Sodium Acetate Enhances Neutrophil Extracellular Trap Formation via Histone Acetylation Pathway in Neutrophil-like HL-60 Cells.

Neutrophil extracellular trap formation has been identified as a new cell death mediator, termed NETosis, which is distinct from apoptosis and necrosis. NETs capture foreign substances, such as bacteria, by releasing DNA into the extracellular environment, and have been associated with inflammatory diseases and altered immune responses. Short-chain fatty acids, such as acetate, are produced by the gut microbiota and reportedly enhance innate immune responses; however, the underlying molecular mechanisms remain unclear. Here, we investigated the effects of sodium acetate, which has the highest SCFA concentration in the blood and gastrointestinal tract, on NETosis by focusing on the mechanisms associated with histone acetylation in neutrophil-like HL-60 cells. Sodium acetate enhanced NETosis, as shown by fluorescence staining with SYTOX green, and the effect was directly proportional to the treatment duration (16-24 h). Moreover, the addition of sodium acetate significantly enhanced the acetylation of Ace-H3, H3K9ace, and H3K14ace. Sodium acetate-induced histone acetylation rapidly decreased upon stimulation with the calcium ionophore A23187, whereas histone citrullination markedly increased. These results demonstrate that sodium acetate induces NETosis via histone acetylation in neutrophil-like HL-60 cells, providing new insights into the therapeutic effects based on the innate immunity-enhancing effect of dietary fiber.

Inhibiting Neutrophil Extracellular Traps Protects against Ultraviolet B-Induced Skin Damage: Effects of Hochu-ekki-to and DNase I.

UV-B radiation induces sunburn, and neutrophils are pivotal in this inflammation. In this study, we examined the potential involvement of neutrophil extracellular traps (NETs) in ultraviolet B (UVB)-induced skin inflammation, correlating the skin inflammation-mitigating effects of Hochu-ekki-to on UV-B irradiation and NETs. To elucidate NET distribution in the dorsal skin, male ICR mice, exposed to UVB irradiation, were immunohistologically analyzed to detect citrullinated histone H3 (citH3) and peptidylarginine deiminase 4 (PAD4). Reactive oxygen species (ROS) production in the bloodstream was analyzed. To establish the involvement of NET-released DNA in this inflammatory response, mice were UV-B irradiated following the intraperitoneal administration of DNase I. In vitro experiments were performed to scrutinize the impact of Hochu-ekki-to on A23187-induced NETs in neutrophil-like HL-60 cells. UV-B irradiation induced dorsal skin inflammation, coinciding with a significant increase in citH3 and PAD4 expression. Administration of DNase I attenuated UV-B-induced skin inflammation, whereas Hochu-ekki-to administration considerably suppressed the inflammation, correlating with diminished levels of citH3 and PAD4 in the dorsal skin. UV-B irradiation conspicuously augmented ROS and hydrogen peroxide (H2O2) production in the blood. Hochu-ekki-to significantly inhibited ROS and H2O2 generation. In vitro experiments demonstrated that Hochu-ekki-to notably inhibited A23187-induced NETs in differentiated neutrophil-like cells. Hence, NETs have been implicated in UV-B-induced skin inflammation, and their inhibition reduces cutaneous inflammation. Additionally, Hochu-ekki-to mitigated skin inflammation by impeding neutrophil infiltration and NETs in the dorsal skin of mice.

Why the Photochemical Reaction of Phenol Becomes Ultrafast at the Air-Water Interface: The Effect of Surface Hydration.

Photochemical reactions at the air-water interface can show remarkably different rates from those in bulk water. The present study elucidates the reaction mechanism of phenol characteristic at the air-water interface by the combination of molecular dynamics simulation and quantum chemical calculations of the excited states. We found that incomplete hydrogen bonding to phenol at the air-water interface affects excited states associated with the conical intersection and significantly reduces the reaction barrier, resulting in the distinctively facilitated rate in comparison with the bulk phase. The present study indicates that the reaction dynamics can be substantially different at the interfaces in general, reflecting the difference in the stabilization energy of the electronic states in markedly different solvation at the interface.

Boundary effects and quadrupole contribution in sum frequency generation spectroscopy.

