SAFT-γ Force Field for the Simulation of Molecular Fluids 6. Binary and ternary mixtures comprising water, carbon dioxide, and n-alkanes

AbstractThe SAFT-γ coarse graining methodology (Avendaño et al., 2011) is used to develop force fields for the fluid-phase behaviour of binary and ternary mixtures comprising water, carbon dioxide, and n-alkanes. The effective intermolecular interactions between the coarse grained (CG) segments are directly related to macroscopic thermodynamic properties by means of the SAFT-γ equation of state for molecular segments represented with the Mie (generalised Lennard–Jones) intermolecular potential (Papaioannou et al., 2014). The unlike attractive interactions between the components of the mixtures are represented with a single adjustable parameter, which is shown to be transferable over a wide range of conditions. The SAFT-γ Mie CG force fields are used in molecular-dynamics simulations to predict the challenging (vapour+liquid) and (liquid+liquid) fluid-phase equilibria characterising these mixtures, and to study phenomena that are not accessible directly from the equation of state, such as the interfacial properties. The description of the fluid-phase equilibria and interfacial properties predicted with the SAFT-γ Mie force fields is in excellent agreement with the corresponding experimental data, and of comparable if not superior quality to that reported for the more sophisticated atomistic and united-atom models

Extension of the SAFT-VR Mie EoS to model homonuclear rings and its parameterization based on the principle of corresponding states

The statistical associating fluid theory of variable range employing a Mie potential (SAFT-VR-Mie) proposed by Lafitte et al. (J. Chem Phys. 2013, 139, 154504) is one of the latest versions of the SAFT family. This particular version has been shown to have a remarkable capability to connect experimental determinations, theoretical calculations, and molecular simulations results. However, the theoretical development restricts the model to chains of beads connected in a linear fashion. In this work, the capabilities of the SAFT-VR Mie equation of state for modeling phase equilibria are extended for the case of planar ring compounds. This modification proposed replaces the Helmholtz energy of chain formation by an empirical contribution based on a parallelism to the second-order thermodynamic perturbation theory for hard sphere trimers. The proposed expression is given in terms of an extra parameter, χ, that depends on the number of beads, ms, and the geometry of the ring. The model is used to describe the phase equilibrium for planar ring compounds formed of Mie isotropic segments for the cases of ms equals to 3, 4, 5 (two configurations), and 7 (two configurations). The resulting molecular model is further parametrized, invoking a corresponding states principle resulting in sets of parameters that can be used indistinctively in theoretical calculations or in molecular simulations without any further refinements. The extent and performance of the methodology has been exemplified by predicting the phase equilibria and vapor pressure curves for aromatic hydrocarbons (benzene, hexafluorobenzene, toluene), heterocyclic molecules (2,5-dimethylfuran, sulfolane, tetrahydro-2H-pyran, tetrahydrofuran), and polycyclic aromatic hydrocarbons (naphthalene, pyrene, anthracene, pentacene, and coronene). An important aspect of the theory is that the parameters of the model can be used directly in molecular dynamics (MD) simulations to calculate equilibrium phase properties and interfacial tensions with an accuracy that rivals other coarse grained and united atom models, for example, liquid densities, are predicted, with a maximum absolute average deviation of 3% from both the theory and the MD simulations, while the interfacial tension is predicted, with a maximum absolute average of 8%. The extension to mixtures is exemplified by considering a binary system of hexane (chain fluid) and tetrahydro-2H-pyran (ring fluid)

Experimental measurements and theoretical modeling of high-pressure mass densities and interfacial tensions of carbon dioxide + n-heptane + toluene and its carbon dioxide binary systems

Experimental determination and theoretical predictions of the isothermal (344.15 K) mass densities and interfacial tensions for the sys tem carbon dioxide (CO2) with heptol (n - heptane + toluene) mixtures varying liquid volume fraction compositions of toluene (0, 25, 50, 75, 100 % v/v) and over the pressure range 0.1 to 8 MPa are reported. Measurements are carried out on a high - pressure dev ice that includes a vibrating tube densimeter and a pendant drop tensiometer. Theoretical modeling of mass densities phase equilibria and interfacial properties (i.e., interfacial tension and interfacial concentration profiles) are performed by employing t he Square Gradient Theory using an extension of the Statistical Associating Fluid Theory equation of state that accounts for ring fluids. The experimental bulk phase equilibrium densities and interfacial tensions obtained are in very good agreement with th e theoretical predictions. Although there are no previous experimental data of these mixtures at the conditions explored herein, the results follow the same trends observed from experimental data at other conditions. The combination of experimental and mod eling approaches provides a route to simultaneously predict phase equilibrium and interfacial properties within acceptable statistical deviations. For the systems and conditions studied here, we observe that the phase equilibrium of the mixtures display z eotropic vapor - liquid equilibria with positive deviations from ideal behavior. The mass bulk densities behave ordinarily whereas the interfacial tensions decrease as the pressure or liquid mole fraction of CO2 increases and/or the ratio toluene/heptane dec reases. The interfacial concentration along the interfacial region exhibits a remarkable high excess adsorption of CO2, which increases with pressure and it is larger in n - heptane than in toluene. Toluene does not exhibit any special adsorption activity wh ereas n - heptane displays surface activity only at low pressure in a very narrow range for the case of CO2 + (25% n - heptane + 75% toluene) mixture

