Search Results (416)

Specific expression of genes is fundamental for defining the identity and the functional state of cells. Sequence-specific transcription factors interpret the information contained in DNA sequence motifs and recruit cofactors to modify chromatin and control RNA polymerases. This multi-step process typically involves several transcription factors and cofactors with different enzymatic activities. Post-translational modifications (PTMs) of histones are one key mechanism to control chromatin structure and polymerase activity and thus gene transcription. The methylation of histone H3 at lysine 4 (H3K4) is a modification of accessible chromatin, including enhancers and promoters, and also sites of recombination and some forms of DNA damage. H3K4 methylation is catalyzed by six lysine methyltransferase complexes, referred to as KMT2 or COMPASS-like complexes. These are important in processes related to transcription and contribute to recombination in T and B cells. PRDM9 and ASH1L are H3K4 methyltransferases involved in meiotic recombination and DNA repair, respectively. In transcription, H3K4 mono- and tri-methylation are located at enhancers and promoters, respectively. These modifications, either alone or in combination with other histone PTMs, provide binding sites for transcriptional cofactors. Through these sites, H3K4 methylation affects chromatin accessibility and histone PTMs, typically resulting in a favorable environment for transcription. H3K4 tri-methylation also recruits and regulates RNA polymerase II (RNAPII) complexes, which interact with KMT2 complexes, generating positive feedforward loops to promote transcription. Thus, H3K4 methylation has broad activities that are key to different chromatin-associated processes. Full article

Our understanding of the molecular mechanisms by which DNA meiotic recombination occurs has significantly increased in the past decades. A more representative molecular model has also undergone repeated revisions and upgrades with the continuous expansion of experimental data. Considering several apparent issues in the field, we intend to make necessary upgrades to previous models and reanalyze those data, exploring structural details and molecular mechanisms of DNA meiotic recombination. Eligible studies were identified from PubMed/Medline (up to June 2024). Key related publications and experimental data were retrieved from eligible studies, displaying five major issues. Meanwhile, the biophysical modeling method was used to establish an enlacement model. Then, the model was used to wholly reanalyze the collected data. An updated molecular model was supplemented. In the current model, a copy choice mechanism can initiate DNA meiotic recombination. The copy choice is based on a branched structure of DNA, which results from relative motion between homologous single strands. The reanalysis of previous experimental data based on this model can lead to new interpretations that can better address the discrepancies between previous experimental observations and theoretical models, including (1) the intertwinement model having embodied the particular characteristics of the SDSA model; (2) hDNA arising from JM resolution rather than being followed by a JM; (3) strand specificity of hDNA mismatch repair seeming to be an illusion and copy choice more likely to be the actual state; (4) parity in resolution patterns of a dHJ leading to parity of gene conversion; (5) the cooperation of multiple HJs readily generating a high correlation between gene conversion and crossover; and (6) transpositional recombination and site-specific recombination seeming to have a common pathway to meiotic recombination. The results indicate that both revisions and reanalysis are necessary. The novel interpretations would be critical to the understanding of the mechanisms of DNA recombination as well as its role in DNA repair. Additionally, the work could have implications for how the field views the importance of factors such as Spo11 or the mechanisms that drive meiotic pairing. Full article

Electrocatalytic CO₂ reduction driven by renewable electricity offers a sustainable approach to producing valuable chemicals, though it is often hindered by low activity and selectivity. CuO, an important transition metal oxide, exhibits unique advantages in photoelectrocatalysis due to its high intrinsic catalytic activity and ability to serve as an active site for CO₂ reduction. SiO₂, a widely used substrate, facilitates Cu loading and increases the specific surface area of the catalyst. Meanwhile, g-C₃N₄ provides excellent visible-light responsiveness and efficient charge carrier mobility. Together, CuO, SiO₂, and g-C₃N₄ are earth-abundant, low-cost, and chemically stable, making them ideal for solar-to-fuel applications. Here, a novel ternary heterojunction photocatalyst was constructed using SiO₂, CuO, and g-C₃N₄. The heterostructure significantly improves light-harvesting efficiency, promotes efficient charge separation and transport, and simultaneously mitigates photogenerated carrier recombination and catalyst corrosion. The resulting SiO₂@CuO/g-C₃N₄ catalyst demonstrates outstanding CO₂ conversion performance, achieving a CO yield of 17 mmolg⁻¹h⁻¹ at 1.2 V_RHE with nearly 100% selectivity. Moreover, this work systematically investigates the electrocatalytic CO₂ reduction reaction (CO₂RR) mechanism on Cu-based catalysts, offering insights into the formation of high-value multicarbon products and highlighting the potential of rational heterojunction design in enhancing solar-driven fuel production efficiency. Full article