Calculation of time correlation functions is a primary task in the computational analysis of sum frequency generation spectroscopy. This paper resolved basic issues to extract interface signals from the calculation. These issues stem from the boundary to restrict the bulk region, which renders the practical computation feasible at a finite and affordable cost. The boundary is found to have significant influences on the time correlation functions, which is closely related to the quadrupole contribution in the nonlinear susceptibility. Thus, we thoroughly examined these influences to establish a proper treatment in performing reliable spectroscopic analysis. We elucidated the distinction of the present boundary effects from the quadrupole contribution and also established a proper center of molecule to minimize the quadrupole effect in the time correlation functions. In the case of liquid water, the proper center was found to be close to the center of mass of a water molecule.

Development of efficient computational analysis of difference infrared and Raman spectroscopies.

Computational analysis of difference spectra between two analogous systems is a challenging issue, as reliable estimation of a tiny difference spectrum requires an extraordinary precision of the two original spectra. We have developed an alternative new method to calculate the difference spectra under background-free conditions, which greatly improved the efficiency of computation. In this paper, we report further improvement by using efficient parallel implementation and the time correlation formula based on time derivative quantities. As a consequence, the present work achieved further remarkable acceleration in the calculations of difference infrared and Raman spectra in the order of magnitude and thereby allowed us by analyzing these difference spectra at a practical cost of computation.

Reply to the 'Comment on "Bi-layering at ionic liquid surfaces: a sum-frequency generation vibrational spectroscopy- and molecular dynamics simulation-based study"' by M. Deutsch, O. M. Magnussen, J. Haddad, D. Pontoni, B. M. Murphy and B. M. Ocko, Phys. Chem. Chem. Phys., 2021, DOI.

In our recent paper titled "Bi-layering at ionic liquid surfaces: a sum-frequency generation vibrational spectroscopy- and molecular dynamics simulation-based study" co-authored by T. Iwahashi, T. Ishiyama, Y. Sakai, A. Morita, D. Kim, and Y. Ouchi, Phys. Chem. Chem. Phys., 2020, 22, 12565 (hereafter referred to as IW), the sum-frequency (SF) spectra for a homologous series of 1-alkyl-3-methylimidazolium bis(trifluoromethanesulfonyl)amide ([Cnmim][TFSA] n = 4, 6, 8, 10, and 12) were reported. In particular, a clear decrease in the SF signals from the [TFSA]- anions with increasing chain length of the [Cnmim]+ cation (Fig. 5 of IW) was explained in terms of "head-to-head" bi-layer formation at the air/ionic liquid (IL) interface. A comment by M. Deutsch et al. (hereafter referred to as DE) questioned this report, claiming that our proposed structure is not consistent with a multilayered electron density (ED) profile obtained by X-ray reflectivity (XR).

Recent progress in simulating microscopic ion transport mechanisms at liquid-liquid interfaces.

Transport of ions through liquid-liquid interfaces is of fundamental importance to a wide variety of applications. However, since it is quite challenging for experimentalists to directly and selectively observe molecules at the interfaces, microscopic mechanisms of ion transport have been largely presumed from kinetic information. This Perspective illustrates recent examples that molecular dynamics simulations with proper free energy surfaces clarified mechanistic pictures of ion transport. The key is a proper choice of coordinates and defining/calculating free energy surfaces in multidimensional space. Once the free energy surfaces for realistic systems are available, they naturally provide new insight into the ion transport in unprecedented details, including water finger, transient ion pairing, and electron transfer.

Glycyrrhizin ameliorates melanoma cell extravasation into mouse lungs by regulating signal transduction through HMGB1 and its receptors.

Metastasis, which accounts for the majority of all cancer-related deaths, occurs through several steps, namely, local invasion, intravasation, transport, extravasation, and colonization. Glycyrrhizin has been reported to inhibit pulmonary metastasis in mice inoculated with B16 melanoma. This study aimed to identify the mechanism through which glycyrrhizin ameliorates the extravasation of melanoma cells into mouse lungs. Following B16 melanoma cell injection, mice were orally administered glycyrrhizin once every two days over 2 weeks; lung samples were then obtained and analyzed. Blood samples were collected on the final day, and cytokine plasma levels were determined. We found that glycyrrhizin ameliorated the extravasation of melanoma cells into the lungs and suppressed the plasma levels of interleukin-6, tumor necrosis factor-α, and transforming growth factor-ß. Furthermore, glycyrrhizin ameliorated the lung tissue expression of high mobility group box-1 protein (HMGB1), receptor for advanced glycation end products (RAGE), Toll-like receptor (TLR)-4, RAS, extracellular signal-related kinase, NF-κB, myeloid differentiation primary response 88, IκB kinase complex, epithelial-mesenchymal transition markers, and vascular endothelial growth factor-A. Our study demonstrates that glycyrrhizin ameliorates melanoma metastasis by regulating the HMGB1/RAGE and HMGB1/TLR-4 signal transduction pathways.

