Role of Local Conductivities in the Plasmon Reflections at the Edges and Stacking Domain Boundaries of Trilayer Graphene.

We employed infrared scattering-type scanning near-field optical microscopy (IR-sSNOM) to study surface plasmon polaritons (SPPs) in trilayer graphene (TLG). Our study reveals systematic differences in near-field IR spectra and SPP wavelengths between Bernal (ABA) and rhombohedral (ABC) TLG domains on SiO2, which can be explained by stacking-dependent intraband conductivities. We also observed that the SPP reflection profiles at ABA-ABC boundaries could be mostly accounted for by an idealized domain boundary defined by the conductivity discontinuity. However, we identified distinct shapes in the SPP profiles at the edges of the ABA and ABC TLG, which cannot be solely attributed to idealized edges with stacking-dependent conductivities. Instead, this can be explained by the presence of various edge structures with local conductivities differing from those of bulk TLGs. Our findings unveil a new structural element that can control SPP, and provide insights into the structures and electronic states of the edges of few-layer graphene.

One-STAGE Tip Method for TMT-Based Proteomic Analysis of a Minimal Amount of Cells.

Liquid chromatography-tandem mass spectrometry (LC-MS)-based profiling of proteomes with isobaric tag labeling from low-quantity biological and clinical samples, including needle-core biopsies and laser capture microdissection, has been challenging due to the limited amount and sample loss during preparation. To address this problem, we developed OnM (On-Column from Myers et al. and mPOP)-modified on-column method combining freeze-thaw lysis of mPOP with isobaric tag labeling of On-Column method to minimize sample loss. OnM is a method that processes the sample in one-STAGE tip from cell lysis to tandem mass tag (TMT) labeling without any transfer of the sample. In terms of protein coverage, cellular components, and TMT labeling efficiency, the modified On-Column (or OnM) displayed similar performance to the results from Myers et al. To evaluate the lower-limit processing capability of OnM, we utilized OnM for multiplexing and were able to quantify 301 proteins in a TMT 9-plex with 50 cells per channel. We optimized the method as low as 5 cells per channel in which we identified 51 quantifiable proteins. OnM method is a low-input proteomics method widely applicable and capable of identifying and quantifying proteomes from limited samples, with tools that are readily available in a majority of proteomic laboratories.

Vibrationally Hot Reactants in a Plasmon-Assisted Chemical Reaction.

Recent studies on plasmon-assisted chemical reactions postulate that the hot electrons of plasmon-excited nanostructures may induce a non-thermal vibrational activation of metal-bound reactants. However, the postulate has not been fully validated at the level of molecular quantum states. We directly and quantitatively prove that such activation occurs on plasmon-excited nanostructures: The anti-Stokes Raman spectra of reactants undergoing a plasmon-assisted reaction reveal that a particular vibrational mode of the reactant is selectively excited, such that the reactants possess >10 times more energy in the mode than is expected from the fully thermalized molecules at the given local temperature. Furthermore, a significant portion (∼20%) of the excited reactant is in vibrational overtone states with energies exceeding 0.5 eV. Such mode-selective multi-quantum excitation could be fully modeled by the resonant electron-molecule scattering theory. Such observations suggest that the vibrationally hot reactants are created by non-thermal hot electrons, not by thermally heated electrons or phonons of metals. The result validates the mechanism of plasmon-assisted chemical reactions and further offers a new method to explore the vibrational reaction control on metal surfaces.

Thermodynamics of π-π Interactions of Benzene and Phenol in Water.

The π-π interaction is a major driving force that stabilizes protein assemblies during protein folding. Recent studies have additionally demonstrated its involvement in the liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs). As the participating residues in IDPs are exposed to water, π-π interactions for LLPS must be modeled in water, as opposed to the interactions that are often established at the hydrophobic domains of folded proteins. Thus, we investigated the association of free energies of benzene and phenol dimers in water by integrating van der Waals (vdW)-corrected density functional theory (DFT) and DFT in classical explicit solvents (DFT-CES). By comparing the vdW-corrected DFT and DFT-CES results with high-level wavefunction calculations and experimental solvation free energies, respectively, we established the quantitative credibility of these approaches, enabling a reliable prediction of the benzene and phenol dimer association free energies in water. We discovered that solvation influences dimer association free energies, but not significantly when no direct hydrogen-bond-type interaction exists between two monomeric units, which can be explained by the enthalpy-entropy compensation. Our comprehensive computational study of the solvation effect on π-π interactions in water could help us understand the molecular-level driving mechanism underlying the IDP phase behaviors.

