Extended Ensemble Molecular Dynamics for Thermodynamics of Phases

The first-order phase transitions and related thermodynamics properties are primary concerns of materials sciences and engineering. In traditional atomistic simulations, the phase transitions and the estimation of their thermodynamic properties are challenging tasks because the trajectories get trapped in local minima close to the initial states. In this study, we investigate various extended ensemble molecular dynamics (MD) methods based on the multicanonical ensemble method using the Wang-Landau (WL) approach. We performed multibaric-multithermal (MBMT) method to fluid phase, gas-liquid transition, and liquid-solid transition of the Lennard-Jones (LJ) system. The derived thermodynamic properties of the fluid phase and the gas-liquid transition from the MBMT agree well with the previously reported equation of states (EOSs). However, the MBMT cannot correctly predict the liquid-solid transition. The multiorder-multithermal (MOMT) ensemble shows significantly enhanced sampling between liquid and solid states with an accurate estimation of transition temperatures. We further investigated the dynamics of each system based on their free energy shapes, providing fundamental insights for their sampling behaviors. This study guides the prediction of broader crystalline materials, e.g., alloys, for their phases and thermodynamic properties from atomistic modeling

IRT5 Probiotics Changes Immune Modulatory Protein Expression in the Extraorbital Lacrimal Glands of an Autoimmune Dry Eye Mouse Model

PURPOSE. While the association between the gut microbiome and the immune system has been studied in autoimmune disorders, little is known about ocular disease. Previously we reported that IRT5, a mixture of five probiotic strains, could suppress autoimmune dry eye. In this study, we investigated the mechanism by which IRT5 performs its immunomodulatory function in a mouse model of autoimmune dry eye. METHODS. NOD.B10.H2b mice were used as an autoimmune dry eye model. Either IRT5 or PBS was gavaged orally for 3 weeks, with or without 5 days of antibiotic pretreatment. The effects on clinical features, extraorbital lacrimal gland and spleen proteins, and fecal microbiota were analyzed. RESULTS. The ocular staining score was lower, and tear secretion was higher, in the IRT5-treated groups than in the PBS-treated groups. After IRT5 treatment, the downregulated lacrimal gland proteins were enriched in the biological processes of defense response and immune system process. The relative abundances of 33 operational taxonomic units were higher, and 53 were lower, in the feces of the IRT5-treated groups than in those of the PBS-treated groups. IRT5 administration without antibiotic pretreatment also showed immunomodulatory functions with increases in the Lactobacillus helveticus group and Lactobacillus hamsteri. Additional proteomic assays revealed a decrease of proteins related to antigen-presenting processes in the CD11b(+) and CD11c(+) cells of spleen in the IRT5-treated groups. CONCLUSIONS. Changes in the gut microbiome after IRT5 treatment improved clinical manifestations in the autoimmune dry eye model via the downregulation of antigen-presenting processes in immune networks.11Ysciescopu

Cell-free synthesis of functional phospholipase A1 from Serratia sp.

Additional file 1: Figure S1 Gas chromatography analysis of sesame oil incubated with cell-free synthesized PLA1

Optical biochemical sensor based on half-circled microdisk laser diode

In this study, a half-circled cavity based microdisk laser diode is proposed and demonstrated experimentally for an integrated photonic biochemical sensor. Conventional microdisk sensors have limitations in optical coupling and reproducibility. In order to overcome these drawbacks, we design a novel half-circled micro disk laser (HC-MDL) which is easy to manufacture and has optical output directionality. The Q-factor of the fabricated HC-MDL was measured as 7.72 × 106 using the self-heterodyne method and the side mode suppression ratio was measured as 23 dB. Moreover, gas sensing experiments were performed using the HC-MDL sensor. A wavelength shift response of 14.21 pm was obtained for 100 ppb dimethyl methylphosphonate (DMMP) gas and that of 14.70 pm was obtained for 1 ppm ethanol gas. These results indicate the possibility of highly sensitive gas detection at ppb levels using HC-MDL. This attractive feature of the HC-MDL sensor is believed to be very useful for a wide variety of optical biochemical sensor applications. © 2017 Optical Society of America.1

