Conformational selection of glycomimetics at enzyme catalytic sites: experimental demonstration of the binding of distinct high-energy distorted conformations of C-, S-, and O-glycosides by E. Coli beta-galactosidases

We show that the conformational features of the molecular complexes of E. coli beta-galactosidase and O-glycosides may differ from those formed with closely related compounds in their chemical nature, such as C- and S-glycosyl analogues. In the particular case presented here, NMR and ab initio quantum mechanical results show that the 3D-shapes of the ligand/inhibitor within the enzyme binding site depend on the chemical nature of the compounds. In fact, they depend on the relative size of the stereoelectronic barriers for chair deformation or for rotation around Phi glycosidic linkage.     

Analytical perfect fluid perturbation for the matter dominated epoch

We present the analytical solution to the linear evolution equation of a one component Friedmann perturbation using an equation of state of the form p = (1/3)μσ²(t), where μ is the mass density and σ(t) is the root mean square (rms) velocity in the matter dominated epoch. It is assumed that this rms velocity depends only on the time coordinate and decreases as 1/a, a being the expansion factor of the Friedmann background. The evolution equations are written for scales below the horizon using the longitudinal gauge. The general solution, in the coordinate space, of the evolution equation for the scalar mode is obtained. In the case of spherical symmetry, this solution is expressed in terms of unidimensional integrals of the initial conditions: the initial values of the Newtonian potential and its first time derivative. This perfect fluid solution is a good approximation to the evolution of warm dark matter perturbations obtained by solving the Vlasov’s equation for collisionless particles.     

The effect of rate of stimulation on perception of spectral shape by cochlear implantees

The effect of rate of stimulation on spectral shape perception was measured in six users of the Nucleus CI24 cochlear implant. Three spectral shapes were created by using three profiles of current across seven electrode positions. Each current profile was replicated in three stimuli that interleaved stimulus pulses across the seven electrodes with cycle rates (rate per electrode) of 450, 900, and 1800 Hz. The stimulus space resulting from a multidimensional scaling experiment showed a clear dimension related to the rate of stimulation that was orthogonal to the dimension related to the spectral shapes. A second experiment was performed with the same subjects to investigate whether the perceptual dimension related to rate in Experiment 1 could be attributed to different perceptual flatness of the profiles at different rates. In Experiment 2, the rate of stimulation was fixed at 900 Hz and three profiles were created for each spectral shape that differed in flatness. This experiment did not, however, result in an independent perceptual dimension related to the flatness of the profile. In conclusion, rate of stimulation provided an independent perceptual dimension in the multiple-electrode stimuli, in spite of the rates being not discriminable or barely discriminable in single-electrode stimulation.     

Quantitative measurement of different ceramide species from crude cellular extracts by normal-phase high-performance liquid chromatography coupled to atmospheric pressure ionization mass spectrometry

Normal-phase high-performance liquid chromatography (NP-HPLC) coupled to atmospheric pressure ionization mass spectrometry (APCI-MS) allows quantitative analysis of endogenous ceramide and dihydroceramide species from crude lipid extracts. Qualitative information for the species comes from observation of differences in chromatographic and mass spectrometric behavior between species (Pettus et al. Rapid Commun. Mass Spectrom. 2003; 17: 1017-1026). Quantitative analysis is achieved by (1) use of a synthetic internal standard as an extraction and injection control, (2) lack of salt adduction, ion suppression, or other matrix effects in APCI mode, and (3) consistent fragmentation and ionization of external standards across the physiologically relevant concentration range found in endogenous lipid samples. Application to the analysis and quantitation of ceramide and dihydroceramide from various cell lines is demonstrated. The results from APCI-MS analysis corroborate and enhance information acquired from use of the diacylglycerol kinase assay for total ceramide measurement. This technique readily allows simultaneous quantitation of ceramide and dihydroceramide species.     

Effect of non-significant proportional bias in the final measurement uncertainty

The trueness of an analytical method can be assessed by calculating the proportional bias of the method in terms of apparent recovery. If the apparent recovery does not differ significantly from one, the analytical method has not a significant bias. If this is the case, the bias is neglected and the uncertainty associated with this bias is included in the uncertainty budget of results. However, when assessing trueness there is always a probability of incorrectly concluding that the proportional bias is not significant. Therefore, the uncertainty of results may be underestimated. In this paper, we study how non-significant bias affects the uncertainty of analytical results. Moreover, we study how to avoid the underestimation of uncertainty by including the non-significant bias calculated in the uncertainty budget. To answer these questions, we have used the Monte-Carlo method to simulate the process of estimating the apparent recovery of a biased analytical method and, subsequently, the future results this method provides. The results of the simulation show that non-significant bias may underestimate the uncertainty of analytical results when bias contributes in more than 20% to the overall uncertainty. Uncertainty is specially underestimated when bias contributes in more than 50% to the overall uncertainty.