Research on the Coupled Water–Soil SPH Algorithm Improvement and Application Based on Two-phase Mixture Theory

An improved water–soil coupling algorithm was proposed based on the two-phase mixture theory within the framework of smoothed particle hydrodynamics (SPH). In this algorithm, the buoyant density was considered in saturated soil and the stress of two phases was completely exfoliated with the Terzaghi’s effective stress principle. Then the interaction between water and soil was only constituted by viscous drag force. The proposed algorithm was validated by several numerical tests to effectively solve a series of numerical problems caused by the truncation of the kernel approximation on the interface between submerged soil and water, and it can also be a feasible measure to simulate underwater soil excavation problems without drainage and underwater landside problems. Meanwhile, combined with frictional sliding contact algorithm, the interaction between water/soil and structure which was considered as rigid can be effectively modeled, and the calculated contact forces acting on the structure are more accurate. Furthermore, this improved algorithm can be applied to deal with large deformation problems involving complex water–soil–structure interaction in hydraulic and geotechnical engineering such as underwater excavation, shield dig, caisson sinking and other practical engineering problems. It is also significant to engineering design and the improvement of construction level.

A Comprehensive Analysis of Human Endogenous Retroviruses HERV-K (HML.2) from Teratocarcinoma Cell Lines and Detection of Viral Cargo in Microvesicles

About 8% of our genome is composed of sequences from Human Endogenous Retroviruses (HERVs). The HERV-K (HML.2) family, here abbreviated HML.2, is able to produce virus particles that were detected in cell lines, malignant tumors and in autoimmune diseases. Parameters and properties of HML.2 released from teratocarcinoma cell lines GH and Tera-1 were investigated in detail. In most experiments, analyzed viruses were purified by density gradient centrifugation. HML.2 structural proteins, reverse transcriptase (RT) activity, viral RNA (vRNA) and particle morphology were analyzed. The HML.2 markers were predominantly detected in fractions with a buoyant density of 1.16 g/cm3. Deglycosylation of TM revealed truncated forms of transmembrane (TM) protein. Free virions and extracellular vesicles (presumably microvesicles—MVs) with HML.2 elements, including budding intermediates, were detected by electron microscopy. Viral elements and assembled virions captured and exported by MVs can boost specific immune responses and trigger immunomodulation in recipient cells. Sequencing of cDNA clones demonstrated exclusive presence of HERV-K108 env in HML.2 from Tera-1 cells. Not counting two recombinant variants, four known env sequences were found in HML.2 from GH cells. Obtained results shed light on parameters and morphology of HML.2. A possible mechanism of HML.2-induced diseases is discussed.

Role of cation-chloride cotransporters, Na/K-pump, and channels in cell water/ionic balance regulation under hyperosmolar conditions: in silico and experimental studies of opposite RVI and AVD responses of U937 cells to hyperosmolar media

The work provides a modern mathematical description of animal cell electrochemical system under a balanced state and during the transition caused by an increase in external osmolarity, considering all the main ionic pathways in the cell membrane: the sodium pump, K+, Na+, Cl- electroconductive channels and cotransporters NC, KC, and NKCC. The description is applied to experimental data obtained on U937 cells cultured in suspension, which allows the required assays to be performed, including determination of cell water content using buoyant density, cell ion content using flame photometry, and optical methods using flow cytometry. The study of these cells can serve as a useful model for understanding the general mechanisms of regulation of cellular water and ionic balance, which cannot be properly analyzed in many important practical cases, such as ischemic disturbance of cellular ionic and water balance, when cells cannot be isolated. An essential part of the results is the developed software supplied with an executable file, which allows researchers with no programming experience to calculate unidirectional fluxes of monovalent ions through separate pathways and ion-electrochemical gradients that move ions through them, which is important for studying the functional expression of channels and transporters. It is shown how the developed approach is used to reveal changes in channels and transporters underlying the RVI and AVD responses to the hyperosmolar medium in the studied living U937 cells.