DNA demethylation increases NETosis.

Neutrophil extracellular traps (NETs) occur during the development of autoimmune diseases, cancer and diabetes. A novel form of cell death that is induced by NETs is called NETosis. Although these diseases are known to have an epigenetic component, epigenetic regulation of NETosis has not previously been explored. In the present study, we investigated the effects of epigenetic change, especially DNA demethylation, on NETosis in neutrophil-like cells differentiated from HL-60 cells, which were incubated for 72 h in the presence of 1.25% DMSO. DMSO-differentiated neutrophil-like cells tended to have increased methylation of genomic DNA. NETosis in the neutrophil-like cells was induced by the treatment with A23187, calcium ionophore, and increased by the addition of the DNMT inhibitor 5-azacytidine (Aza) during differentiation. Interestingly, Aza-stimulated neutrophil-like cell induced NETosis without treatment with A23187. Although reactive oxygen species (ROS), especially superoxide and hypochlorous acid, are important in NETosis induction, treatment with Aza decreased production of ROS, while mitochondria ROS scavenger tended to decrease Aza-induced NETosis. Moreover, the genomic DNA in Aza-stimulated neutrophil-like cell was demethylated, and the expression of peptidylarginine deiminase4 (PAD4) and citrullinated histone H3 (R2+R8+R17) was increased, but myeloperoxidase expression was unaffected. Additionally, PAD4 inhibition tended to decrease Aza-induced NETosis. The DNA demethylation induced by the DNMT inhibitor in neutrophil-like cells enhanced spontaneous NETosis through increasing PAD4 expression and histone citrullination. This study establishes a relationship between NETosis and epigenetics for the first time, and indicates that various diseases implicated to have an epigenetic component might be exacerbated by excessive NETosis also under epigenetic control.

Large-Scale Parallel Implementation of Hartree-Fock Exchange Energy on Real-Space Grids Using 3D-Parallel Fast Fourier Transform.

Two types of implementation of the Hartree-Fock (HF) exchange energy were developed with the real-space grid approach for the purpose of achieving high efficiency in the parallel execution of the hybrid exchange functional in the density functional theory. First, a parallel implementation of the three-dimensional fast Fourier transform (FFT), referred to as PFFT, was adapted to solve the Poisson equations for the electrostatic potentials of the densities of the orbital pairs. In the other approach, the Poisson equations were solved iteratively through the conjugate gradient (CG) procedures where the operation of Laplacian was parallelized by the domain decomposition scheme. Comparison of the parallel performances for the exchange energy calculation was made between these two approaches, and it was revealed that the calculation with the FFT method is faster than that with CG. The method with FFT is more advantageous than CG because a larger bandwidth can be made available in the collective message passing interface communication associated with the parallel execution of FFT. We also implemented the projection operator to circumvent the laborious calculation of the exchange energy at every self-consistent field step, which made a significant contribution to expedite the convergence. To assess the accuracy of our implementation, the association energies of a hydrated ion were computed, which showed excellent agreement with those given by the Gaussian 09 program employing sophisticated basis sets.

Bi-layering at ionic liquid surfaces: a sum-frequency generation vibrational spectroscopy- and molecular dynamics simulation-based study.

Room-temperature ionic liquids (RTILs) are being increasingly employed as novel solvents in several fields, including chemical engineering, electrochemistry, and synthetic chemistry. To further increase their usage potential, a better understanding of the structure of their surface layer is essential. Bi-layering at the surfaces of RTILs consisting of 1-alkyl-3-methylimidazolium ([Cnmim]+; n = 4, 6, 8, 10, and 12) cations and bis(trifluoromethanesulfonyl)amide ([TFSA]-) anions was demonstrated via infrared-visible sum-frequency generation (IV-SFG) vibrational spectroscopy and molecular dynamics (MD) simulations. It was found that the sum-frequency (SF) signal from the [TFSA]- anions decreases as the alkyl chain length increases, whereas the SF signal from the r+ mode (the terminal CH3 group) of the [Cnmim]+ cations is almost the same regardless of chain length. MD simulations show the formation of a bi-layered structure consisting of the outermost first layer and a submerged second layer in a "head-to-head" molecular arrangement. The decrease in the SF signals of the normal modes of the [TFSA]- anions is caused by destructive and out-of-phase interference of vibrations of corresponding molecular moieties oriented toward each other in the first and second layers. In contrast, the r+ mode of [Cnmim]+ does not experience destructive interference because the peak position of the r+ mode differs marginally at the surface and in the bulk. Our conclusions are not limited to the system presented here. Similar bi-layered structures can be expected for the surfaces of conventional RTILs, which necessitates the consideration of bi-layering in the design and application.