Antiplatelet and Antithrombotic Activity of a Traditional Medicine, Hwangryunhaedok-Tang

Platelet activation and accumulation at the site of vascular injury are central to thrombus formation resulted in thrombotic disorders. Medicinal herbs could be one of the most important pharmaceutical agents that ameliorate thrombotic disorders, such as unstable angina, myocardial infarction, stroke, and peripheral vascular diseases. Hwangryunhaedok-tang (HRT) is a traditional herbal medicine that displays multiple biological properties including anti-inflammatory abilities. However, its role in platelet activation has not been fully studied. Hence, we examined whether HRT has a potent inhibitory effect on platelet aggregation and thrombus formation. We demonstrated that HRT (30, 50, and 100 μg/ml) significantly impaired thrombin- and collagen-related peptide-induced platelet aggregation, granule secretion, thromboxane B2 generation, and intracellular Ca2+ mobilization. Biochemical studies revealed that HRT is involved in inhibiting the phosphorylation of phospholipase C and protein kinase B. The oral administration of HRT (30, 50, and 100 mg/kg once daily for 1 and/or 7 days) efficiently ameliorates ferric chloride induced arterial thrombus formation in vivo. Tail bleeding time was not significantly increased. The qualitative phytochemical constituents of the HRT extract were investigated using high-performance liquid chromatography. Our results demonstrated that HRT shows potential antiplatelet and antithrombotic effects without affecting hemostasis. Hence, HRT could be an effective therapeutic agent for the treatment of thrombotic diseases

The ancient phosphatidylinositol 3-kinase signaling system is a master regulator of energy and carbon metabolism in algae

Algae undergo a complete metabolic transformation under stress by arresting cell growth, inducing autophagy and hyperaccumulating biofuel precursors such as triacylglycerols and starch. However, the regulatory mechanisms behind this stress-induced transformation are still unclear. Here, we use biochemical, mutational, and “omics” approaches to demonstrate that PI3K signaling mediates the homeostasis of energy molecules and influences carbon metabolism in algae. In Chlamydomonas reinhardtii, the inhibition and knockdown (KD) of algal class III PI3K led to significantly decreased cell growth, altered cell morphology, and higher lipid and starch contents. Lipid profiling of wild-type and PI3K KD lines showed significantly reduced membrane lipid breakdown under nitrogen starvation (-N) in the KD. RNA-seq and network analyses showed that under -N conditions, the KD line carried out lipogenesis rather than lipid hydrolysis by initiating de novo fatty acid biosynthesis, which was supported by tricarboxylic acid cycle down-regulation and via acetyl-CoA synthesis from glycolysis. Remarkably, autophagic responses did not have primacy over inositide signaling in algae, unlike in mammals and vascular plants. The mutant displayed a fundamental shift in intracellular energy flux, analogous to that in tumor cells. The high free fatty acid levels and reduced mitochondrial ATP generation led to decreased cell viability. These results indicate that the PI3K signal transduction pathway is the metabolic gatekeeper restraining biofuel yields, thus maintaining fitness and viability under stress in algae. This study demonstrates the existence of homeostasis between starch and lipid synthesis controlled by lipid signaling in algae and expands our understanding of such processes, with biotechnological and evolutionary implications.Ministry of Science, ICT and Future Planning 2015M3A6A2065697Ministry of Oceans and Fisheries 2015018

Visual tracking of non-rigid objects with partial occlusion through elastic structure of local patches and hierarchical diffusion

In this paper, a tracking method based on sequential Bayesian inference is proposed. The proposed method focuses on solving both the problem of tracking under partial occlusions and the problem of non-rigid object tracking in real-time on a desktop personal computer (PC). The proposed method is mainly composed of two parts: (1) modeling the target object using elastic structure of local patches for robust performance; and (2) efficient hierarchical diffusion method to perform the tracking procedure in real-time. The elastic structure of local patches allows the proposed method to handle partial occlusions and non-rigid deformations through the relationship among neighboring patches. The proposed hierarchical diffusion method generates samples from the region where the posterior is concentrated to reduce computation time. The method is extensively tested on a number of challenging image sequences with occlusion and non-rigid deformation. The experimental results show the real-time capability and the robustness of the proposed method under various situations