With the aim of reducing catalysts’ cost while maintaining high performance in water splitting, ZnO and RuO₂ were combined into composites with ZnO to RuO₂ mass ratios of 1:1, 2:1, and 10:1. The ZnO/RuO₂ composites were prepared by microwave processing of a suspension containing Zn(OH)₂ in situ precipitated onto RuO₂ powder, and subsequently thermally modified at 600 °C to promote heterojunction formation and alter the defect chemistry. Phase composition, crystal structure, morphology, and optical properties were analyzed in detail employing XRD, TEM/HRTEM, HAADF-STEM with EDS, PL and XPS spectroscopy. The photoelectrocatalytic (PEC) activity of the composites toward the hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) was evaluated by linear sweep voltammetry in alkaline electrolyte (0.1 M NaOH, pH 13), before and after one hour of electrochemical system illumination. The analysis focused on surface and bulk oxygen vacancies, which may have a crucial impact in PEC activity, by (1) promoting charge separation and increasing the number of active sites thus enhancing PEC activity, or (2) acting as electron–hole traps and recombination centers, reducing the lifetime of photo-induced charge carriers and thus deteriorating PEC activity. The presented results demonstrate that the combination of ZnO with RuO₂ in a specific mass ratio, along with controlled defect structure, offers a worthwhile route for developing bifunctional, noble-metal-reduced catalysts for green hydrogen and oxygen production. Full article

TiO₂ photocatalysts exhibit great potential in solar fuel production and environmental remediation, yet their practical applications are often hindered by high electron-hole recombination rates. This study presents a novel strategy for fabricating hollow anatase TiO₂-modified ZnS heterostructures (TiO₂/ZnS) via a simple hydrothermal method. The heterostructure effectively combines the high electron mobility of ZnS, which facilitates rapid photogenerated electron transfer, with the high specific surface area of hollow TiO_2, which enhances pollutant adsorption. As a result, TiO₂/ZnS demonstrates superior tetracycline degradation efficiency due to optimized charge separation and improved accessibility to reactive sites, compared to pristine TiO₂ and ZnS. Furthermore, the enhanced photocatalytic activity is attributed to efficient charge separation facilitated by Type-II heterojunctions between ZnS and anatase TiO₂. Cycling tests reveal that TiO₂/ZnS retains over 94% of its activity after 5 cycles. This work offers a versatile approach for stabilizing metal oxides through heterostructure engineering, with significant implications for scalable environmental catalysis. Full article

This study explores the structural transitions and aggregation behaviour of recombinant β- and γ-synucleins from five vertebrate species—Cyprinus carpio, Danio rerio, Xenopus laevis, Anolis carolinensis, and Homo sapiens—using thioflavin T fluorescence and circular dichroism spectroscopy, with and without copper ions. Although synucleins are well-conserved proteins among vertebrates, species-specific differences in amino acid composition and predicted secondary structures were observed, particularly within β-strand-forming regions. During a six-day incubation, human β-synuclein exhibited a time-dependent increase in β-sheet-rich structures, while non-mammalian β-synucleins showed limited variation. In contrast, γ-synucleins from all species displayed greater aggregation propensity, with variations in kinetics and magnitude. The presence of copper reduced the rate of aggregation in human β-synuclein, likely due to high-affinity metal-binding sites, whereas γ-synuclein aggregation was only mildly affected. Notably, copper enhanced late-phase aggregation in A. carolinensis β-synuclein. These findings suggest that sequence divergence among synuclein isoforms may underlie species-specific aggregation mechanisms and metal sensitivity. The differential aggregation behaviour observed across taxa may reflect evolutionary adaptations in synuclein function and folding propensity, with implications for understanding the molecular basis of synucleinopathies and their potential modulation by metal ions. Full article

