The Role of the Dielectric Barrier in Narrow Biological Channels: a Novel Composite Approach to Modeling Single-channel Currents

A composite continuum theory for calculating ion current through a protein channel of known structure is proposed, which incorporates information about the channel dynamics. The approach is utilized to predict current through the Gramicidin A ion channel, a narrow pore in which the applicability of conventional continuum theories is questionable. The proposed approach utilizes a modified version of Poisson-Nernst-Planck (PNP) theory, termed Potential-of-Mean-Force-Poisson-Nernst-Planck theory (PMFPNP), to compute ion currents. As in standard PNP, ion permeation is modeled as a continuum drift-diffusion process in a self-consistent electrostatic potential. In PMFPNP, however, information about the dynamic relaxation of the protein and the surrounding medium is incorporated into the model of ion permeation by including the free energy of inserting a single ion into the channel, i.e., the potential of mean force along the permeation pathway. In this way the dynamic flexibility of the channel environment is approximately accounted for. The PMF profile of the ion along the Gramicidin A channel is obtained by combining an equilibrium molecular dynamics (MD) simulation that samples dynamic protein configurations when an ion resides at a particular location in the channel with a continuum electrostatics calculation of the free energy. The diffusion coefficient of a potassium ion within the channel is also calculated using the MD trajectory. Therefore, except for a reasonable choice of dielectric constants, no direct fitting parameters enter into this model. The results of our study reveal that the channel response to the permeating ion produces significant electrostatic stabilization of the ion inside the channel. The dielectric self-energy of the ion remains essentially unchanged in the course of the MD simulation, indicating that no substantial changes in the protein geometry occur as the ion passes through it. Also, the model accounts for the experimentally observed saturation of ion current with increase of the electrolyte concentration, in contrast to the predictions of standard PNP theory

Results on the nucleon spin structure

SMC performed an investigation of the spin structure of the nucleon by measuring deep inelastic scattering of polarised muons off polarised protons and deuterons. A summary of the results for spin structure functions and sum rules is given.Comment: 8 pages, LaTeX, Talk given at the Workshop on "Symmetry and Spin - PRAHA98", Prag, September 1998. Proceedings to be published by Czech. Journ. Phy

Factors affecting sperm recovery rates and survival after centrifugation of equine semen

Conventional centrifugation protocols result in important sperm losses during removal of the supernatant. In this study, the effect of centrifugation force (400 or 900 × g), duration (5 or 10 min), and column height (20 or 40 mL; Experiment 1); sperm concentration (25, 50, and 100 × 10[superscript 6]/mL; Experiment 2), and centrifugation medium (EZ-Mixin CST [Animal Reproduction Systems, Chino, CA, USA], INRA96 [IMV Technologies, Maple Grove, MN, USA], or VMDZ [Partnar Animal Health, Port Huron, MI, USA]; Experiment 3) on sperm recovery and survival after centrifugation and cooling and storage were evaluated. Overall, sperm survival was not affected by the combination of centrifugation protocol and cooling. Total sperm yield was highest after centrifugation for 10 min at 400 × g in 20-mL columns (95.6 ± 5%, mean ± SD) or 900 × g in 20-mL (99.2 ± 0.8%) or 40-mL (91.4 ± 4.5%) columns, and at 900 × g for 5 min in 20-mL columns (93.8 ± 8.9%; P < 0.0001). Total (TMY) and progressively motile sperm yield followed a similar pattern (P < 0.0001). Sperm yields were not significantly different among samples centrifuged at various sperm concentrations. However, centrifugation at 100 × 10[superscript 6]/mL resulted in significantly lower total sperm yield (83.8 ± 10.7%) and TMY (81.7 ± 6.8%) compared with noncentrifuged semen. Centrifugation in VMDZ resulted in significantly lower TMY (69.3 ± 22.6%), progressively motile sperm yield (63.5 ± 18.2%), viable yield (60.9 ± 36.5%), and survival of progressively motile sperm after cooling (21 ± 10.8%) compared with noncentrifuged semen. In conclusion, centrifuging volumes of ≤ 20 mL minimized sperm losses with conventional protocols. With 40-mL columns, it may be recommended to increase the centrifugal force to 900 × g for 10 min and dilute the semen to a sperm concentration of 25 to 50 × 10[superscript 6]/mL in a milk- or fractionated milk-based medium. The semen extender VMDZ did not seem well suited for centrifugation of equine semen

Variability in supply and cross-shelf transport of pink shrimp (Farfantepenaeus duorarum) postlarvae into western Florida Bay

The variability in the supply of pink shrimp (Farfantepenaeus duorarum) postlarvae and the transport mechanisms of planktonic stages were investigated with field data and simulations of transport. Postlarvae entering the nursery grounds of Florida Bay were collected for three consecutive years at channels that connect the Bay with the Gulf of Mexico, and in channels of the Middle Florida Keys that connect the southeastern margin of the Bay with the Atlantic Ocean. The influx of postlarvae in the Middle Florida Keys was low in magnitude and varied seasonally and among years. In contrast, the greater postlarval influx occurred at the northwestern border of the Bay, where there was a strong seasonal pattern with peaks in influx from July through September each year. Planktonic stages need to travel up to 150 km eastward between spawning grounds (northeast of Dry Tortugas) and nursery grounds (western Florida Bay) in about 30 days, the estimated time of planktonic development for this species. A Lagrangian trajectory model was developed to estimate the drift of planktonic stages across the SW Florida shelf. The model simulated the maximal distance traveled by planktonic stages under various assumptions of behavior. Simulation results indicated that larvae traveling with the instantaneous current and exhibiting a diel behavior travel up to 65 km and 75% of the larvae travel only 30 km. However, the eastward distance traveled increased substantially when a larval response to tides was added to the behavioral variable (distance increased to 200 km and 85% of larvae traveled 150 km). The question is, when during larval development, and where on the shallow SW Florida shelf, does the tidal response become incorporated into the behavior of pink shrimp

