitative detection, we developed a species-specific TaqMan qPCR assay targeting the 28S rDNA region of G. polygramma and applied it to field samples collected during a four-year survey in Korean coastal waters. The developed primer–probe set showed high specificity without cross-reactivity with tested non-target microalgae. The assay exhibited high linearity (R² = 0.999), amplification efficiencies of 92.01–99.36%, and a detection limit of ${10 \mathrm{c}\mathrm{o}\mathrm{p}\mathrm{i}\mathrm{e}\mathrm{s} \mathrm{r}\mathrm{e}\mathrm{a}\mathrm{c}\mathrm{t}\mathrm{i}\mathrm{o}\mathrm{n}}^{-1}$. Field application revealed clear regional differences in distribution patterns. G. polygramma was rarely detected in the semi-enclosed Jinhae Bay, whereas relatively high abundances were observed at offshore-influenced stations in the Tongyeong–Yeosu–Wando region during summer. These results suggest that G. polygramma occurs locally in offshore-influenced coastal waters rather than being uniformly distributed along the southern coast of Korea. The developed qPCR assay provides a reliable molecular tool for detecting G. polygramma and can complement morphology-based monitoring of Gonyaulax species in coastal HAB surveillance programs. Full article

Global warming has increasingly positioned heat stress (HS) as a major threat to public health, as it can inflict damage on multiple organs including the kidneys, liver, and heart. However, effective targeted therapeutic strategies remain limited. This investigation employed an integrated approach combining Network pharmacology, in silico binding simulations, and cell-based assays to elucidate the cytoprotective properties and molecular basis of oxymatrine action under heat-stressed conditions. Network analysis identified 36 overlapping targets common to oxymatrine and the pathological processes of HS-related acute kidney injury (AKI), acute liver injury (ALI), and acute myocardial injury (AMI). These targets were strongly enriched in the PI3K-AKT signaling cascade. Molecular docking showed that oxymatrine binds tightly to key pathway proteins such as PIK3CA and GSK3B, with Vina scores below −8 kcal/mol. In 293T cells, the half-maximal cytotoxic concentration (CC₅₀) of oxymatrine exceeded 2000 μM. Under heat stress, oxymatrine (31.25–1000 μM) dose-dependently increased cell viability by about 30% and significantly lowered HSP90 and HSP70 expression. Similar protective effects were observed in H9C2 cardiomyocytes under heat stress. RT-qPCR further confirmed that oxymatrine reduced the transcript levels of PI3K-AKT pathway-related genes, including CASP3, EGFR, RXRα, and MMP9 in 293T cells. We also found 18 overlapping targets between oxymatrine and ferroptosis, most of which matched the core targets above. Molecular docking analysis predicted binding of oxymatrine to the ferroptosis regulator GPX4. Together, these results suggested that oxymatrine potentially alleviates HS injury by modulating the PI3K-AKT signaling pathway andregulating potential ferroptotic targets such as GPX4. Full article

Discrete breathers (DBs) are nonlinear vibrational excitations localized on small groups of atoms in perfect crystal lattices. While theoretically proven, a systematic understanding of DB formation in binary crystals with the B2 structure remains limited. We employ molecular dynamics simulations using the LAMMPS package to investigate the nonlinear dynamics of three representative B2 crystals: ionic CsCl, and intermetallic LiPb and NiTi. We calculate the amplitude-frequency dependencies of delocalized nonlinear vibrational modes (DNVMs) and analyze DB existence conditions based on phonon spectrum features and anharmonicity type. Our analysis reveals that a significant atomic mass difference creates a phonon band gap, enabling gap DBs in CsCl and LiPb, whereas NiTi, with similar atomic masses, exhibits no gap. A simplified model assuming identical bond stiffnesses accurately predicts frequency ratios in CsCl and LiPb but fails for NiTi due to strong bond stiffness asymmetry. We demonstrate the successful excitation of long-lived gap DBs in LiPb by initializing atomic displacements based on the G1 DNVM pattern on heavy Pb atoms. These gap DBs remain stable for over 20 ps with negligible energy dissipation. In contrast, DBs with frequencies above the phonon spectrum (excited on light Li atoms) exhibit shorter lifetimes (~2 ps). The study establishes that both atomic mass ratio and interatomic bond stiffness asymmetry are critical parameters governing nonlinear dynamics in B2 crystals. The predicted long-lived gap DBs in LiPb provide a target for future experimental detection via inelastic neutron or X-ray scattering, offering new insights into energy localization and transport in biatomic alloys. Full article

