Search Results (177)

Despite current vaccines and therapeutics targeting SARS-CoV-2, the causative agent of the COVID-19 pandemic, cases remain high causing a burden on health care systems. Spike-protein mediated membrane fusion of SARS-CoV-2 is a critical step in viral entry. Herein, we describe entry inhibitors identified by first screening a library of about 160 compounds and then analogue synthesis. Specifically, compound 261 was found to inhibit SARS-CoV-2 infection in a tissue model with IC₅₀ of 0.3 µM. Using NMR, we found that 261 interacts with key residues in the aromatic-rich region of the spike protein directly next to the transmembrane domain. Molecular dynamic simulations of the 261 binding pocket in the spike protein was also mapped to the transmembrane domain, consistent with NMR findings. The amino acids in the binding site are conserved among different coronaviruses known to infect humans; therefore, inhibitors targeting this conserved binding site could be a useful addition to current therapeutics and may have pan-coronavirus antiviral activities. Full article

Background/Objectives: For viral entry into host cells, the spike (S) protein of coronavirus (CoV) uses its S1 domain to bind to the host receptor and S2 domain to mediate the fusion between virion and cellular membranes. The S1 domain acquired multiple mutations as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolved to give rise to Variant of Concerns (VOCs) but the S2 domain has limited changes. In particular, the stem helix in S2 did not change significantly and it is fairly well-conserved across multiple beta-CoVs. In this study, we generated a murine mAb 7B2 binding to the stem helix of SARS-CoV-2. Methods: MAb 7B2 was isolated from immunized mouse and its neutralization activity was evaluated using microneutralization, plaque reduction and cell–cell fusion assays. Bio-layer interferometry was used to measure binding affinity and AlphaFold3 was used to model the antibody–antigen interface. Results: MAb 7B2 has lower virus neutralizing and membrane block activities when compared to a previously reported stem helix-binding human mAb S2P6. Alanine scanning and AlphaFold3 modeling reveals that residues K1149 and D1153 in S form a network of polar interactions with the heavy chain of 7B2. Conversely, S2P6 binding to S is not affected by alanine substitution at K1149 and D1153 as indicated by the high ipTM scores in the predicted S2P6-stem helix structure. Conclusions: Our detailed characterization of the mechanism of inhibition of 7B2 reveals its distinctive binding model from S2P6 and yields insights on multiple neutralizing and highly conserved epitopes in the S2 domain which could be key components for pan-CoV vaccine development. Full article

Background/Objectives: Identification and characterization of broadly neutralizing monoclonal antibodies from individuals exposed to SARS-CoV-2, either by infection or vaccination, can inform the development of next-generation vaccines and antibody therapeutics with pan-SARS-CoV-2 protection. Methods: Through single B cell sorting and RT-PCR, monoclonal antibodies (mAbs) were isolated from a donor who experienced a BA.5 or BF.7 breakthrough infection after three doses of inactivated vaccines. Their binding and neutralizing capacities were measured with ELISA and a pseudovirus-based neutralization assay, respectively. Their epitopes were mapped by competition ELISA and site-directed mutation. Results: Among a total of 67 spike-specific mAbs cloned from the donor, four mAbs (KXD643, KXD652, KXD681, and KXD686) can neutralize all tested SARS-CoV-2 variants from wild-type to KP.3. Moreover, KXD643, KXD652, and KXD681 belong to a clonotype encoded by IGHV5-51 and IGKV1-13 and recognize the cryptic and conserved RBD-8 epitope on the receptor-binding domain (RBD). In contrast, KXD686 is encoded by IGHV1-69 and IGKV3-20 and targets a conserved epitope (NTD Site iv) outside the antigenic supersite (NTD Site i) of the N-terminal domain (NTD). Notably, antibody cocktails containing these two groups of mAbs can neutralize SARS-CoV-2 more potently due to synergistic effects. In addition, bispecific antibodies derived from KXD643 and KXD686 demonstrate further improved neutralizing potency compared to antibody cocktails. Conclusions: These four mAbs can be developed as candidates of pan-SARS-CoV-2 antibody therapeutics through further antibody engineering. On the other hand, vaccines designed to simultaneously elicit neutralizing antibodies towards RBD-8 and NTD Site iv have the potential to provide pan-SARS-CoV-2 protection. Full article

