Quantifying growth of symmetric and asymmetric lipid bilayer domains

Here, we examine by atomic force microscopy (AFM) the kinetics and morphology of lipid domain growth during lipid phase separation by rapid thermal cooling of fully mixed two-component supported lipid bilayers. At the undercooled temperatures chosen, symmetric 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC)-rich domains favored slower reaction-limited growth whereas asymmetric galactosylceramide (GalCer)-rich domains favored faster diffusion-limited growth, indicated by shape factors and kinetic exponents. Because kinetically limited conditions could be accessed, we were able to estimate the activation energy barrier (approximately 16kT) and lateral diffusion coefficient (approximately 0.20 microm2/s) of lipid molecular addition to a growing domain. We discuss these results with respect to transition states, obstructed diffusion, and the necessity for coordinating growth in both leaflets in a symmetric lipid domain.     

Low energy electron and O- reactions in films of O2 coadsorbed with benzene or toluene

A detailed understanding of nascent reactive events leading to DNA damage is required to describe ionizing radiation effects on living cells. These early, sub-picosecond events involve mainly low energy (E < 20 eV) secondary electrons (SE), and low energy (E < 5 eV) secondary ion (and neutral) fragments; the latter are created either by the primary radiation, or by SE via dissociative electron attachment (DEA). While recent work has shown that SE initiate DNA strand break formation via DEA, the subsequent damage induced by the DEA ion fragments in DNA, or its basic components is unknown. Here, we report 0-20 eV electron impact measurements of anion desorption from condensed films containing O2 and either benzene (C6H6), or toluene (C6H5CH3); these molecules represent the most fundamental structural analogs of pyrimidine bases. Our experiments show that all of the observed OH- yields are the result of reactive scattering of 1-5 eV O- fragments produced initially by DEA to O2. These O- reactions involve hydrogen abstraction from benzene or toluene, and result in the formation of benzyl radicals, or toluene radicals centered on either the ring or exocyclic methyl group. O- scatters over nm distances comparable to DNA dimensions, and reactions involve a transient anion collision complex. Anion desorption is found to depend on both, the temperature of hydrocarbon film formation (morphology), and the order of overlayer adsorption, e.g. O2 on benzene, or benzene on O2. Our measurements support the notion that in irradiated DNA similar secondary-ion reactions can be initiated by the abundant secondary electrons, and may lead to clustered damage.     

Phenolysis and aminolysis of 4‐nitrophenyl and 2,4‐dinitrophenyl S‐methyl thiocarbonates in aqueous ethanol

The reactions of S‐methyl O‐(4‐nitrophenyl) thiocarbonate ( 1 ) and S‐methyl O‐(2,4‐dinitrophenyl) thiocarbonate ( 2 ) with a series of secondary alicyclic (SA) amines and phenols are subjected to a kinetic investigation. Under nucleophile excess, pseudo‐first‐order rate coefficients (k_obs) are obtained. Plots of k_obs against the free nucleophile concentration at constant pH are linear with slopes k_N. The Brønsted plots (log k_N vs. nucleophile pK_a) for the reactions are linear with slope (β) values in the 0.5–0.7 range, in accordance with concerted mechanisms. Comparison of the SA aminolysis of 1 with the same one carried out in water shows that the change of solvent from water to aqueous ethanol destabilizes the zwitterionic tetrahedral intermediate, changing the mechanism from stepwise to concerted. This destabilization is greater than that due to the change from SA amines to quinuclidines. For the phenolysis reactions, the k_N values in aqueous ethanol are smaller than those for the same reactions in water. Considering that the nucleophile is an anion, this result is unexpected because the anion should be more stabilized in the more polar solvent. This result is explained by the facts that the phenoxide reactant has a negative charge that is delocalized in the aromatic ring and the transition state is highly polar. © 2011 Wiley Peiodicals, Inc. Int J Chem Kinet 43: 353–358, 2011     

Heavy-tailed longitudinal data modeling using copulas

In this paper, we consider “heavy-tailed” data, that is, data where extreme values are likely to occur. Heavy-tailed data have been analyzed using flexible distributions such as the generalized beta of the second kind, the generalized gamma and the Burr. These distributions allow us to handle data with either positive or negative skewness, as well as heavy tails. Moreover, it has been shown that they can also accommodate cross-sectional regression models by allowing functions of explanatory variables to serve as distribution parameters.The objective of this paper is to extend this literature to accommodate longitudinal data, where one observes repeated observations of cross-sectional data. Specifically, we use copulas to model the dependencies over time, and heavy-tailed regression models to represent the marginal distributions. We also introduce model exploration techniques to help us with the initial choice of the copula and a goodness-of-fit test of elliptical copulas for model validation. In a longitudinal data context, we argue that elliptical copulas will be typically preferred to the Archimedean copulas. To illustrate our methods, Wisconsin nursing homes utilization data from 1995 to 2001 are analyzed. These data exhibit long tails and negative skewness and so help us to motivate the need for our new techniques. We find that time and the nursing home facility size as measured through the number of beds and square footage are important predictors of future utilization. Moreover, using our parametric model, we provide not only point predictions but also an entire predictive distribution.     

Association of Acenaphthoporphyrins with Liposomes for the Photodynamic Treatment of Leishmaniasis

Acenaphthoporphyrins are potential photosensitizers for photodynamic therapy, but their hydrophobicity limits their potential. Liposomes have been widely investigated as delivery vehicles that can transport hydrophobic drugs in biological systems. Here we study the association of acenaphthoporphyrins with liposomes made up of dimyristoyl phosphatidylcholine (DMPC), and to liposomes made up of a mixture of DMPC, cholesterol (Chol) and distearoyl phosphatidylglycerol (DSPG) in a 2:1:0.8 molar ratio to evaluate how liposome composition affects association constants. In liposomes consisting only of DMPC, the smaller monoacenaphthoporphyrin had the largest association constant of 5.5 × 10⁴ m ⁻¹ while the larger adj-diacenaphthoporphyrin and opp-diacenaphthoporphyrin (ODP) had smaller association constants at 1.8 × 10⁴ and 1.5 × 10⁴ m ⁻¹, respectively. The addition of liposomal Chol and DSPG has little effect on the magnitudes of the association constants. Polarization studies show that the acenaphthoporphyrins are driven far into the lipid bilayer to minimize polar–nonpolar interactions. Confocal microscopy confirms that the DMPC liposomes transport the porphyrins into promastigotes of Leishmania tarentolae. The compounds associated with DMPC:Chol:DSPG liposomes are effective in vitro against axenic and intracellular amastigotes of the pathogenic Leishmania panamensis. The effectiveness of the compounds is enhanced upon exposure of cultures to visible light.     

Investigation of RNA-Ligand Interactions by (19) F NMR Spectroscopy Using Fluorinated Probes

Spy swap: The interaction between an unlabeled RNA and unlabeled ligands (red hexagon) can be monitored by (19) F?NMR spectroscopy using small fluorinated diamines (green star) as spy reporters. This technique also enables the visualization of the conformational capture of a riboswitch by its ligand.