Development of quadrupole susceptibility automatic calculator in sum frequency generation spectroscopy and application to methyl C-H vibrations.

Sum frequency generation (SFG) spectroscopy has been established as a powerful interface probe technique based on the electric dipole approximation, while possible signals of quadrupole and bulk origin have also been known for a long time. In this work, we developed a computational tool, namely, Qsac (quadrupole susceptibility automatic calculator), to evaluate the comprehensive contributions of the dipole/quadrupole and interface/bulk in the arbitrary vibrational bands of SFG spectra. The calculations of relevant susceptibility terms are performed on the basis of the theory of energy representation using quantum chemical calculation and molecular dynamics simulation, which allows for semi-quantitative comparison among these terms on the same footing. We applied the Qsac to the methyl C-H stretching bands of organic molecules and found a general trend that the weak asymmetric bands are more sensitive to the bulk contribution than the symmetric ones. The phases of interface and bulk terms tend to cancel in the asymmetric band, which results in the reduced band intensity in the SFG spectra.

Experimental and theoretical evidence for bilayer-by-bilayer surface melting of crystalline ice.

On the surface of water ice, a quasi-liquid layer (QLL) has been extensively reported at temperatures below its bulk melting point at 273 K. Approaching the bulk melting temperature from below, the thickness of the QLL is known to increase. To elucidate the precise temperature variation of the QLL, and its nature, we investigate the surface melting of hexagonal ice by combining noncontact, surface-specific vibrational sum frequency generation (SFG) spectroscopy and spectra calculated from molecular dynamics simulations. Using SFG, we probe the outermost water layers of distinct single crystalline ice faces at different temperatures. For the basal face, a stepwise, sudden weakening of the hydrogen-bonded structure of the outermost water layers occurs at 257 K. The spectral calculations from the molecular dynamics simulations reproduce the experimental findings; this allows us to interpret our experimental findings in terms of a stepwise change from one to two molten bilayers at the transition temperature.

Formation of neutrophil extracellular traps in mitochondrial DNA-deficient cells.

Neutrophil extracellular trap (NET) formation plays an important role in inflammatory diseases. Although it is known that NET formation occurs via NADPH oxidase (NOX)-dependent and NOX-independent pathways, the detailed mechanism remains unknown. Therefore, in this study, we aimed to elucidate the role of mitochondria in NOX-dependent and NOX-independent NET formation. We generated mitochondrial DNA-deficient cells (ρ0 cells) by treating HL-60 cells with dideoxycytidine and differentiated them to neutrophil-like cells. These neutrophil-like ρ0 cells showed markedly reduced NOX-independent NET formation but not NOX-dependent NET formation. However, NET-associated intracellular histone citrullination was not inhibited in ρ0 cells. Furthermore, cells membrane disruption in NOX-dependent NET formation occurred in a Myeloperoxidase (MPO) and mixed lineage kinase domain like pseudokinase (MLKL)-dependent manner; however, cell membrane disruption in NOX-independent NET formation partially occurred in an MLKL-dependent manner. These results highlight the importance of mitochondria in NOX-independent NET formation.

17-ß-estradiol enhances neutrophil extracellular trap formation by interaction with estrogen membrane receptor.

Cell death-associated neutrophil extracellular trap formation (NETosis) occurs during various autoimmune diseases including systemic lupus erythematosus and rheumatoid arthritis, as well as during gestation. Although increasing estrogen concentrations associated with pregnancy might induce NETosis via nuclear estrogen receptor (ERα/ERß), little is known about the mechanisms associated with estrogen-induced NETosis. Here, we investigated the effects of estrogen (17-ß-estradiol; E2) on NETosis, focusing on mechanisms associated with estrogen membrane receptor (GPR30) in neutrophil-like HL-60 cells. Our results show that E2 and the GPR30 agonist G-1 increases level of NETosis and NET formation. Moreover, NETosis-associated intracellular and extracellular histone citrullination and peptidyl arginine deiminase 4 (PAD4) expression were also increased by E2 or G-1 treatment. Furthermore, GPR30 antagonist pre-treatment inhibited increases in NETosis and PAD4 expression mediated by G-1 and partially inhibited these effects mediated by E2. These results demonstrate that E2 treatment induces NETosis via not only ERα/ERß but also GPR30 in neutrophil-like HL-60 cells.