Burden of waterpipe smoking and chewing tobacco use among women of reproductive age group using data from the 2012-13 Pakistan Demographic and Health Survey

Background: Despite the general decline in cigarette smoking, use of alternative forms of tobacco has increased particularly in developing countries. Waterpipe (WP) and Chewing Tobacco (CT) are two such alternative forms, finding their way into many populations. However, the burden of these alternative forms of tobacco and their socio demographic determinants are still unclear. We assessed the prevalence of WP and CT use among women of reproductive age group in Pakistan. Methods: Data from the most recent Pakistan Demographic and Health Survey 2012–13 (n = 13,558) was used for this analysis. Information obtained from ever married women, aged between 15 and 49 years were analyzed using two separate data subgroups; exclusive WP smokers (total n = 12,995) and exclusive CT users (total n = 12,771). Univariate and Multivariate logistic regression analyses were conducted and results were reported as crude and adjusted Odds Ratio with 95 % confidence intervals. Results: Prevalence of WP smoking and CT were 4 % and 2 %, respectively. After multivariate adjustments, ever married women who were: older than 35 years (OR; 4.68 95 % CI, 2.62–8.37), were poorest (OR = 4.03, 95 % CI 2.08–7.81), and had no education (OR = 9.19, 95 % CI 5.10–16.54), were more likely to be WP smokers. Similarly, ever married women who were: older than 35 years (OR = 3.19, 95 % CI 1.69–6.00), had no education (OR = 4.94, 95 % CI 2.62–9.33), were poor (OR = 1.64, 95 % CI 1.07–2.48) and had visited health facility in last 12 months (OR = 1.81, 95 % CI 1.22–2.70) were more likely to be CT users as well. Conclusion: Older women with lower socio-economic profile were more likely to use WP and CT. Focused policies aiming towards reducing the burden of alternate forms of tobacco use among women is urgently needed to control the tobacco epidemic in the country

Injection of Pseudomonas aeruginosa Exo Toxins into Host Cells Can Be Modulated by Host Factors at the Level of Translocon Assembly and/or Activity

Pseudomonas aeruginosa type III secretion apparatus exports and translocates four exotoxins into the cytoplasm of the host cell. The translocation requires two hydrophobic bacterial proteins, PopB and PopD, that are found associated with host cell membranes following infection. In this work we examined the influence of host cell elements on exotoxin translocation efficiency. We developed a quantitative flow cytometry based assay of translocation that used protein fusions between either ExoS or ExoY and the ß-lactamase reporter enzyme. In parallel, association of translocon proteins with host plasma membranes was evaluated by immunodetection of PopB/D following sucrose gradient fractionation of membranes. A pro-myelocytic cell line (HL-60) and a pro-monocytic cell line (U937) were found resistant to toxin injection even though PopB/D associated with host cell plasma membranes. Differentiation of these cells to either macrophage- or neutrophil-like cell lines resulted in injection-sensitive phenotype without significantly changing the level of membrane-inserted translocon proteins. As previous in vitro studies have indicated that the lysis of liposomes by PopB and PopD requires both cholesterol and phosphatidyl-serine, we first examined the role of cholesterol in translocation efficiency. Treatment of sensitive HL-60 cells with methyl-ß-cyclodextrine, a cholesterol-depleting agent, resulted in a diminished injection of ExoS-Bla. Moreover, the PopB translocator was found in the membrane fraction, obtained from sucrose-gradient purifications, containing the lipid-raft marker flotillin. Examination of components of signalling pathways influencing the toxin injection was further assayed through a pharmacological approach. A systematic detection of translocon proteins within host membranes showed that, in addition to membrane composition, some general signalling pathways involved in actin polymerization may be critical for the formation of a functional pore. In conclusion, we provide new insights in regulation of translocation process and suggest possible cross-talks between eukaryotic cell and the pathogen at the level of exotoxin translocation

Heat Shock Response in Yeast Involves Changes in Both Transcription Rates and mRNA Stabilities

We have analyzed the heat stress response in the yeast Saccharomyces cerevisiae by determining mRNA levels and transcription rates for the whole transcriptome after a shift from 25°C to 37°C. Using an established mathematical algorithm, theoretical mRNA decay rates have also been calculated from the experimental data. We have verified the mathematical predictions for selected genes by determining their mRNA decay rates at different times during heat stress response using the regulatable tetO promoter. This study indicates that the yeast response to heat shock is not only due to changes in transcription rates, but also to changes in the mRNA stabilities. mRNA stability is affected in 62% of the yeast genes and it is particularly important in shaping the mRNA profile of the genes belonging to the environmental stress response. In most cases, changes in transcription rates and mRNA stabilities are homodirectional for both parameters, although some interesting cases of antagonist behavior are found. The statistical analysis of gene targets and sequence motifs within the clusters of genes with similar behaviors shows that both transcriptional and post-transcriptional regulons apparently contribute to the general heat stress response by means of transcriptional factors and RNA binding proteins