The aim of this study was the quality assessment and antioxidant activity of chokeberry, raspberry and blackberry low-alcohol beverages produced from native berry fruits from the southeastern region of the Republic of North Macedonia. This is the first study on the fermentation of chokeberries, raspberries and blackberries in order to achieve low-alcohol beverages enriched by polyphenols such as monomeric and polymeric anthocyanins, low and high molecular proanthocyanidins derived from these berry fruits. The pre-fermentative addition of sugar was avoided in order to achieve the amount of ethanol less than 4%. The commercial Saccharomyces cerevisiae yeast strain Lalvin ICV D80 was used for fermentation as the most suitable for contributing significant tannin volume and stabilization of the color of the beverages. Chemical analyses revealed the acetic and lactic acids were the most abundant in the chokeberry beverage, while malic acid was the most dominant in the blackberry beverage. All low-alcohol beverages had an amount of residual sugar less than 1 g/L, while the highest total acidity was noticed in the raspberry beverage (25.45 g/L). High and low molecular proanthocyanidins were in similar amounts in the chokeberry and blackberry beverages, while total anthocyanins and total phenols were in favor to the blackberry beverage. Despite the total phenolic content, the highest antioxidant activity was measured in the raspberry beverage which can be linked to the amount and particular classes of phenolic compounds. The results presented in this study can provide insight in the new formulations of health-promoting beverages with low levels of alcohol. Full article

The biggest challenge faced by classical anticancer therapy is drug resistance, which causes cancer recurrence and metastasis. Two underlying mechanisms could be responsible, including the stemness of pro-survival autophagy-associated cancer stem cells (CSCs). Background/Objectives: The relationship between CSCs and autophagy in gynecological cancer is still unknown. However, it has been shown that CSCs’ in vitro self-renewal ability is decreased when autophagy is inhibited. Helping to maintain normal tissue homeostasis, autophagy is a catabolic process involved in degrading long-lived proteins and cytoplasmic organelles. Autophagy acts as a key player in the human body’s self-regenerating tissues. It also has a reproductive function, contributing to decidualization for a successful pregnancy. The aim of our review is to identify similarities and differences between these processes, using these findings to discover new therapeutic strategies through nanotechnology. Method: We conducted a narrative review, identifying heterogeneity in the data in the literature, and found 153 relevant articles. Discussions: While autophagy has been proven to be capable of acting as a tumor suppressor, it also promotes tumor progression. Moreover, it has been linked to cancer stem cell regulation, therapy resistance, cancer invasion, and metastasis. Several molecular mechanisms have been linked to autophagy. Remarkably, some cellular processes required for proper placentation, including autophagy, are common between placental development and tumor growth. Just as trophoblast cells invade and migrate, so do cancer cells. While in the trophoblast, this phenomenon is programmed and controlled; in cancer, this regulation is lost. As shown, we thus observed commonalities and discrepancies in the phenotypes and underlying molecular mechanisms of autophagy regulation in preeclampsia versus cancer contexts. Translational applicability of nanomedicine research strategies and design paradigms between preeclampsia intervention and cancer therapy has been sought. Conclusions: Autophagy-based nanotechnology seems to be feasible in both placental ischemia in preeclampsia and cancers. This review draws parallels between targeted treatments in malignancies and placenta-derived PE. Comparing these diseases provides a novel molecular rationale and the possibility of identifying treatment through autophagy modulation. Full article

The primary control mechanism for synaptic uptake of GABA is through γ-aminobutyric acid transporter 1 (GAT-1, SLC6A1), a known target for anti-epileptic drugs. Although there is a clinically used GAT-1 inhibitor, tiagabine, the development of a new ligand with an advanced pharmacological profile is desirable. For this purpose, a multi-tiered virtual approach to screening has been created, involving pharmacophore-based search; application of the Informational Spectrum Method for Small Molecules, followed by EIIP/AQVN filtering (ISM-SM); molecular docking using an ensemble of several experimentally obtained structures of GAT-1; and ADMET predictions. Pharmacophore-based screening of the ZINC database of natural products, combined with ISM-SM/EIIP filtering, yielded 237 candidate compounds. Structural separation analysis discriminated between the positives and negatives, enabling enrichment-based prioritization. The use of a composite normalized rank score based on docking affinity and structural similarity allowed for the identification of the top candidates: ZINC03643214 and ZINC67840571. Collectively, these refinements establish a more sophisticated computational model for identifying novel GAT-1 inhibitors and highlight promising candidates for future experimental evaluation. Full article