Molecular structure and vibrational spectra at water/poly(2-methoxyethylacrylate) and water/poly(methyl methacrylate) interfaces: A molecular dynamics simulation study.

Classical molecular dynamics simulations at the interfaces of two (meth)acrylate polymers, poly(2-methoxyethylacrylate) (PMEA) and poly(methyl methacrylate) (PMMA), upon contact with water are performed to elucidate interfacial molecular structures from the interface-specific nonlinear spectroscopic point of view. PMEA has methoxy oxygen in the side chain, while PMMA does not have it, and its impacts on the interfacial structure are particularly focused on. The force fields of PMEA and PMMA used in the classical simulation are modeled so as to reproduce the radial distribution functions and the vibrational density of states calculated by ab initio molecular dynamics simulations, where a stronger hydrogen-bonding interaction between water and methoxy oxygen of PMEA than the conventional molecular modeling predicts is found. The imaginary part of the second order nonlinear susceptibility is theoretically calculated for these two interfaces, showing a definite difference between them. The origin of the spectral difference is discussed on the basis of the decomposition analysis of the spectra and the interfacial molecular structures.

Calculation of solvation free energy utilizing a constrained QM/MM approach combined with a theory of solutions.

In an extended QM/MM (quantum mechanical/molecular mechanical) description of a solution, the solvent molecules surrounding the solute are incorporated into the QM region besides the solute. In a recent development, we introduced a simple and efficient method, referred to as boundary constraint with correction (BCC), to prevent the diffusion of the QM solvent into the bulk. The major purpose of the present work is to develop a method to compute the solvation free energy of a QM solute in an extended QM/MM simulation by means of the BCC method. The strategy of our development is to utilize the QM/MM-ER method which combines the QM/MM simulation and the theory of solutions termed energy representation (ER) to expedite the free energy calculation. A theory is, then, formulated to couple QM/MM-ER and the BCC method on the basis of the statistical mechanics. A notable feature of our method is that the effect of the constraint potentials on the free energy completely vanishes when the force field of the QM solvent coincides with that of the MM solvent. The method is applied to the calculations of the solvation free energies of a water molecule and a hydronium ion in water solutions. It turns out that the present method can offer a significant improvement in describing the free energy Δν of the hydronium ion, in particular, as compared with the conventional QM/MM approach. Explicitly, Δν is obtained as -98.0 kcal/mol showing a good agreement with an experimental value of -103.5 kcal/mol, while -86.1 kcal/mol by the conventional method.

Origin of the Overpotential for the Oxygen Evolution Reaction on a Well-Defined Graphene Electrode Probed by in Situ Sum Frequency Generation Vibrational Spectroscopy.

To develop an efficient material for the cathode of the lithium-oxygen (Li-O2) secondary battery, the oxygen reduction and evolution reactions (ORR and OER) on a well-defined graphene electrode have been investigated in a typical organic solvent, dimethyl sulfoxide (DMSO). The adsorption and desorption behaviors of the solvents on the graphene electrode surface were evaluated by an intrinsically surface-selective vibrational spectroscopy of sum frequency generation (SFG) during the ORR and OER. After the initial ORR depositing lithium peroxide (Li2O2) on the graphene electrode surface in a LiClO4/DMSO solution, the SFG spectroscopy revealed that the subsequent OER oxidizing the Li2O2 preferentially proceeds at the interface between the Li2O2 and graphene rather than that between the Li2O2 and bulk solution. Therefore, the OER tends to reduce the electric conductivity between the Li2O2 and graphene by decreasing their contact area before a large part of the deposited Li2O2 was oxidized, which elucidates the origin of the high overpotential for the OER.

Computational Analysis of Vibrational Sum Frequency Generation Spectroscopy.

Vibrational sum frequency generation (VSFG) spectroscopy is a widely used probe of interfaces and, having ideal surface sensitivity and selectivity, is particularly powerful when applied to wet and soft interfaces. Although VSFG spectroscopy can sensitively detect molecular details of interfaces, interpretation of observed spectra has, until recently, been challenging and often ambiguous. The situation has been greatly improved by remarkable advances in computational VSFG analysis on the basis of molecular modeling and molecular dynamics simulation. This article reviews the basic idea of computational VSFG analysis and recent applications to both aqueous and organic interfaces.