Phthalic acid esters (PAEs), ubiquitously employed as a plasticizer, have been classified as priority environmental pollutants because of their persistence, bioaccumulation, and endocrine-disrupting properties. As a characterized PAE-degrading strain of marine origin, Mycolicibacterium phocaicum RL-HY01 utilizes di-(2-ethylhexyl) phthalate (DEHP) as its sole carbon and energy source. Genome sequencing and RT-qPCR analysis revealed a previously uncharacterized hydrolase gene (dehpH) in strain RL-HY01, which catalyzes ester bond cleavage in PAEs. Subsequently, recombinant expression of the cloned dehpH gene from strain RL-HY01 was established in Escherichia coli BL21(DE3). The purified recombinant DehpH exhibited optimal activity at 30 °C and pH 8.0. Its activity was enhanced by Co²⁺ and tolerant to most metal ions but strongly inhibited by EDTA, SDS, and PMSF. Organic solvents (Tween-80, Triton X-100, methanol, ethanol, isopropanol, acetone, acetonitrile, ethyl acetate, and n-hexane) showed minimal impact. Substrate specificity assay indicated that DehpH could efficiently degrade the short and long side-chain PAEs but failed to hydrolyze the cyclic side-chain PAE (DCHP). The kinetics parameters for the hydrolysis of DEHP were determined under the optimized conditions, and DehpH had a V_max of 0.047 ± 0.002 μmol/L/min, K_m of 462 ± 50 μmol/L, and k_cat of 3.07 s⁻¹. Computational prediction through structural modeling and docking identified the active site, with mutagenesis studies confirming Ser228, Asp324, and His354 as functionally indispensable residues forming the catalytic triad. The identification and characterization of DehpH provided novel insights into the mechanism of DEHP biodegradation and might promote the application of the target enzyme. Full article

Infectious bronchitis virus (IBV) remains a major threat to poultry health worldwide due to frequent genetic changes mainly driven by recombination and limited cross-protection between genotypes. In this study, we analyzed IBV strains collected from clinical outbreaks in Chile between 1986 and 2021 to assess the long-term impacts of live-attenuated vaccines (Massachusetts and 4/91) on viral evolution. Phylogenetic analysis of the S1 and N genes revealed four major lineages circulating in Chile—GI-1, GI-13, GI-16, and a novel monophyletic clade we propose as GI-31. The latter, identified in isolates from 1986 to 1988, is highly divergent (22–24%) from other known lineages, representing a previously unreported South American IBV variant. Despite widespread Mass vaccination, genetically distinct field strains circulated during the 1980s, facilitating potential recombination with GI-1 vaccine-derived strains, including evidence of shared ancestry with GI-11, an endemic lineage from Brazil. Non-recombinant GI-16, likely introduced from Asia, was detected in isolates from 2009. Notably, a recombinant strain emerged in 2015, four years after 4/91 vaccine introduction, indicating vaccine–field-strain genetic exchange. By 2017, isolates with >99% identity to the 4/91 strain were recovered, suggesting vaccine-derived variants. In 2021, GI-1 re-emerged, showing recombination signatures between GI-1 and GI-13 (4/91-derived) strains, likely reflecting suboptimal or inconsistent vaccination strategies. Selection analyses showed strong purifying selection across most of the S1 gene, with limited sites under positive selection in the receptor-binding domain. Phylodynamic reconstruction revealed time-structured evolution and multiple introduction events over 35 years, with lineage-specific tMRCA estimates. Collectively, these findings highlight the emergence of a novel lineage in South America and demonstrate that vaccine use, while mitigating disease, has significantly shaped the evolution of IBV in Chile. Our results underscore the importance of continuous genomic surveillance to inform vaccine strategies and limit recombinant emergence. Full article