Spatially Controlled Fabrication of Surface-Enhanced Raman Scattering Hot Spots through Photoinduced Dewetting of Silver Thin Films.

A well-designed narrow gap between noble metal nanostructures plays a prominent role in surface-enhanced Raman scattering (SERS) to concentrate electromagnetic fields at the local point, called a "hot spot". However, SERS-active substrate fabrication remains a substantial hurdle due to the high process cost and the difficulty of engineering efficient plasmonic hot spots at the target area. In this study, we demonstrate a simple photolithographic method for generating ultrasensitive SERS hot spots at desired positions. The solid-state dewetting of a Ag thin film (thickness of ∼10 nm) using a continuous-wave laser (∼1 MW/cm2) generates a closely packed assembly of hemispherical Ag nanoislands. Some of these nanoislands provide substantial plasmonic-field enhancement that is sufficient for single-molecule detection and plasmon-catalyzed chemical reaction. Such hot spot structures can be patterned on the substrate with a spatial resolution of better than 1 µm. In integrated analytical devices, the patterned SERS hot spots can be used as position-specific chemical-sensing elements.

Phosphoproteome Profiling Using an Isobaric Carrier without the Need for Phosphoenrichment.

Phosphorylation is a crucial component of cellular signaling cascades. It controls a variety of biological cellular functions, including cell growth and apoptosis. Owing to the low stoichiometry of phosphorylated proteins, the enrichment of phosphopeptides prior to LC-MS/MS is necessary for comprehensive phosphoproteome analysis, and quantitative phosphoproteomic workflows are typically limited by the amount of sample required. To address this issue, we developed an easy-to-establish, widely applicable, and reproducible strategy to increase phosphoproteomic signals from a small amount of sample without a phosphoenrichment step. By exploiting the multiplexing nature of isobaric labeling to generate a merged signal from multiple samples, and using a larger amount of enriched phosphopeptides as a carrier, we were able to increase trace amounts of phosphopeptides in the unpurified sample to an identifiable level and perform quantification using the reporter ion intensity of the isobaric tag. Our results showed that >1400 phosphopeptides were quantified from 250 ng of tryptic peptides prepared from cells. In a proof-of-concept of our strategy, we distinguished three types of lung cancer cell lines based on their quantitative phosphoproteomic data and identified changes in the phosphoproteome induced by drug treatment.

Rag2 Deficiency Enhances Susceptibility to Systemic Mouse Adenovirus Type 1 Infection.

INTRODUCTION: Recombination-activating gene (Rag) 1 and Rag2, which are essential in V(D)J recombination, play a crucial role in B- and T-cell maturation. METHOD: We investigated the effects of Rag2 deficiency in clustered regularly interspaced short palindromic repeats/Cas9-mediated FVB-Rag2 knockout (KO) and wild-type (WT) mice infected with mouse adenovirus type 1 (MAV-1) via the intranasal route. RESULTS: MAV-1 infection caused more severe histopathological changes in FVB-Rag2 KO mice than in WT mice. FVB-Rag2 KO mice exhibited moderate to severe inflammation on day 4 and severe inflammation on day 8 post infection. In contrast, WT mice showed mild inflammation on day 4 and mild to severe inflammation on day 8 post infection, including interstitial pneumonia and inflammatory cell infiltration in the lungs and liver. Viral loads in the spleen and kidneys were significantly higher in FVB-Rag2 KO mice than in WT mice on day 8 post infection. Levels of cytokines and chemokines, including macrophage inflammatory protein-1α, induced protein 10, interferon (IFN)-α, IFN-γ, and tumor necrosis factor alpha, were upregulated in the spleens of FVB-Rag2 KO mice compared with those of WT mice. The upregulation of several cytokines occurred concurrently with the histopathological changes. MAV-1 infection induced more severe systemic infection in FVB-Rag2 KO mice than in WT mice. CONCLUSION: In mice, Rag2 deficiency induces inflammatory cell recruitment via the upregulation of cytokine and chemokine levels. The MAV-1 infection model can be utilized to assess the efficacy and safety of therapeutic agents for human adenoviral diseases.

