Hydrophobicity within the three-dimensional Mercedes-Benz model: potential of mean force

We use the three-dimensional Mercedes-Benz model for water and Monte Carlo simulations to study the structure and thermodynamics of the hydrophobic interaction. Radial distribution functions are used to classify different cases of the interaction, namely, contact configurations, solvent separated configurations, and desolvation configurations. The temperature dependence of these cases is shown to be in qualitative agreement with atomistic models of water. In particular, while the energy for the formation of contact configurations is favored by entropy, its strengthening with increasing temperature is accounted for by enthalpy. This is consistent with our simulated heat capacity. An important feature of the model is that it can be used to account for well-converged thermodynamics quantities, e.g., the heat capacity of transfer. Microscopic mechanisms for the temperature dependence of the hydrophobic interaction are discussed at the molecular level based on the conceptual simplicity of the model.     

Determination of operating characteristic, retesting, and testing amount probabilities associated with testing for the presence of Salmonella in foods

The relatively small perceived probability associated with retesting a food for the presence of Salmonella at low levels is often considered as one of the reasons that a confirmatory or check-analysis tends to disagree in practice with the results of an original test. Given a retesting process where a retest is only performed to confirm an original positive Salmonella test, the probability that both the original and retest will test positive for Salmonella has been traditionally determined by some as the product of the probabilities of a positive Salmonella test for the original and retest samples. When examining the probabilities associated with the retesting process, we found that our results disagreed with those based on intuitions apparently held by others concerning how these probabilities should be calculated. For Salmonella testing, operating characteristic values were computed to demonstrate the protections afforded by the Salmonella sampling plans presented in the U.S. Food and Drug Administration's Bacteriological Analytical Manual and to obtain the probability of a positive Salmonella test. The geometric distribution was examined for possible utility in determining the probabilities associated with testing amounts, i.e., the number of Salmonella tests needed to obtain a positive test.     

CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling

Monosaccharide derivatives such as xylose, fucose, N-acetylglucosamine (GlcNAc), N-acetylgalactosamine (GlaNAc), glucuronic acid, iduronic acid, and N-acetylneuraminic acid (Neu5Ac) are important components of eukaryotic glycans. The present work details development of force-field parameters for these monosaccharides and their covalent connections to proteins via O-linkages to serine or threonine sidechains and via N-linkages to asparagine sidechains. The force field development protocol was designed to explicitly yield parameters that are compatible with the existing CHARMM additive force field for proteins, nucleic acids, lipids, carbohydrates, and small molecules. Therefore, when combined with previously developed parameters for pyranose and furanose monosaccharides, for glycosidic linkages between monosaccharides, and for proteins, the present set of parameters enables the molecular simulation of a wide variety of biologically-important molecules such as complex carbohydrates and glycoproteins. Parametrization included fitting to quantum mechanical (QM) geometries and conformational energies of model compounds, as well as to QM pair interaction energies and distances of model compounds with water. Parameters were validated in the context of crystals of relevant monosaccharides, as well NMR and/or x-ray crystallographic data on larger systems including oligomeric hyaluronan, sialyl Lewis X, O- and N-linked glycopeptides, and a lectin:sucrose complex. As the validated parameters are an extension of the CHARMM all-atom additive biomolecular force field, they further broaden the types of heterogeneous systems accessible with a consistently-developed force-field model.     

Circadian variations in biologically closed electrochemical circuits in Aloe vera and Mimosa pudica

The circadian clock regulates a wide range of electrophysiological and developmental processes in plants. This paper presents, for the first time, the direct influence of a circadian clock on biologically closed electrochemical circuits in vivo. Here we show circadian variation of the plant responses to electrical stimulation. The biologically closed electrochemical circuits in the leaves of Aloe vera and Mimosa pudica, which regulate their physiology, were analyzed using the charge stimulation method. The electrostimulation was provided with different timing and different voltages. Resistance between Ag/AgCl electrodes in the leaf of Aloe vera was higher during the day than at night. Discharge of the capacitor in Aloe vera at night was faster than during the day. Discharge of the capacitor in a pulvinus of Mimosa pudica was faster during the day. The biologically closed electrical circuits with voltage gated ion channels in Mimosa pudica are also activated the next day, even in the darkness. These results show that the circadian clock can be maintained endogenously and has electrochemical oscillators, which can activate ion channels in biologically closed electrochemical circuits. We present the equivalent electrical circuits in both plants and their circadian variation to explain the experimental data.     

Tissue-Specific stem cell differentiation in an in vitro airway model

The respiratory tract is the primary site of exposure to airborne compounds, with the bronchial epithelium providing one of the first lines of defence. A growing need exists for an accurate in vitro model of the bronchial epithelium. Here, normal human bronchial epithelial (NHBE) cells cultured at an air/liquid interface create a fully differentiated, in-vivo-like model of the human bronchial epithelium. Developmental characterisation includes (i) trans-epithelial electrical resistance, (ii) morphology and (iii) bronchial cell specific stains/markers. It is concluded that the basal/progenitor cells create a pseudo-stratified, mucociliary NHBE model containing basal, serous, Clara, goblet and ciliated cells, reflective of the normal human bronchial epithelium (days 24-33 ALI culture).     

Affinity of Cu+ for the copper-binding domain of the amyloid-β peptide of Alzheimer's disease

The role of metal ions in Alzheimer's disease etiology is unresolved. For the redox-active metal ions iron and copper, the formation of reactive oxygen species by metal amyloid complexes has been proposed to contribute to Alzheimer's disease neurodegeneration. For copper, reactive oxygen species are generated by copper redox cycling between its 1+ and 2+ oxidation states. Thus, the AβCu(I) complex is potentially a critical reactant associated with Alzheimer's disease etiology. Through competitive chelation, we have measured the affinity of the soluble copper-binding domain of the amyloid-β peptide for Cu(I). The dissociation constants are in the femtomolar range for both wild-type and histidine-to-alanine mutants. These results indicate that Cu(I) binds more tightly to monomeric amyloid-β than Cu(II) does, which leads us to propose that Cu(I) is a relevant in vivo oxidation state.     

I(-)·(CH3I)2 photoexcitation: the influence of dipole bound states on detachment and fragmentation

We present the results of a photoelectron imaging study of the I(-)·(CH(3)I)(2) cluster anion over excitation wavelengths 355-260 nm. The resulting spectra and photoelectron angular distributions (PADs) suggest extensive electron-molecule interaction following photoexcitation. Fragmentation channels are observed subsequent to excitation between 355 and 330 nm. The origin of these features, which begin 200 meV and peak 70 meV below the X band direct detachment threshold, is described in terms of a predissociative dipole bound state. The nature of the fragments detected and the energetics of the channel opening argue strongly in favor of an asymmetric, head to tail cluster anion geometry posited by Dessent et al. [Acc. Chem. Res. 31, 527 (1998)]. Above the direct detachment threshold, PADs display evidence of phenomena akin to electron-molecule scattering. The fragment anions disappear above the X band threshold but reappear some distance below the second (A) direct detachment band. At these energies there is also rapid variation of the X band PAD, an observation attributed to autodetachment via spin-orbit relaxation of the iodine core of the cluster.     

The E.S.R. spectrum of the tropolonyl radical

The many-body diagrammatic Rayleigh-Schrödinger perturbation theory (RSPT) is used for the calculation of ionization potentials of open-shell systems with one unpaired electron. This theoretical approach is tested on the simple examples of NO₂ and NF₂ molecules described by the INDO semi-empirical hamiltonian. The first- and second-order results are presented.