Background: Chronic hepatitis B (CHB) remains being a major public health threat, and currently existing CHB therapies have limited efficacy and side effects. We have recently developed a vaccine termed VVX001 based on a recombinant fusion protein consisting of the preS domain of the large surface protein of hepatitis B virus (HBV) fused to grass pollen allergen peptides. VVX001 has been shown to induce preS-specific antibodies in grass pollen allergic patients, and sera of immunized subjects inhibited HBV infection in vitro. Methods: In this study we investigated if immunization with VVX001 can induce preS-specific antibodies in CHB using the adeno-associated virus (AAV)-HBV murine model of CHB. Six groups of C57BL/6 female mice (n = 6) were transduced with AAV-HBV or AAV-Empty, and after six weeks, they were immunized five times with 20 µg of aluminum hydroxide-adsorbed VVX001 or preS or vehicle (Alum alone). Serum samples were taken continuously. Two weeks after the last immunization, spleen and liver mononuclear cells were collected. Serum reactivity to preS and preS-derived peptides was assessed by ELISA. B-cell responses were measured by ELISPOT assay, and intrahepatic lymphocyte (ILH) counts were determined by FACS. HBV DNA, HBsAg, HBeAg, ALT, and AST were assessed using commercial kits. Results: Our results show that VVX001 induces preS-specific IgG antibodies that cross-react with different HBV genotypes A-H and are directed against the sodium taurocholate co-transporting polypeptide (NTCP) receptor binding site of preS both in mice with and without HBV. Actively immunized AAV-HBV-treated mice had a higher number of intrahepatic lymphocytes than vehicle-vaccinated and mock-transduced animals. Conclusions: These findings encourage performing further trials to study the potential of VVX001 for therapeutic vaccination against CHB. Full article

 Porcine epidemic diarrhea virus (PEDV) continues to circulate globally, causing substantial economic losses to the swine industry. Historically, PEDV strains are classified into the classical G1, epidemic G2, and S-INDEL genotypes. Among these genotypes, the highly virulent and prevalent G2 genotype has been extensively studied. However, recent clinical outbreaks in China necessitate a reevaluation of the epidemiological and evolutionary dynamics of circulating strains. This study analyzed 37 newly sequenced S genes and public sequences to characterize the genetic variations of S-INDEL strains. Our analysis revealed that S-INDEL strains are endemic throughout China, with a phylogenetic analysis identifying two distinct clades: clade 1, comprising early endemic strains, and clade 2, representing a recently dominant, geographically restricted lineage in China. While inter-genotypic recombination has been documented, our findings also demonstrate that intra-genotypic and intra-clade recombination events contributed significantly to the emergence of clade 2, distinguishing its evolutionary pattern from clade 1. A comparative analysis identified 22 clade-specific amino acid changes, 11 of which occurred in the D0 domain. Notably, mutations at positively selected sites—113 and 114 within the D0 domain, a domain associated with pathogenicity—were specific to clade 2. A phylodynamic analysis indicated Germany as the epicenter of S-INDEL dispersal, with China acting as a sink population characterized by localized transmission networks and frequent recombination events. These results demonstrate that contemporary S-INDEL strains, specifically clade 2, exhibit unique recombination patterns and mutations potentially impacting virulence. Continuous surveillance is essential to assess the pathogenic potential of these evolving recombinant variants and the efficacy of vaccines against them.  Full article