Nuclear effects in charged-current quasielastic neutrino-nucleus scattering

After a short review of the recent developments in studies of neutrino-nucleus interactions, the predictions for double-differential and integrated charged current-induced quasielastic cross sections are presented within two different relativistic approaches: one is the so-called SuSA method, based on the superscaling behavior exhibited by electron scattering data; the other is a microscopic model based on relativistic mean field theory, and incorporating final-state interactions. The role played by the meson-exchange currents in the two-particle two-hole sector is explored and the results are compared with the recent MiniBooNE data.Comment: 12 pages, 9 figures, to appear in the Proceedings of "XIII Convegno di Cortona su Problemi di Fisica Nucleare Teorica", Cortona (Italy), April 6-8, 201

Oxygen content variation and cation doping dependence of (La)1.4(Sr1-yCay)1.6Mn2O7 (y = 0, 0.25, 0.5) bilayered manganites properties

The results of the synthesis and characterization of the optimally doped (La)1.4(Sr1-yCay)1.6Mn2O7 solid solution with y=0, 0.25 and 0.5 are reported. By progressively replacing the Sr with the smaller Ca, while keeping fixed the hole-concentration due to the divalent dopant, the 'size effect' of the cation itself on the structural, transport and magnetic properties of the bilayered manganite has been analysed. Two different annealing treatments of the solid solution, in pure oxygen and in pure argon, allowed also to study the effect of the oxygen content variation. Structure and electronic properties of the samples have been investigated by means of X-ray powder diffraction and X-ray absorption spectroscopy measurements. Magnetoresistivity and static magnetization measurements have been carried out to complete the samples characterization. Oxygen annealing of the solid solution, that showed a limit for about y=0.5, induces an increase of the Mn average valence state and a transition of the crystal structure from tetragonal to orthorhombic while the argon annealing induces an oxygen under-stoichiometry and, in turn, a reduction of the Mn average valence state. Along with the Ca substitution, the Jahn-Teller distortion of the MnO6 octahedra is reduced. This has been directly connected to a general enhancement of the transport properties induced by the Ca-doping. For the same cation composition, oxygen over-stoichiometry leads to higher metal-insulator transition temperatures and lower resistivity values. Curie temperatures (TC) reduce by increasing the Ca-doping. The lower TC for all the annealed samples with respect to the 'as prepared' ones are connected to the strong influence on the magnetic interaction of the point defects due to the oxygen content variation.Comment: 49 pages, 13 figure

Extensive structure‐activity relationship study of albicidin’s C‐terminal dipeptidic p‐aminobenzoic acid moiety

Albicidin is a recently described natural product that strongly inhibits bacterial DNA gyrase. The pronounced activity, particularly against Gram‐negative bacteria, turns it into a promising lead structure for an antibacterial drug. Hence, structure–activity relationship studies are key for the in‐depth understanding of structural features/moieties affecting gyrase inhibition, antibacterial activity and overcoming resistance. The 27 newly synthesized albicidins give profound insights into possibilities for variations of the C‐terminus. Furthermore, in the present study, a novel derivative has been identified as overcoming resistance posed by the Klebsiella‐protease AlbD. Structural modifications include, for example, azahistidine replacing the previous instable cyanoalanine as the central amino acid, as well as a triazole amide bond isostere between building blocks D and E.BMBF, 03VP00030, Validierung einer neuen antibakteriellen Wirkstoffklasse - AlbiPharmTU Berlin, Open-Access-Mittel - 201

Experimental joint signal-idler quasi-distributions and photon-number statistics for mesoscopic twin beams

Joint signal-idler photoelectron distributions of twin beams containing several tens of photons per mode have been measured recently. Exploiting a microscopic quantum theory for joint quasi-distributions in parametric down-conversion developed earlier we characterize properties of twin beams in terms of quasi-distributions using experimental data. Negative values as well as oscillating behaviour in quantum region are characteristic for the subsequently determined joint signal-idler quasi-distributions of integrated intensities. Also the conditional and difference photon-number distributions are shown to be sub-Poissonian and sub-shot-noise, respectively.Comment: 7 pages, 6 figure

Obesity Prevalence and Dietary Intake of Antioxidants in Native American Adolescents

Antioxidants are well known for possessing anti-inflammatory properties, which can reduce the risk of chronic disease and obesity. However, very little research has been done to examine antioxidant intake among adolescent minority populations such as Native American adolescents. Our study examined the significance of antioxidant intake among Native American adolescents at an urban residential high school in Southern California. Our study population consisted of 183 male and female Native American adolescents, 14-18 years of age, representing 43 tribes from across the United States. Students' primary source of meals was provided by the school food service. Based on the BMI calculations, the rate of obesity within our population was 38% for males and 40% for females, more than two-fold the national rate indicated by NHANESIII data. We used the Harvard School of Public Health Youth/Adolescent Questionnaire (HSPH YAQ), a semi-quantitative food frequency questionnaire, to examine antioxidant nutrient intake and evaluate the differences in the intake between normal and obese weight students. Statistical analysis of the results showed that intakes of vitamins C, E, and lycopene were the antioxidant nutrients found to be significantly different between normal and obese weight students and intakes of these nutrients were found to be higher among normal weight students (p-values = 0.02451, 0.00847, and 0.04928, respectively). These results suggest that dietary intake of antioxidants could be increased among Native American adolescents. Further research is needed to confirm our findings and identify effective ways for school food service to incorporate antioxidant rich foods into school menus