Extracellular vesicles from neurons promote neural induction of stem cells through cyclin D1

Extracellular vesicles (EVs) are thought to mediate the transport of proteins and RNAs involved in intercellular communication. Here, we show dynamic changes in the buoyant density and abundance of EVs that are secreted by PC12 cells stimulated with nerve growth factor (NGF), N2A cells treated with retinoic acid to induce neural differentiation, and mouse embryonic stem cells (mESCs) differentiated into neuronal cells. EVs secreted from in vitro differentiated cells promote neural induction of mESCs. Cyclin D1 enriched within the EVs derived from differentiated neuronal cells contributes to this induction. EVs purified from cells overexpressing cyclin D1 are more potent in neural induction of mESC cells. Depletion of cyclin D1 from the EVs reduced the neural induction effect. Our results suggest that EVs regulate neural development through sorting of cyclin D1.

Extracellular vesicles from neuronal cells promote neural induction of mESCs through cyclinD1

Extracellular vesicles (EVs) that are thought to mediate the transport of proteins and RNAs involved in intercellular communication. Here, we show dynamic changes in the buoyant density and abundance of extracellular vesicles that are secreted by PC12 cells stimulated with nerve growth factor (NGF), N2A cells treated with retinoic acid to induce neural differentiation and mESCs differentiated into neuronal cells. EVs secreted from in vitro differentiated cells promote neural induction of mouse embryonic stem cells (mESCs). Cyclin D1 enriched within the EVs derived from differentiated neuronal cells contributes to this induction. EVs purified from cells overexpressing cyclin D1 are more potent in neural induction of mESC cells. Depletion of cyclin D1 from the EVs reduced the neural induction effect. Our results suggest that extracellular vesicles regulate neural development through sorting of cyclin D1.

Precise Layer Separation of Two-Dimensional Nanomaterials for Scalable Optoelectronics

The biggest challenge in the field of low-dimensional nanomaterials, in terms of practical application, is scalable production with structural uniformity. As the size of materials is becoming smaller, the tendency of their structure-dependent properties, which directly affects the device reliability of largescale applications, is to become stronger due to quantum confinement effects. For example, one-dimensional (1D) carbon nanotubes have various electrical/optical properties based on their structures (e.g., diameter, chirality, etc.). Likewise, two-dimensional (2D) layered materials also exhibit different properties based on their thickness. To overcome such structural heterogeneity, isopycnic density gradient ultracentrifugation (i-DGU) will be introduced to achieve monodispersity of nanomaterials in structure based on their buoyant density differentiations. The i-DGU approach makes it possible to sort 1D carbon nanotubes and 2D layered materials such as graphene, transition metal dichalcogenides and hexagonal boron nitride with high structural purity, based on their structure. Various largescale optoelectronic applications, electrically driven light emitters and photodetectors demonstrated based on the monodisperse nanomaterials will be discussed.

Biomanufacturing of Tomato-Derived Nanovesicles

Micro- and nano-sized vesicles (MVs and NVs, respectively) from edible plant resources are gaining increasing interest as green, sustainable, and biocompatible materials for the development of next-generation delivery vectors. The isolation of vesicles from complex plant matrix is a significant challenge considering the trade-off between yield and purity. Here, we used differential ultracentrifugation (dUC) for the bulk production of MVs and NVs from tomato (Solanum lycopersicum L.) fruit and analyzed their physical and morphological characteristics and biocargo profiles. The protein and phospholipid cargo shared considerable similarities between MVs and NVs. Phosphatidic acid was the most abundant phospholipid identified in NVs and MVs. The bulk vesicle isolates were further purified using sucrose density gradient ultracentrifugation (gUC) or size-exclusion chromatography (SEC). We showed that SEC using gravity column efficiently removed co-purifying matrix components including proteins and small molecular species. dUC/SEC yielded a high yield of purified vesicles in terms of number of particles (2.6 × 1015 particles) and protein quantities (6.9 ± 1.5 mg) per kilogram of tomato. dUC/gUC method separated two vesicle populations on the basis of buoyant density. Proteomics and in silico studies of the SEC-purified MVs and NVs support the presence of different intra- and extracellular vesicles with highly abundant lipoxygenase (LOX), ATPases, and heat shock proteins (HSPs), as well as a set of proteins that overlaps with that previously reported in tomato chromoplast.