GUCY2C Opposes Systemic Genotoxic Tumorigenesis by Regulating AKT-Dependent Intestinal Barrier Integrity

The barrier separating mucosal and systemic compartments comprises epithelial cells, annealed by tight junctions, limiting permeability. GUCY2C recently emerged as an intestinal tumor suppressor coordinating AKT1-dependent crypt-villus homeostasis. Here, the contribution of GUCY2C to barrier integrity opposing colitis and systemic tumorigenesis is defined. Mice deficient in GUCY2C (Gucy2c−/−) exhibited barrier hyperpermeability associated with reduced junctional proteins. Conversely, activation of GUCY2C in mice reduced barrier permeability associated with increased junctional proteins. Further, silencing GUCY2C exacerbated, while activation reduced, chemical barrier disruption and colitis. Moreover, eliminating GUCY2C amplified, while activation reduced, systemic oxidative DNA damage. This genotoxicity was associated with increased spontaneous and carcinogen-induced systemic tumorigenesis in Gucy2c−/− mice. GUCY2C regulated barrier integrity by repressing AKT1, associated with increased junction proteins occludin and claudin 4 in mice and Caco2 cells in vitro. Thus, GUCY2C defends the intestinal barrier, opposing colitis and systemic genotoxicity and tumorigenesis. The therapeutic potential of this observation is underscored by the emerging clinical development of oral GUCY2C ligands, which can be used for chemoprophylaxis in inflammatory bowel disease and cancer

Association of Six Single Nucleotide Polymorphisms with Gestational Diabetes Mellitus in a Chinese Population

To investigate whether the candidate genes that confer susceptibility to type 2 diabetes mellitus are also correlated with gestational diabetes mellitus (GDM) in pregnant Chinese women.In this study, 1764 unrelated pregnant women were recruited, of which 725 women had GDM and 1039 served as controls. Six single nucleotide polymorphisms (rs7754840 in CDKAL1, rs391300 in SRR, rs2383208 in CDKN2A/2B, rs4402960 in IGF2BP2, rs10830963 in MTNR1B, rs4607517 in GCK) were genotyped using TaqMan allelic discrimination assays. The genotype and allele distributions of each SNP between the GDM cases and controls and the combined effects of alleles for the risk of developing GDM were analyzed. We found that the rs4402960, rs2383208 and rs391300 were statistically associated with GDM (OR = 1.207, 95%CI = 1.029-1.417, p = 0.021; OR = 1.242, 95%CI = 1.077-1.432, p = 0.003; OR = 1.202, 95%CI = 1.020-1.416, P = 0.028, respectively). In addition, the effect was greater under a recessive model in rs391300 (OR = 1.820, 95%CI = 1.226-2.701, p = 0.003). Meanwhile, the joint effect of these three loci indicated an additive effect of multiple alleles on the risk of developing GDM with an OR of 1.196 per allele (p = 1.08×10(-4)). We also found that the risk alleles of rs2383208 (b = -0.085, p = 0.003), rs4402960 (b = -0.057, p = 0.046) and rs10830963 (b = -0.096, p = 0.001) were associated with HOMA-B, while rs7754840 was associated with decrease in insulin AUC during a 100 g OGTT given at the time of GDM diagnosis (b = -0.080, p = 0.007).Several risk alleles of type 2 diabetes were associated with GDM in pregnant Chinese women. The effects of these SNPs on GDM might be through the impairment of beta cell function and these risk loci contributed additively to the disease

Intramolecular Folding in Human ILPR Fragment with Three C-Rich Repeats

Enrichment of four tandem repeats of guanine (G) rich and cytosine (C) rich sequences in functionally important regions of human genome forebodes the biological implications of four-stranded DNA structures, such as G-quadruplex and i-motif, that can form in these sequences. However, there have been few reports on the intramolecular formation of non-B DNA structures in less than four tandem repeats of G or C rich sequences. Here, using mechanical unfolding at the single-molecule level, electrophoretic mobility shift assay (EMSA), circular dichroism (CD), and ultraviolet (UV) spectroscopy, we report an intramolecularly folded non-B DNA structure in three tandem cytosine rich repeats, 5'-TGTC4ACAC4TGTC4ACA (ILPR-I3), in the human insulin linked polymorphic region (ILPR). The thermal denaturation analyses of the sequences with systematic C to T mutations have suggested that the structure is linchpinned by a stack of hemiprotonated cytosine pairs between two terminal C4 tracts. Mechanical unfolding and Br2 footprinting experiments on a mixture of the ILPR-I3 and a 5′-C4TGT fragment have further indicated that the structure serves as a building block for intermolecular i-motif formation. The existence of such a conformation under acidic or neutral pH complies with the strand-by-strand folding pathway of ILPR i-motif structures