Pansharpening provides a computational solution to the resolution limitations of imaging hardware by enhancing the spatial quality of low-resolution hyperspectral (LRMS) images using high-resolution panchromatic (PAN) guidance. From an information-theoretic perspective, the task involves maximizing the mutual information between PAN and LRMS inputs while minimizing spectral distortion and redundancy in the fused output. However, traditional spatial-domain methods often fail to preserve high-frequency texture details, leading to entropy degradation in the resulting images. On the other hand, frequency-based approaches struggle to effectively integrate spatial and spectral cues, often neglecting the underlying information content distributions across domains. To address these shortcomings, we introduce a novel architecture, termed the Cross-Domain Fusion Attention Network (CDFAN), specifically designed for the pansharpening task. CDFAN is composed of two core modules: the Multi-Domain Interactive Attention (MDIA) module and the Spatial Multi-Scale Enhancement (SMCE) module. The MDIA module utilizes discrete wavelet transform (DWT) to decompose the PAN image into frequency sub-bands, which are then employed to construct attention mechanisms across both wavelet and spatial domains. Specifically, wavelet-domain features are used to formulate query vectors, while key features are derived from the spatial domain, allowing attention weights to be computed over multi-domain representations. This design facilitates more effective fusion of spectral and spatial cues, contributing to superior reconstruction of high-resolution multispectral (HRMS) images. Complementing this, the SMCE module integrates multi-scale convolutional pathways to reinforce spatial detail extraction at varying receptive fields. Additionally, an Expert Feature Compensator is introduced to adaptively balance contributions from different scales, thereby optimizing the trade-off between local detail preservation and global contextual understanding. Comprehensive experiments conducted on standard benchmark datasets demonstrate that CDFAN achieves notable improvements over existing state-of-the-art pansharpening methods, delivering enhanced spectral–spatial fidelity and producing images with higher perceptual quality. Full article

The Oryza genus serves not only as a gene pool for rice improvement but also as a model system for plant evolutionary research. Calcium-dependent protein kinases (CPKs) function as both effectors and sensors in calcium signaling and play versatile roles in plant development and stress responses. Four kinase families, namely CPK-related kinases (CRKs), phosphoenolpyruvate carboxylase kinases (PPCKs), PPCK-related kinases (PEPRKs), and calcium- and calmodulin-dependent kinases (CCaMKs), are frequently called CPK-related kinases. This study utilized evolutionary genomics approaches and provided the pan-genome repertoires of CPKs and their related kinases in 34 Oryza genomes by leveraging the rich genomics resources of the Orzya genus. Gene duplication analysis revealed that distinct duplication types contributed to expanding CPKs and their related kinases in wild rice. We depicted the protein domain architectures of CPKs and their related kinases, highlighting the complexity of EF-hand motifs in CPKs and CCaMKs. Transcriptome analysis determined that alternative splicing was a mechanism contributing to the diversity in the domain architectures of CPKs and CCaMKs. We also generated the expression atlas of CPKs and their related kinases in multiple species of Oryza genus, emphasizing divergent homoeolog expression patterns across tissues and species in allotetraploid wild rice. Collectively, our Oryza-wide analysis of CPKs and their related kinases revealed their evolutionary trajectories and highlighted their diversified domain architectures and expression dynamics, providing gene resources of wild relatives for rice improvement. Full article

Bovine rotavirus (BRV) is one of the main pathogens that cause acute diarrhea in calves under one month of age. Passive immunization has been recognized as an effective way to prevent and treat BRV infection. Recent studies have shown that 10% of bovine antibodies possess an ultra-long CDR H3 domain, which has been shown to be the smallest antigen-binding domain. Due to the extremely small size of ultra-long CDR H3 antibodies, the phage display method was utilized to obtain ultra-long CDR H3 antibodies targeting BRV, providing a new approach for the prevention and/or treatment of BRV. Here, we report the preparation of BRV-specific bovine ultra-long CDR H3 antibodies obtained by constructing and screening a phage display library containing approximately 8.55 × 10⁹ individual clones. Through three rounds of bio-panning, we identified 92 candidate clones, of which 79 exhibited specific binding activity in phage ELISAs. The recombinant bovine ultra-long CDR H3 antibodies could specifically bind to BRV in ELISAs and cell immunofluorescence assays. The neutralizing activity was further confirmed through virus neutralization tests. In the calf model experiment, the recombinant bovine ultra-long CDR H3 antibodies could relieve the symptoms of diarrhea, reduce both the amount and duration of virus release, and increase the survival in calves experimentally infected with BRV. Therefore, BRV-specific bovine ultra-long CDR H3 antibodies could serve as an effective agent for the prevention and treatment of BRV infection. At the same time, the development of ultra-long CDR H3 antibodies using phage display screening technology provides a new approach for developing biological agents for the prevention and control of infectious diseases in bovines. Full article