Stoichiometric Doping of Highly Coupled Cu2-xS Nanocrystal Assemblies.

The hole density of individual copper sulfide nanocrystals (Cu2-xS NCs) is determined from the stoichiometric mismatch (x) between copper and sulfide atoms. Consequently, the electronic properties of the material vary over a range of x. To exploit Cu2-xS NCs in devices, assemblies of NCs are typically required. Herein, we investigate the influence of x, referred to as the stoichiometric doping effect, on the structural, optical, electrical, and thermoelectric properties of electronically coupled Cu2-xS NC assemblies. The doping process is done by immersing the solid NC assemblies into a solution containing a Cu(I) complex for different durations (0-10 min). As Cu+ gradually occupied the copper-deficient sites of Cu2-xS NCs, x could be controlled from 0.9 to less than 0.1. Consequently, the near-infrared (NIR) absorbance of Cu2-xS NC assemblies changes systematically with x. With increasing x, electrical conductivity increased and the Seebeck coefficient decreased systematically, leading to the maximal thermoelectric power factor from a film of Cu2-xS NCs at an optimal doping condition yielding x = 0.1. The physical characteristics of the Cu2-xS NC assemblies investigated herein will provide guidelines for exploiting this emerging class of nanocrystal system based on doping.

Lentivirus-Mediated VEGF Knockdown Suppresses Gastric Cancer Cell Proliferation and Tumor Growth in vitro and in vivo.

PURPOSE: Gastric cancer has a high mortality rate worldwide. Although treatments, such as molecular-targeted therapy, have been introduced, the resulting long-term survival and prognosis remain unsatisfactory. Downregulation of the target genes using lentivirus-mediated short hairpin RNA (shRNA) can be an effective therapeutic strategy for patients with gastric cancer. Overexpressed vascular endothelial growth factor A (VEGF) in human gastric cancer cells can be an effective novel therapeutic target for human gastric cancer. Thus, this study aimed to evaluate the therapeutic effects of lentivirus-mediated knockdown of VEGF gene expression in human gastric cancer growth. MATERIALS AND METHODS: Specific shRNA sequences targeting VEGF were designed to construct a lentiviral expression vector. After human gastric carcinoma cells (cell line NCI-N87) were infected with the lentiviral vector, the therapeutic effects of the lentivirus-mediated shRNA targeting VEGF were analyzed both in vitro and in vivo. RESULTS: Stable suppression of VEGF gene expression in NCI-N87 cells using shRNA (ShVEGF) showed significant inhibition of cell proliferation, clonogenicity, and cell motility. ShVEGF also showed increased G0/G1 cell cycle arrest and apoptosis. In addition, in vivo results from nude mice xenografted ShVEGF showed significant inhibition of tumor growth. Assessing the therapeutic effects of intratumoral injection of lentivirus-targeting VEGF (Virus_VEGF) revealed that it significantly inhibited tumor growth compared to that in the Virus_Scramble or saline injection control groups. CONCLUSION: The constructed ShVEGF showed significant inhibition of NCI-N87 gastric cancer cell growth both in vitro and in vivo. These experimental results suggest a novel therapeutic strategy for patients with gastric cancer using lentivirus-mediated shRNA targeting VEGF.

Comparison of the virulence of Streptococcus pneumoniae in ICR mouse stocks of three different origins.

