Co-eluent effect in partition chromatography. Rhamnose-xylose separation with strong and weak cation-exchangers in aqueous ethanol

The effect of ethanol in aqueous eluent on the chromatographic separation was studied at 298 K. Two sugars, L-rhamnose and D-xylose, were separated by using strong and weak cation-exchangers as a stationary phase. The ionic form of the resins was Na+ or Ca2+. The separations were carried out with sugar feed concentrations up to 35 wt% and with both low (about 1%) and high (about 10%) feed volume to bed volume ratios. The separation of the sugars was improved by adding ethanol into the eluent. The separation was also significantly enhanced when the weak cation-exchangers with the greatest affinity for water were used instead of strong cation-exchangers as a separation medium for the sugars having different hydrophilicities. The experimental data were successfully explained with a rate-based column model, which accounted for the volume changes of the stationary phase. A thermodynamic sorption model was utilized in column calculations.     

MM-PBSA free energy analysis of endo-1,4-xylanase II (XynII)-substrate complexes: binding of the reactive sugar in a skew boat and chair conformation

The binding of xylotetraose in different conformations to the active site of endo-1,4-beta-xylanase II (XynII) from Trichoderma reesei was studied using molecular dynamics (MD) simulations and free energy analyses employing the MM-PBSA (Molecular Mechanics-Poisson-Boltzmann Surface Area) method. MD simulations of 1 ns were done for the substrate xylotetraose having the reactive sugar, which is bound in the -1 subsite of XynII in the 4C1 (chair) and 2So (skew boat) ground state conformations, and for the transition state of the XynII catalysed hydrolysis of the beta-glycosidic linkage. According to the simulations and free energy analysis, XynII binds the substrate with the -1 sugar in the 2So conformation 59.8 kJ mol(-1) tighter than the substrate with the sugar in the 4C1 conformation. The reactive 2So conformation resembles closely the reaction transition state and has the breaking glycosidic bond in a pseudo-axial orientation ready for facile bond cleavage. The transition state was calculated to be bound 77.1 kJ mol(-1) tighter than the 4C1 ground state conformation. The molecular mechanical interaction energy between the enzyme and the reactive pyranoside unit at the -1 subsite was 75.7 kJ mol(-1) more favorable for the binding of the 2So conformation than the 2C1 conformation, explaining the clearly tighter binding of the reactive structure The results of this study indicate that in the Michaelis complex XynII, a member of the family 11 xylanase, the substrate is bound in a skew boat conformation and in the catalytic reaction, the -1 sugar proceeds from the 4C1 conformation through 2So to the transition state with the -1 sugar in the 2,5B conformation.     

On applicability of PCA,voxel-wise variance normalization and dimensionality assumptions for sliding temporal window sICA in resting-state fMRI

Subject-level resting-state fMRI (RS-fMRI) spatial independent component analysis (sICA) may provide new ways to analyze the data when performed in the sliding time window. However, whether principal component analysis (PCA) and voxel-wise variance normalization (VN) are applicable pre-processing procedures in the sliding-window context, as they are for regular sICA, has not been addressed so far. Also model order selection requires further studies concerning sliding-window sICA. In this paper we have addressed these concerns. First, we compared PCA-retained subspaces concerning overlapping parts of consecutive temporal windows to answer whether in-window PCA and VN can confound comparisons between sICA analyses in consecutive windows. Second, we compared the PCA subspaces between windowed and full data to assess expected comparability between windowed and full-data sICA results. Third, temporal evolution of dimensionality estimates in RS-fMRI data sets was monitored to identify potential challenges in model order selection in a sliding-window sICA context. Our results illustrate that in-window VN can be safely used, in-window PCA is applicable with most window widths and that comparisons between windowed and full data should not be performed from a subspace similarity point of view. In addition, our studies on dimensionality estimates demonstrated that there are sustained, periodic and very case-specific changes in signal-to-noise ratio within RS-fMRI data sets. Consequently, dimensionality estimation is needed for well-founded model order determination in the sliding-window case. The observed periodic changes correspond to a frequency band of ≤ 0.1 Hz, which is commonly associated with brain activity in RS-fMRI and become on average most pronounced at window widths of 80 and 60 time points (144 and 108 s, respectively). Wider windows provided only slightly better comparability between consecutive windows, and 60 time point or shorter windows also provided the best comparability with full-data results. Further studies are needed to determine the cause for dimensionality variations.     