Adaptive mutations promote hepatitis C virus assembly by accelerating Core translocation to the endoplasmic reticulum

The envelopment of hepatitis C virus (HCV) is believed to occur primarily in the endoplasmic reticulum (ER)-associated membrane, and the translocation of viral Core protein from lipid droplets (LDs) to the ER is essential for the envelopment of viral particles. However, the factors involved in are not completely understood. Herein, we identified eight adaptive mutations that enhanced virus spread and infectivity of genotype 1a clone TNcc in hepatoma Huh7 cells through long-term culture adaptation and reverse genetic study. Of eight mutations, I853V in NS2 and C2865F in NS5B were found to be minimal mutation sets that enabled an increase in virus production without apparently affecting RNA replication, thus suggesting its roles in the post-replication stage of the HCV life cycle. Using a protease K protection and confocal microscopy analysis, we demonstrated that C2865F and the combination of I853V/C2865F enhanced virus envelopment by facilitating Core translocation from LDs to the ER. Buoyant density analysis revealed that I853V/C2865F contributed to the release of virion with a density of ~1.10 g/ml. Moreover, we demonstrated that NS5B directly interacted with NS2 at the protease domain, and that mutations I853V, C2865F, I853V/C2865F enhanced the interaction. In addition, C2865F also enhanced the interaction between NS5B and Core. In conclusion, this study demonstrated that adaptive mutations in NS2 and NS5B promoted HCV envelopment by accelerating Core translocation from LDs to the ER and reinforced the interaction between NS2 and NS5B. The findings facilitate our understanding of the assembly of HCV morphogenesis.

Neuroprotection by Neurotropin through Crosstalk of Neurotrophic and Innate Immune Receptors in PC12 Cells

Infected or damaged tissues release multiple “alert” molecules such as alarmins and damage-associated molecular patterns (DAMPs) that are recognized by innate immune receptors, and induce tissue inflammation, regeneration, and repair. Recently, an extract from inflamed rabbit skin inoculated with vaccinia virus (Neurotropin®, NTP) was found to induce infarct tolerance in mice receiving permanent ischemic attack to the middle cerebral artery. Likewise, we report herein that NTP prevented the neurite retraction in PC12 cells by nerve growth factor (NGF) deprivation. This effect was accompanied by interaction of Fyn with high-affinity NGF receptor TrkA. Sucrose density gradient subcellular fractionation of NTP-treated cells showed heretofore unidentified membrane fractions with a high-buoyant density containing Trk, B subunit of cholera toxin-bound ganglioside, flotillin-1 and Fyn. Additionally, these new membrane fractions also contained Toll-like receptor 4 (TLR4). Inhibition of TLR4 function by TAK-242 prevented the formation of these unidentified membrane fractions and suppressed neuroprotection by NTP. These observations indicate that NTP controls TrkA-mediated signaling through the formation of clusters of new membrane microdomains, thus providing a platform for crosstalk between neurotrophic and innate immune receptors. Neuroprotective mechanisms through the interaction with innate immune systems may provide novel mechanism for neuroprotection.

The impact of progenitor asymmetries on the neutrino-driven convection in core-collapse supernovae

ABSTRACT The explosion of massive stars in core-collapse supernovae may be aided by the convective instabilities that develop in their innermost nuclear burning shells. The resulting fluctuations support the explosion by generating additional turbulence behind the supernova shock. It was suggested that the buoyant density perturbations arising from the interaction of the pre-collapse asymmetries with the shock may be the primary contributor to the enhancement of the neutrino-driven turbulent convection in the post-shock region. Employing three-dimensional numerical simulations of a toy model, we investigate the impact of such density perturbations on the post-shock turbulence. We consider a wide range of perturbation parameters. The spatial scale and the amplitude of the perturbations are found to be of comparable importance. The turbulence is particularly enhanced when the perturbation frequency is close to that of the convective turnovers in the gain region. Our analysis confirms that the buoyant density perturbations is indeed the main source of the additional turbulence in the gain region, validating the previous order-of-magnitude estimates.