Streptococcus pneumoniae causes many people to suffer from pneumonia, septicemia, and other diseases worldwide. To identify the difference in susceptibility of and treatment efficacy against S. pneumoniae in three ICR mouse stocks (Korl:ICR, A:ICR, and B:ICR) with different origins, mice were infected with 2 × 106, 2 × 107, and 2 × 108 CFU of S. pneumoniae D39 intratracheally. The survival of mice was observed until three weeks after the infection. The three stocks of mice showed no significant survival rate difference at 2 × 106 and 2 × 107 CFU. However, the lung and spleen weight in the A:ICR stock was significantly different from that in the other two stocks, whereas the liver weight in B:ICR stock was significantly lower than that in the other two stocks. Interestingly, no significant CFU difference in the organs was observed between the ICR stocks. The level of interferon gamma inducible protein 10 in Korl:ICR was significantly lower than that in the other two stocks. The level of granulocyte colony stimulating factor in B:ICR was significantly lower than in the other two stocks. However, tumor-necrosis factor-alpha and interleukin-6 levels showed no significant difference between the ICR stocks. In the vancomycin efficacy test after the S. pneumoniae infection, both the single-dose and double-dose vancomycin-treated groups showed a significantly better survival rate than the control group. There was no significant survival difference between the three stocks. These data showed that Korl:ICR, A:ICR, and B:ICR have no susceptibility difference to the S. pneumoniae D39 serotype 2.

Radioprotective effect of newly synthesized toll-like receptor 5 agonist, KMRC011, in mice exposed to total-body irradiation.

Exposure to ionizing radiation leads to severe damages in radiosensitive organs and induces acute radiation syndrome, including effects on the hematopoietic system and gastrointestinal system. In this study, the radioprotective ability of KMRC011, a novel toll-like receptor 5 (TLR5) agonist, was investigated in C57BL6/N mice exposed to lethal total-body gamma-irradiation. In a 30-day survival study, KMRC011-treated mice had a significantly improved survival rate compared with control after 11 Gy total-body irradiation (TBI), and it was found that the radioprotective activity of KMRC011 depended on its dosage and repeated treatment. In a 5-day short-term study, we demonstrated that KMRC011 treatment stimulated cell proliferation and had an anti-apoptotic effect. Furthermore, KMRC011 increased the expressions of genes related to DNA repair, such as Rad21, Gadd45b, Sod2 and Irg1, in the small intestine of lethally irradiated mice. Interestingly, downregulation of NF-κB p65 in the mouse intestine by KMRC011 treatment was observed. This data indicated that KMRC011 exerted a radioprotective activity partially by regulating NF-κB signaling. Finally, peak expression levels of G-CSF, IL-6, IFN-γ, TNF-α and IP-10 induced by KMRC011 treatment were different depending on the route of administration and type of cytokine. These cytokines could be used as candidate biomarkers for the evaluation of KMRC011 clinical efficacy. Our data indicated that KMRC011 has radioprotective activity in lethally irradiated mice and may be developed as a therapeutic agent for radioprotection.

Enthalpy-Entropy Interplay in π-Stacking Interaction of Benzene Dimer in Water.

Aromatic groups can engage in an interesting class of noncovalent interactions termed π-π interactions, which play a pivotal role in stabilizing a variety of molecular architectures, including nucleic acids, proteins, and supramolecular assemblies. When the aromatic compounds interact with each other in an aqueous environment, their association is facilitated by the hydrophobic effect-the trend of nonpolar solutes to aggregate in a polar solution. To develop an in-depth understanding of hydrophobic association, we investigate in the present work π-π interactions in water, employing as a paradigm the benzene dimer. Using DFT-CES, a mean-field QM/MM method recently developed by our group, we describe the benzene solute at a quantum-mechanical level. Full consideration of detailed solute-electron density enables an optimal description of the solute-solvent interactions, leading to an accurate prediction of hydration free energies. In π-stacking of benzene, we find an entropic stabilization associated with the shrinkage of the solvent-excluded volume, which agrees with the theory of hydrophobic effect at subnanoscales. However, at the equilibrium binding distance of the benzene dimer, we find that the entropic stabilization nearly cancels out due to the enthalpic cost required for dewetting the internal space. Such an enthalpy-entropy compensation leads the association free energy to be predominantly dictated by the solute-solute interaction enthalpy. The present work offers new insight into the mechanistic role of water and the primary thermodynamic driving force of hydrophobic association.