Background/Objectives: Poor outcomes in liver cancer are often driven by late-stage diagnoses and high recurrence rates following surgical resection, highlighting a critical clinical need for non-invasive surveillance tools. This proof-of-concept study investigates the utility of circulating extracellular vesicles (EVs) to track dynamic molecular shifts and monitor patient response following tumour resection. Methods: Small ribonucleic acid (RNA) sequencing was conducted on matched tumour tissue, tissue-derived EVs, and plasma EVs collected at the time of surgery from patients with liver cancer. To capture longitudinal transcriptomic changes, plasma EVs were also collected at a post-operative follow-up appointment. Results: At the time of surgery, the transcriptomic profile of circulating plasma EVs strongly correlated with both the matched tumour tissue and tissue-derived EVs, exhibiting substantial transcript overlap. However, at post-operative follow-up, the circulating EV cargo significantly diverged from the primary tumour profile. This loss of similarity was characterised by a distinct shift in RNA cargo, including 173 uniquely detected transcripts absent at baseline. Conclusions: Circulating EVs accurately reflect the local hepatic transcriptome at the time of surgery, but their profile dynamically and fundamentally diverges once the tumour is removed. This post-surgical divergence provides an initial proof-of-concept that utilising patients as their own internal control to longitudinally profile EV cargo may track the clearance of tumour signals and monitor post-surgical systemic changes, highlighting their potential utility for future longitudinal studies aimed at tracking cancer progression and recurrence. Full article

The family GH126 represents a potential fourth, but still non-confirmed α-amylase family in CAZy with the founding, partially characterized member, the assumed amylolytic enzyme CPF_2247 from Clostridium perfringens. Proteins of this family adopt an (α/α)₆-barrel domain, structurally distinct from the rather more complex domain arrangement of families GH13, GH57, and GH119. Interestingly, GH126 exhibits structural similarity, including sharing potential functionally important residues with inverting β-glucanases from GH8 and GH48 (clan GH-M); this fact has prompted previous bioinformatics analyses. In the present study, two GH126 members with experimentally determined tertiary structure—the CPF_2247 and the exopolysaccharide-specific hydrolase PssZ from Listeria monocytogenes—were compared with seven GH8 and ten GH48 enzyme-substrate complexes. Family GH126 enzymes display a wide, open binding cleft, with a central tunnel-like cavity along the barrel axis, distinct from the narrow cleft in GH8 and the tunnel-shaped site in GH48. Conserved residues involved in substrate binding and catalysis of GH8 and GH48 were identified in GH126. Molecular docking with α-glucans using the CPF_2247 confirmed predicted binding at the potential active site and revealed also eventual additional binding sites. Targeted docking showed the strongest interactions for acarbose and maltoheptaose, particularly involving a GH126 unique α11-α12 loop in the assumed amylolytic enzyme CPF_2247. Full article

Accurate prediction of protein–protein interaction (PPI) interface residues is essential for understanding molecular recognition and supporting structure-guided design. To integrate contextual sequence representations with structure-related physicochemical information, we propose a multimodal framework termed MD-Transformer. The model combines residue-level ProtBERT embeddings with physicochemical descriptors, including B-factor, solvent-accessible surface area (SASA), and hydrophobicity. A hybrid fusion module first aligns heterogeneous features, followed by Transformer encoding and cross-modal attention for multimodal integration. Using the DB5.5 benchmark, physicochemical descriptors were Z-score normalized exclusively with training-set statistics. Under the complex-level split protocol (Official A), MD-Transformer achieved an AUPRC of 0.564, outperforming the ablation model without physicochemical descriptors by 0.159 and reducing false-positive predictions on exposed non-interface residues. Under the homology-aware split protocol (Official B v1), the model maintained an AUPRC of 0.480 and an MCC of 0.242, indicating retained predictive capability under reduced sequence similarity constraints. Under the same aligned evaluation workflow, PeSTo achieved an AUPRC of 0.264. Further SASA-stratified analyses identified SASA as a major contributor to suppressing false-positive predictions across residue exposure environments, while also revealing a precision-recall trade-off in highly exposed residues. These results suggest that contextual sequence representations and residue-level physicochemical descriptors provide complementary predictive signals. Full article