Background/Objectives: Monkeypox, twice declared a public health emergency of international concern by the WHO, currently lacks approved targeted therapeutics. This study focused on the development of monkeypox virus (MPXV) E8-specific human monoclonal antibodies (mAbs) derived from recipients of the recombinant vaccinia vaccine (rTV), with subsequent evaluation of their cross-neutralizing activity against orthopoxviruses, including the vaccinia virus (VACV) and MPXV. Methods: Three mAbs (C5, C9, and F8) were isolated from rTV vaccinees. Structural mapping characterized their binding domains on the MPXV E8 and VACV D8 proteins. Neutralization potency was assessed against the VACV TianTan strain and MPXV clade IIb. A combo was further evaluated in a VACV-infected mice model for clinical recovery and viral load reduction. Complement-dependent enhancement mechanisms were also investigated in vitro. Results: C9 targets the virion surface region of E8 and both the virion surface region and intravirion region of D8, showing cross-neutralization activity against the MPXV (IC₅₀ = 3.0 μg/mL) and VACV (IC₅₀ = 51.1 ng/mL) in vitro. All three antibodies demonstrated potent neutralization against the VACV in vitro: C5 (IC₅₀ = 3.9 ng/mL), C9 (IC₅₀ = 51.1 ng/mL), and F8 (IC₅₀ = 101.1 ng/mL). Notably, complement enhanced neutralization against the VACV by >50-fold, although no enhancement was observed for the MPXV. In vivo administration accelerated clinical recovery by 24 h and achieved significant viral clearance (0.9-log reduction). Conclusions: E8-targeting mAbs exhibited broad-spectrum neutralization against orthopoxviruses, demonstrating therapeutic potential against both historical (VACV) and emerging (MPXV) pathogens. However, MPXV’s resistance to complement-dependent enhancement highlights the necessity for pathogen-adapted optimization. These findings establish E8 as a critical conserved target for pan-poxvirus VACV and MPXV countermeasure development. Full article

Neuroinflammation is a key feature of all neurodegenerative disorders, including Alzheimer’s disease, and is tightly regulated by epigenetic mechanisms. Among them, bromodomain and extraterminal domain (BET) proteins play a crucial role by recognizing acetylated histones and acting as transcriptional co-regulators to modulate gene expression. This study investigates the potential of inhibiting BET proteins in preventing microglia-mediated neuronal damage in vitro. Murine BV2 microglial cells were exposed to lipopolysaccharide (LPS) or amyloid-β (Aβ) to induce an inflammatory response, and the subsequent effects on murine HT22 neuronal cells were examined. Among the BET proteins tested, only Brd4 was significantly upregulated in BV2 cells upon pro-inflammatory stimulation. JQ1, a potent pan-inhibitor of BET proteins, suppressed LPS-induced upregulation of pro-inflammatory cytokine mRNA levels, including Il1b, Il6, and Tnf, in BV2 microglia. Pre-treatment with JQ1 attenuated the cytotoxicity of LPS-activated BV2 cells toward neurons. Additionally, conditioned media from Aβ fibril-stimulated BV2 cells induced neuronal cell death, which was partially prevented by pre-treatment with JQ1. Co-culture assays further demonstrated the beneficial effect of BET inhibition. Our findings suggest that targeting BET proteins may offer a neuroprotective strategy by modulating microglial activation, potentially providing therapeutic benefits in neurodegenerative diseases. Full article

The discovery of profound differences in the brain microbiota of Alzheimer’s disease (AD) patients and age-matched controls (AMCs) raised questions of postmortem contamination and bacterial transport processes which could be informed by microspatial heterogeneities. We performed semiquantitative species-specific bacterial analyses on multiple micro biopsies from each of the 30 brain specimens (AD and controls). We trimmed ~1 mm of each specimen’s edges for surface contaminants and made multiple sterile biopsy punches of the resultant core of each specimen. To identify species-specific abundances, we used our validated, semiquantitative, full-length 16S rRNA gene pan-domain amplification protocol followed by high-fidelity circular consensus sequencing performed on a Pacific Biosciences Sequel IIe instrument. Statistical analyses showed no significant increase in bacterial abundance on trimmed surfaces compared to core specimens, including C. acnes, the most abundant species previously identified in AD. We did find evidence of substantial bacterial species abundance differences among micro-biopsies obtained from within individual tissue blocks supporting our hypothesis of microspatial heterogeneities. The autopsy brain specimens used in our analyses in this study and our previous publication were not contaminated prior to or postharvesting but we suggest that future microbiological analyses of brain specimens include similar types of edge-core comparison analyses. Further, the species-level bacterial abundance heterogeneities among specimens of the same tissue suggest that multiple symbiotic processes may be occurring. Full article