Background: Against the backdrop of the large-scale and intensive development of the livestock industry, enhancing the reproductive efficiency of cattle has become a crucial factor in industrial development. Holstein cows, as the most predominant dairy cattle breed globally, are characterized by high milk yield and excellent milk quality. However, their reproductive efficiency is comprehensively influenced by a variety of complex factors, and improving their reproductive performance faces numerous challenges. The ovary, as the core organ of the female reproductive system, plays a decisive role in embryonic development and pregnancy maintenance. It is not only the site where eggs are produced and developed but it also regulates the cow’s estrous cycle, ovulation process, and the establishment and maintenance of pregnancy by secreting various hormones. The normal functioning of the ovary is crucial for the smooth development of the embryo and the successful maintenance of pregnancy. Methods: Currently, traditional sequencing technologies have obvious limitations in deciphering ovarian function and reproductive regulatory mechanisms. To overcome the bottlenecks of traditional sequencing technologies, this study selected Holstein cows as the research subjects. Ovarian samples were collected from one pregnant and one non-pregnant Holstein cow, and single-nucleus transcriptome sequencing technology was used to conduct an in-depth study on the ovarian cells of Holstein cows. Results: By constructing a cell type-specific molecular atlas of the ovaries, nine different cell types were successfully identified. This study compared the proportions of ovarian cell types under different physiological states and found that the proportion of endothelial cells decreased during pregnancy, while the proportions of granulosa cells and luteal cells increased significantly. In terms of functional enrichment analysis, oocytes during both pregnancy and non-pregnancy play roles in the “cell cycle” and “homologous recombination” pathways. However, non-pregnant oocytes are also involved in the “progesterone-mediated oocyte maturation” pathway. Luteal cells during pregnancy mainly function in the “cortisol synthesis and secretion” and “ovarian steroidogenesis” pathways; non-pregnant luteal cells are mainly enriched in pathway processes such as the “AMPK signaling pathway”, “pyrimidine metabolism”, and “nucleotide metabolism”. Cell communication analysis reveals that there are 51 signaling pathways involved in the pregnant ovary, with endothelial cells, granulosa cells, and luteal cells serving as the core communication hubs. In the non-pregnant ovary, there are 48 pathways, and the interaction between endothelial cells and stromal cells is the dominant mode. Conclusions: This study provides new insights into the regulatory mechanisms of reproductive efficiency in Holstein cows. The differences in the proportions of ovarian cell types, functional pathways, and cell communication patterns under different physiological states, especially the increase in the proportions of granulosa cells and luteal cells during pregnancy and the specificity of related functional pathways, indicate that these cells play a crucial role in the reproductive process of cows. These findings also highlight the importance of ovarian cells in pathways such as “cell cycle”, “homologous recombination”, and “progesterone-mediated oocyte maturation”, as well as the cell communication mechanisms in regulating ovarian function and reproductive performance. Full article

Phospholipase A1 (Ves a 1), a major toxin from Vespa affinis venom, poses significant risks to allergic individuals. Nevertheless, the epitope determinants of Ves a 1 have not been characterized. Thus, identifying its linear B-cell epitopes is crucial for understanding envenomation mechanisms. In this study, we predicted and identified B-cell epitopes EP5 and EP6 as potential candidates. EP5 formed an α-helix at the active site of Ves a 1, whereas EP6 adopted an extended loop conformation. Both synthetic peptides were synthesized and evaluated for their inhibitory effects using immune-inhibitory assays with polyclonal antibodies (pAbs) targeting both native (nVes a 1) and recombinant (rVes a 1) forms. The Ves a 1 polyclonal antibodies (pAb-nVes a 1 and pAb-Ves a 1) were produced, and their specificity binding to Ves a 1 was confirmed by Western blot. Next, ELISA inhibition assays showed that EP5 and EP6 significantly blocked pAb binding to both nVes a 1 and rVes a 1. Dot blot and Western blot assays supported these findings, particularly with stronger inhibition toward rVes a 1. Furthermore, enzymatic assays indicated that nVes a 1 and rVes a 1 retained phospholipase activity. Immunoinformatics docking showed that EP5 and EP6 specifically bind to a single-chain variable fragment antibody (scFv) targeting Naja naja PLA2. Molecular analysis revealed similar amino acid interactions to the template, suggesting effective paratope–epitope binding. These results support the potential of EP5 and EP6 for future diagnosis and therapy of V. affinis venom allergy. Full article

Recombinant protein hydrogels have emerged as transformative biomaterials that overcome the bioinertness and unpredictable degradation of traditional synthetic systems by leveraging genetically engineered backbones, such as elastin-like polypeptides, SF, and resilin-like polypeptides, to replicate extracellular matrix (ECM) dynamics and enable programmable functionality. Constructed through a hierarchical crosslinking strategy, these hydrogels integrate reversible physical interactions with covalent crosslinking approaches, collectively endowing the system with mechanical strength, environmental responsiveness, and controlled degradation behavior. Critically, molecular engineering strategies serve as the cornerstone for functional precision: domain-directed self-assembly exploits coiled-coil or β-sheet motifs to orchestrate hierarchical organization, while modular fusion of bioactive motifs through genetic encoding or site-specific conjugation enables dynamic control over cellular interactions and therapeutic release. Such engineered designs underpin advanced applications, including immunomodulatory scaffolds for diabetic wound regeneration, tumor-microenvironment-responsive drug depots, and shear-thinning bioinks for vascularized bioprinting, by synergizing material properties with biological cues. By uniting synthetic biology with materials science, recombinant hydrogels deliver unprecedented flexibility in tuning physical and biological properties. This review synthesizes emerging crosslinking paradigms and molecular strategies, offering a framework for engineering next-generation, adaptive biomaterials poised to address complex challenges in regenerative medicine and beyond. Full article