Hydration Thermodynamics of Non-Polar Aromatic Hydrocarbons: Comparison of Implicit and Explicit Solvation Models.

The precise description of solute-water interactions is essential to understand the chemo-physical nature in hydration processes. Such a hydration thermodynamics for various solutes has been explored by means of explicit or implicit solvation methods. Using the Poisson-Boltzmann solvation model, the implicit models are well designed to reasonably predict the hydration free energies of polar solutes. The implicit model, however, is known to have shortcomings in estimating those for non-polar aromatic compounds. To investigate a cause of error, we employed a novel systematic framework of quantum-mechanical/molecular-mechanical (QM/MM) coupling protocol in explicit solvation manner, termed DFT-CES, based on the grid-based mean-field treatment. With the aid of DFT-CES, we delved into multiple energy parts, thereby comparing DFT-CES and PB models component-by-component. By applying the modified PB model to estimate the hydration free energies of non-polar solutes, we find a possibility to improve the predictability of PB models. We expect that this study could shed light on providing an accurate route to study the hydration thermodynamics for various solute compounds.

Differences between immunodeficient mice generated by classical gene targeting and CRISPR/Cas9-mediated gene knockout.

Immunodeficient mice are widely used for pre-clinical studies to understand various human diseases. Here, we report the generation of four immunodeficient mouse models using CRISPR/Cas9 system without inserting any foreign gene sequences such as NeoR cassettes and their characterization. By eliminating any possible effects of adding a NeoR cassette, our mouse models may allow us to better elucidate the in vivo functions of each gene. Our FVB-Rag2-/-, B6-Rag2-/-, and BALB/c-Prkdc-/- mice showed phenotypes similar to those of the earlier immunodeficient mouse models, including a lack of mature B cells and T cells and an increase in the number of CD45+DX-5+ natural killer cells. However, B6-Il2rg-/- mice had a unique phenotype, with a lack of mature B cells, increased number of T cells, and decreased number of natural killer cells. Additionally, serum immunoglobulin levels in all four immunodeficient mouse models were significantly reduced when compared to those in wild-type mice with the exception of IgM in B6-Il2rg-/- mice. These results indicate that our immunodeficient mouse models are a robust tool for in vivo studies of the immune system and will provide new insights into the variation in phenotypic outcomes resulting from different gene-targeting methodologies.

A Seamless Grid-Based Interface for Mean-Field QM/MM Coupled with Efficient Solvation Free Energy Calculations.

Among various models that incorporate solvation effects into first-principles-based electronic structure theory such as density functional theory (DFT), the average solvent electrostatic potential/molecular dynamics (ASEP/MD) method is particularly advantageous. This method explicitly includes the nature of complicated solvent structures that is absent in implicit solvation methods. Because the ASEP/MD method treats only solvent molecule dynamics, it requires less computational cost than the conventional quantum mechanics/molecular mechanics (QM/MM) approaches. Herein, we present a real-space rectangular grid-based method to implement the mean-field QM/MM idea of ASEP/MD to plane-wave DFT, which is termed "DFT in classical explicit solvents", or DFT-CES. By employing a three-dimensional real-space grid as a communication medium, we can treat the electrostatic interactions between the DFT solute and the ASEP sampled from MD simulations in a seamless and straightforward manner. Moreover, we couple a fast and efficient free energy calculation method based on the two-phase thermodynamic (2PT) model with our DFT-CES method, which enables direct and simultaneous computation of the solvation free energies as well as the geometric and electronic responses of a solute of interest under the solvation effect. With the aid of DFT-CES/2PT, we investigate the solvation free energies and detailed solvation thermodynamics for 17 types of organic molecules, which show good agreement with the experimental data. We further compare our simulation results with previous theoretical models and assumptions made for the development of implicit solvation models. We anticipate that our proposed method, DFT-CES/2PT, will enable vast utilization of the ASEP/MD method for investigating solvation properties of materials by using periodic DFT calculations in the future.