Despite significant progress in characterizing the omics landscape of head and neck squamous cell carcinoma (HNSCC), the development of precision therapies remains limited. One key factor contributing to this challenge is the marked molecular heterogeneity of HNSCC. Further investigation of molecular profiles within HNSCC may facilitate the improvement in more effective precision treatments. Here, we focus on the dysregulation of PDZ and LIM domain protein 3 (PDLIM3) in HNSCC. The expression levels of PDLIM3 were analyzed using public datasets to assess its potential role in tumor progression. We found that PDLIM3 was downregulated in pan–cancer and HNSCC. The prognostic significance of PDLIM3 was evaluated through tissue microarray, and the downregulation of PDLIM3 was correlated with poor HNSCC prognosis. Investigating the implications of PDLIM3 for tumor metastatic ability in vitro, we found that PDLIM3 suppressed the migration and invasion of HNSCC, accompanied by partially impeding the process of epithelial–mesenchymal transition (EMT). Furthermore, PDLIM3 inhibited the transcriptional activity of Yes–associated protein (YAP), suggesting that YAP may be involved in the PDLIM3–mediated suppression of HNSCC metastatic ability. Our findings identify a potential signaling axis wherein PDLIM3 regulates YAP–EMT, thereby influencing tumor metastatic ability, and suggest the potential role of PDLIM3 as a tumor suppressor and prognostic biomarker for HNSCC. Full article

Background: The EGF domain-specific O-GlcNAc transferase (EOGT), a migrasome marker, plays emerging roles in cancer biology through O-GlcNAcylation modifications, yet its pan-cancer functions and therapeutic implications remain underexplored. This study aimed to systematically characterize EOGT’s oncogenic mechanisms across malignancies, with particular focus on hepatocellular carcinoma (HCC) progression and sorafenib resistance. Methods: Multi-omics analysis integrated TCGA/GTEx data from 33 cancer types with spatial/single-cell transcriptomics and 10 HCC cohorts. Functional validation employed Huh7 cell models with EOGT modulation, RNA sequencing, and ceRNA network construction. Drug sensitivity analysis leveraged GDSC/CTRP/PRISM databases, while immune microenvironment assessment utilized ESTIMATE/TIMER algorithms. Results: EOGT showed cancer-specific dysregulation, marked by significant upregulation in HCC correlating with advanced stages and poor survival. Pan-cancer analysis revealed EOGT’s association with genomic instability, tumor stemness, and angiogenesis. Experimental validation demonstrated EOGT’s promotion of HCC proliferation and migration. A novel exosomal circ_0058189/miR-130a-3p/EOGT axis was identified, showing that circ_0058189 was upregulated in HCC tissues, plasma samples and exosomes of sorafenib-resistant cells. Conclusion: This study establishes EOGT as a pan-cancer angiogenesis biomarker, while elucidating its role in therapeutic resistance via exosomal circRNA-mediated regulation, providing mechanistic insights for targeted intervention strategies. Full article

