Genetically engineering encapsulin protein cage nanoparticle as a SCC-7 cell targeting optical nanoprobe

Background - Protein cage nanoparticles are promising nanoplatform candidates for efficient delivery systems of diagnostics and/or therapeutics because of their uniform size and structure as well as high biocompatibility and biodegradability. Encapsulin protein cage nanoparticle is used to develop a cell-specific targeting optical nanoprobe. Results - FcBPs are genetically inserted and successfully displayed on the surface of encapsulin to form FcBP-encapsulin. Selectively binding of FcBP-encapsulin to SCC-7 is visualized with fluorescent microscopy. Conclusions - Encapsulin protein cage nanoparticle is robust enough to maintain their structure at high temperature and easily acquires multifunctions on demand through the combination of genetic and chemical modifications.ope

Disorder-dependent Li diffusion in Li6PS5Cl\mathrm{Li_6PS_5Cl} investigated by machine learning potential

Solid-state electrolytes with argyrodite structures, such as $\mathrm{Li_6PS_5Cl}$, have attracted considerable attention due to their superior safety compared to liquid electrolytes and higher ionic conductivity than other solid electrolytes. Although experimental efforts have been made to enhance conductivity by controlling the degree of disorder, the underlying diffusion mechanism is not yet fully understood. Moreover, existing theoretical analyses based on ab initio MD simulations have limitations in addressing various types of disorder at room temperature. In this study, we directly investigate Li-ion diffusion in $\mathrm{Li_6PS_5Cl}$ at 300 K using large-scale, long-term MD simulations empowered by machine learning potentials (MLPs). To ensure the convergence of conductivity values within an error range of 10%, we employ a 25 ns simulation using a $5\times5\times5$ supercell containing 6500 atoms. The computed Li-ion conductivity, activation energies, and equilibrium site occupancies align well with experimental observations. Notably, Li-ion conductivity peaks when Cl ions occupy 25% of the 4c sites, rather than at 50% where the disorder is maximized. This phenomenon is explained by the interplay between inter-cage and intra-cage jumps. By elucidating the key factors affecting Li-ion diffusion in $\mathrm{Li_6PS_5Cl}$, this work paves the way for optimizing ionic conductivity in the argyrodite family.Comment: 34 pages, 6 figure

Deformable Graph Transformer

Transformer-based models have recently shown success in representation learning on graph-structured data beyond natural language processing and computer vision. However, the success is limited to small-scale graphs due to the drawbacks of full dot-product attention on graphs such as the quadratic complexity with respect to the number of nodes and message aggregation from enormous irrelevant nodes. To address these issues, we propose Deformable Graph Transformer (DGT) that performs sparse attention via dynamically sampled relevant nodes for efficiently handling large-scale graphs with a linear complexity in the number of nodes. Specifically, our framework first constructs multiple node sequences with various criteria to consider both structural and semantic proximity. Then, combining with our learnable Katz Positional Encodings, the sparse attention is applied to the node sequences for learning node representations with a significantly reduced computational cost. Extensive experiments demonstrate that our DGT achieves state-of-the-art performance on 7 graph benchmark datasets with 2.5 - 449 times less computational cost compared to transformer-based graph models with full attention.Comment: 16 pages, 3 figure

Extracellular Vesicles From KSHV-Infected Cells Stimulate Antiviral Immune Response Through Mitochondrial DNA

Kaposi's Sarcoma-associated herpesvirus (KSHV) is the etiologic agent of Kaposi's sarcoma, which is the most common cancer in acquired immune deficiency syndrome patients. KSHV contains a variety of immunoregulatory proteins. There have been many studies on the modulation of antiviral response by these immunoregulatory proteins of KSHV. However, the antiviral effects of extracellular vesicles (EVs) during de novo KSHV infection have not been investigated to our best knowledge. In this study, we showed that KSHV-infected cells induce interferon-stimulated genes (ISGs) response but not type I interferon in uninfected bystander cells using EVs. mRNA microarray analysis showed that ISGs and IRF-activating genes were prominently activated in EVs from KSHV-infected cells (KSHV EVs)-treated human endothelial cells, which were validated by RT-qPCR and western blot analysis. We also found that this response was not associated with cell death or apoptosis by virus infection. Mechanistically, the cGAS-STING pathway was linked with these KSHV EVs-mediated ISGs expressions, and mitochondrial DNA on the surface of KSHV EVs was one of the causative factors. Besides, KSHV EVs-treated cells showed lower infectivity for KSHV and viral replication activity than mock EVs-treated cells. Our results indicate that EVs from KSHV-infected cells could be an initiating factor for the innate immune response against viral infection, which may be critical to understanding the microenvironment of virus-infected cells