Engineering Short Peptide Sequences for Uranyl Binding

Peptides are interesting tools to rationalize uranyl–protein interactions, which are relevant to uranium toxicity in vivo. Structured cyclic peptide scaffolds were chosen as promising candidates to coordinate uranyl thanks to four amino acid side chains pre‐oriented towards the dioxo cation equatorial plane. The binding of uranyl by a series of decapeptides has been investigated with complementary analytical and spectroscopic methods to determine the key parameters for the formation of stable uranyl–peptide complexes. The molar ellipticity of the uranyl complex at 195 nm is directly correlated to its stability, which demonstrates that the β‐sheet structure is optimal for high stability in the peptide series. Cyclodecapeptides with four glutamate residues exhibit the highest affinities for uranyl with log K_C=8.0–8.4 and, therefore, appear as good starting points for the design of high‐affinity uranyl‐chelating peptides.     

A general approach to detect protein expression in vivo using fluorescent puromycin conjugates

Understanding the expression of known and unknown gene products represents one of the key challenges in the post-genomic world. Here, we have developed a new class of reagents to examine protein expression in vivo that does not require transfection, radiolabeling, or the prior choice of a candidate gene. To do this, we constructed a series of puromycin conjugates bearing various fluorescent and biotin moieties. These compounds are readily incorporated into expressed protein products in cell lysates in vitro and efficiently cross cell membranes to function in protein synthesis in vivo as indicated by flow cytometry, selective enrichment studies, and Western analysis. Overall, this work demonstrates that fluorescent-puromycin conjugates offer a general means to examine protein expression in vivo.     

Point-wise measurements of MRS volume selection performance are insensitive to magnetic susceptibility effects of phantom materials

The purpose was to analyse magnetic susceptibility effects on accuracy of point-wise measurements of signal profiles in the assessment of MRS volume selection performance. An existing phantom design consisting of a sphere with a movable signal source was used for the investigation. The influence from the phantom on magnetic field homogeneity was measured with phase sensitive 1H imaging and 31P spectroscopy on a 1.5 T whole body MR system. The susceptibility effects for such a phantom design can be separated in 1/ A variation in the background magnetic field, which is caused by the stationary structures and has a significant influence on spatial accuracy. 2/ A magnetic field distortion, which is caused by the movable signal source and has very little influence on accuracy. The spatial inaccuracy due to susceptibility effects in this phantom, was 0.03 mm for positions of the signal source covering a 40-mm VOI. Susceptibility effects from the movable signal source were substantial but had very little influence on spatial accuracy. Still, improvements of this phantom design are possible. Point-wise measurements using a phantom with a movable signal source is inherently insensitive to susceptibility effects from the signal source and permits accurate signal profile measurements of high spatial (sub-mm) resolution.     

Light scattering by Gaussian random ellipsoid particles: First results with discrete-dipole approximation

We introduce the stochastic geometry of a Gaussian random ellipsoid (GE) and, with the discrete-dipole approximation, carry out preliminary computations for light scattering by wavelength-scale GE particles. In the GE geometry, we describe the base ellipsoid by the three semiaxes a?b?c. The axial ratios b:a and c:a appear as two shape parameters additional to those of the Gaussian random sphere geometry (GS). We compare the scattering characteristics of GE particles to those of ellipsoids. Introducing irregularities on ellipsoids smoothens the angular scattering characteristics, in a way analogous to the smoothening of spherical particle characteristics in the case of GS particles.     

Nonlocal Harnack inequalities

We state and prove a general Harnack inequality for minimizers of nonlocal, possibly degenerate, integro-differential operators, whose model is the fractional p-Laplacian.