Equine lutropin hormone/choriogonadotropin receptor (LH/CGR) is a G protein-coupled receptor that binds to both luteinizing hormone and choriogonadotropin, with multiple potential N-linked glycosylation sites in the long extracellular domain region. The roles of these glycosylation sites in hormone binding have been widely studied; however, their relationships with cyclic adenosine monophosphate (cAMP) activation, loss of cell surface receptors, and phosphorylated extracellular signal-regulated kinases1/2 (pERK1/2) expression are unknown. We used site-directed mutagenesis with the substitution of Asn for Gln to alter the consensus sequences for N-linked glycosylation, and cAMP signaling was analyzed in the mutants. Specifically, the N174Q and N195Q mutants exhibited markedly reduced expression levels, reaching approximately 15.3% and 2.5%, respectively, of that observed for wild-type equine LH/CGR. Correspondingly, the cAMP EC₅₀ values were decreased by 7.6-fold and 5.6-fold, respectively. Notably, the N195Q mutant displayed an almost complete loss of cAMP activity, even at high concentrations of recombinant eCG, suggesting a critical role for this glycosylation site in receptor function. Despite these alterations, Western blot analysis revealed that pERK1/2 phosphorylation peaked at 5 min following agonist stimulation across all mutants, indicating that the ERK1/2 signaling pathway remains functionally intact. This study demonstrates that the specific N-linked glycosylation site, N195, in equine LH/CGR is indispensable for cAMP activity but is normally processed in pERK1/2 signaling. Thus, we suggest that in equine LH/CGR, agonist treatment induces biased signaling, differentially activating cAMP signaling and the pERK1/2 pathway. Full article

The efficient depolymerization of lignin has become a key challenge in the preparation of high-value-added chemicals. Graphitic carbon nitride (g-C₃N₄)-based photocatalytic system shows potential due to its mild and green characteristics over other depolymerization methods. However, its inherent defects, such as a wide band gap and rapid carrier recombination, severely limit its catalytic performance. In this paper, a g-C₃N₄ modification strategy of K⁺ doping and surface alkalinization is proposed, which is firstly applied to the photocatalytic depolymerization of the lignin β-O-4 model compound (2-phenoxy-1-phenylethanol). K⁺ doping is achieved by introducing KCl in the precursor thermal polymerization stage to weaken the edge structure strength of g-C₃N₄, and post-treatment with KOH solution is combined to optimize the surface basic groups. The structural/compositional evolution of the materials was analyzed by XRD, FTIR, and XPS. The morphology/element distribution was visualized by SEM-EDS, and the optoelectronic properties were evaluated by UV–vis DRS, PL, EIS, and transient photocurrent (TPC). K⁺ doping and surface alkalinization synergistically regulate the layered structure of the material, significantly increase the specific surface area, introduce nitrogen vacancies and hydroxyl functional groups, effectively narrow the band gap (optimized to 2.35 eV), and inhibit the recombination of photogenerated carriers by forming electron capture centers. Photocatalytic experiments show that the alkalinized g-C₃N₄ can completely depolymerize 2-phenoxy-1-phenylethanol with tunable product selectivity. By adjusting reaction time and catalyst dosage, the dominant product can be shifted from benzaldehyde (up to 77.28% selectivity) to benzoic acid, demonstrating precise control over oxidation degree. Mechanistic analysis shows that the surface alkaline sites synergistically optimize the C_β-O bond breakage path by enhancing substrate adsorption and promoting the generation of active oxygen species (·OH, ·O₂⁻). This study provides a new idea for the efficient photocatalytic depolymerization of lignin and lays an experimental foundation for the interface engineering and band regulation strategies of g-C₃N₄-based catalysts. Full article