The Banyo area, located in the southern prolongation of the Mayo Nolti shear zone trend, belongs to the western Cameroon domain of the Neoproterozoic Central African Belt (NCAB). It is made of granitic rocks that intrude metamorphic banded rocks. Both are sometimes mylonitized. The pluton is dominantly of paramagnetic behavior, as shown by the hysteresis loops and the Fe-bearing silicates crystals are the susceptibility carriers. AMS ellipsoids are dominantly of oblate shape, pointing to the importance of flattening during pluton emplacement. The anisotropy degree of magnetic susceptibility values (≤1.20) characterize the magmatic fabric flow. The microstructural study of the granite reveals magmatic, sub-magmatic, solid-state and mylonitic deformations. Field and AMS fabrics show evidence of polyphase deformation (D₁–D₃). The D₁ phase is of flattening mechanism (flat-laying foliation). The D₂ phase points to sinistral ductile simple shear accommodating moderate to steep dipping and N-S- to NW-SE-oriented foliations in plutonic and country rocks and conjugated E-W mylonitic foliation in country rocks bearing sub-horizontal- to moderate-plunge mineral stretching lineation. The D₃ phase is of dextral ductile simple shear. σ- and δ-type kinematic markers in the pluton indicate sinistral top-to-south sense of shear movement, indicating a non-coaxial component of the tectonics. The magnetic fabrics of the pluton are parallel to those of the D₂ deformation phase of the study area. The transpressive D₂ and D₃ events correlate with the D₂ and D₃ phases of the Pan-African tectonic dated at 613–585 Ma and 585–540 Ma, respectively. The pluton, then, emplaced during regional sinistral D₂ deformation under transpressive regime. The emplacement of the NE Banyo granite took place as rock strips sheared in sinistral sense of shear movement. Full article

Human coronavirus OC43 (HCoV-OC43) is usually associated with common colds, but also related to severe disease in the frail. Its envelope glycoproteins spike (S) is responsible for host-cell attachment and membrane fusion. To understand the molecular basis of membrane fusion of HCoV-OC43, we solved the 3.34 Å crystal structure of the post-fusion state formed by two heptad repeat domains (HR1P and HR2P) of OC43-S. This fusion core comprises a parallel trimeric coiled coil of three HR1 helices with 61 Å at length, around which three HR2 helices are entwined in an antiparallel manner, as anticipated. Moreover, a pan-CoV fusion inhibitor EK1 derived from OC43-HR2P was also crystalized with OC43-HR1P in the resolution of 2.71 Å. Parallel comparisons rationalize the design of EK1, maintaining various hydrophobic and charged or hydrophilic interactions formed in the initial fusion core to stabilize the overall conformation. Together, our results not only reveal the critical intrahelical and interhelical interactions underlying the mechanism of action of OC43-S fusion, but also help our understanding on the mechanism of HCoV-OC43 inhibition by analogue HR2 mimic peptide. Full article

The gut microbiome, a complex ecosystem of microorganisms, plays a pivotal role in human health and disease. The gut microbiome’s influence extends beyond the digestive system to various organs, and its imbalance is linked to a wide range of diseases, including cancer and neurodevelopmental, inflammatory, metabolic, cardiovascular, autoimmune, and psychiatric diseases. Despite its significance, the interactions between gut bacteria and human proteins remain understudied, with less than 20,000 experimentally validated protein interactions between the host and any bacteria species. This study addresses this knowledge gap by predicting a protein–protein interaction network between gut bacterial and human proteins. Using statistical associations between Pfam domains, a comprehensive dataset of over one million experimentally validated pan-bacterial–human protein interactions, as well as inter- and intra-species protein interactions from various organisms, were used for the development of a machine learning-based prediction method to uncover key regulatory molecules in this dynamic system. This study’s findings contribute to the understanding of the intricate gut microbiome–host relationship and pave the way for future experimental validation and therapeutic strategies targeting the gut microbiome interplay. Full article

Lipoxygenase (LOX) is a dioxygenase that contains non-heme iron and plays a crucial role in regulating plant growth and development, signal transduction, and responses to both biotic and abiotic stresses. In this study, we identified 24 CsLOXs from the pan-genome of 12 cucumber (Cucumis sativus L.) accessions, with most CsLOX proteins exhibiting amino acid variations. To elucidate their functions, we examined the phylogenetic relationships, gene structures, conserved domains, promoter cis-elements, and collinearity of the 24 CsLOXs from the newly updated genome version 4.0 of ‘Chinese Long 9930’. The results indicated that CsLOXs can be categorized into three subfamilies: 9-LOX, Type I 13-LOX, and Type II 13-LOX. Additionally, promoter analysis revealed that the promoters of CsLOXs contain various cis-elements related to stress and hormone responses. The expression of CsLOXs demonstrated tissue specificity, with each CsLOX expressed in at least one tissue, and six CsLOXs expressed across all tissues. Furthermore, in the transcriptome data of cucumber responses to heat, cold, powdery mildew (PM), downy mildew (DM), and gray mold (GM) stresses, eight, four, eight, eight, and four CsLOXs exhibited differential expression, respectively. Notably, CsLOX22 responded to heat, cold, DM, and GM stresses. Our results provided a reference for further exploring the functions of CsLOXs in cucumber. Full article