Sequence-specific retention calculator. A family of peptide retention time prediction algorithms in reversed-phase HPLC: applicability to various chromatographic conditions and columns

Separation selectivity of C18 reversed-phase columns from different manufacturers has been compared to evaluate the applicability of our sequence-specific retention calculator (SSRCalc) peptide retention prediction algorithms. Three different versions of SSRCalc are currently in use: 300-A pore size sorbents (TFA as ion-pairing modifier, pH 2), 100 A (TFA, pH 2), and 100 A (pH 10), which have been applied for the separation of randomly chosen mixture of tryptic peptides. The major factor affecting separation selectivity of C18 sorbents was found to be apparent pore size, while differences in end-capping chemistry do not introduce a significant impact. The introduction of embedded polar groups to the C18 functionality increases the retention of peptides containing hydrophobic amino acid residues with polar groups: Tyr and Trp. We also demonstrate that changing the ion-pairing modifier to formic/acetic acid significantly reduces the algorithm's predictive ability, so models developed for different eluent conditions cannot be compared directly to each other.     

Diffusion of 22Na and 85Sr in montmorillonite: evidence of interlayer diffusion being the dominant pathway at high compaction

A mechanistic understanding of transport phenomena in compacted clays is essential for the use of such materials as engineered barrier systems for the safe geological disposal of radioactive wastes. The present contribution is a first step in the development of an integrative treatment of the properties of tracer cations in compacted bentonites with respect to diffusion and sorption. The diffusion of 22Na and 85Sr in highly compacted montmorillonite and kaolinite is investigated as a function of the "external salt concentration" (NaClO4), i.e., of the solution in equilibrium with the clay. Consistent results were obtained from through-diffusion experiments and tracer profile analysis. Knowledge of genuine diffusion coefficients of the filter plates turned out to be crucial in cases where the diffusive resistance of the filter plates was similar to that of the clay. Diffusion coefficients formally calculated on the basis of the tracer concentration gradient in the external aqueous phase, and the sorption distribution ratios were found to decrease with increasing external salt concentration in the case of montmorillonite. In a logarithmic representation of these data, a slope of -1 was obtained for the monovalent 22Na, whereas the slope was -2 for the divalent 85Sr. In the case of kaolinite, diffusion coefficients were independent of the external salt concentration. It is postulated that the diffusion of the tracer cation through the interlayer water is the dominant pathway in compacted swelling clays under the experimental conditions tested. Effective diffusion coefficients, based on a tracer concentration gradient in the interlayer water of the clay, were found to be independent of the composition of the external aqueous phase. The latter gradient is assumed to be a function of the external salt concentration, according to a calculated distribution of the tracer cation between free pore water and the interlayer water via cation exchange.     

Hydrogen release from a mixture of NaBH4 and Mg(OH)2

Hydrogen generating reaction between sodium borohydride, NaBH₄, and magnesium hydroxide, Mg(OH)₂ (brucite), was studied. Reaction rate was found to depend on the degree of reactants homogenization and/or their particle size. Kinetic of the reaction was studied in isothermal approach in the temperature range of 240–360 °C. It is shown that the reaction obeys 2D diffusion mechanism and its activation energy is 155.9 kJ/mol. Powder XRD analysis and Raman spectroscopy reveal that mechanically activated mixture of NaBH₄ and Mg(OH)₂ reacts yielding MgO as the only crystalline phase in the temperature range of 240–318 °C. At higher temperatures a new crystalline tetragonal phase of as yet undetermined composition is developed.     

Comparison of atmospheric deposition of copper, nickel, cobalt, zinc, and cadmium recorded by Finnish peat cores with monitoring data and emission records

This study aims to determine the extent to which the accumulation rates of Cu, Ni, Co, Zn, and Cd in peat cores agree with established histories of atmospheric emission from local pointsources. Metals accumulating in three Finnish peat cores with known metal deposition histories have been measured using inductively coupled plasma-sector field mass spectrometry. Samples were age-dated using both 210Pb and 14C (bomb pulse curve). At the Outokumpu (OUT) site as well as the low-background site Hietaj?rvi (HIJ), 210Pb age dates are in excellent agreement with the 14C bomb pulse curve method results, and the precision is between 1 and 10 years for most of the samples; at the Harjavalta (HAR) site, precision is > 6 years. Mean regional "background" concentrations have been calculated from deeper peat layers of the HIJ site (microg g(-1)): Cu, 1.3 +/- 0.2 (n = 62); Co, 0.25 +/- 0.04 (n = 71); Cd, 0.08 +/- 0.01 (n = 23); and Zn, 4 +/- 2 (n = 40). For layers accumulated within the past 100 years, accumulation rates (ARs) have been calculated. At sites with < 0.06 g m(-2) cumulative Ni inventory (HIJ and OUT), ARs of Cu and Co trace the known metal deposition histories very well. At HAR, where metal inventories are much greater, Cu and Co are mobile. ARs of Zn were between 3 and 30 mg m(-2) year(-1) and those of Cd between 24 and 140 microg m(-2) year(-1) at all sites and are independent of the chronology of their inputs from the atmosphere.     

Loss of swiss cheese in Neurons Contributes to Neurodegeneration with Mitochondria Abnormalities,Reactive Oxygen Species Acceleration and Accumulation of Lipid Droplets in Drosophila Brain

Various neurodegenerative disorders are associated with human NTE/PNPLA6 dysfunction. Mechanisms of neuropathogenesis in these diseases are far from clearly elucidated. Hereditary spastic paraplegia belongs to a type of neurodegeneration associated with NTE/PNLPLA6 and is implicated in neuron death. In this study, we used Drosophila melanogaster to investigate the consequences of neuronal knockdown of swiss cheese (sws)—the evolutionarily conserved ortholog of human NTE/PNPLA6—in vivo. Adult flies with the knockdown show longevity decline, locomotor and memory deficits, severe neurodegeneration progression in the brain, reactive oxygen species level acceleration, mitochondria abnormalities and lipid droplet accumulation. Our results suggest that SWS/NTE/PNPLA6 dysfunction in neurons induces oxidative stress and lipid metabolism alterations, involving mitochondria dynamics and lipid droplet turnover in neurodegeneration pathogenesis. We propose that there is a complex mechanism in neurological diseases such as hereditary spastic paraplegia, which includes a stress reaction, engaging mitochondria, lipid droplets and endoplasmic reticulum interplay.     

Spectral analysis and physical properties of benzylated starch

A‐ and B‐wheat starch (in native or acetylated form) and potato starch (slightly acetylated) were subjected to benzylation with benzylchloride in various reaction conditions and at various reaction times (40–100°C, 1–90 h). Modified and original starches were characterized by elemental analysis and spectroscopic methods (FT‐IR and 1H NMR). The semicrystalline or amorphous character was indicated by X‐ray powder (XRD) patterns. Rheological properties of benzyl starch of DS ∼ 1 were measured by small amplitude oscillation shear rheology (SAOS) using the rheometer Haake Rheostress RS 80. The results indicated predominantly elastic behavior because the storage modulus was higher than the loss modulus over the whole frequency range; it corresponded to a true gel. The storage and loss moduli increased with increasing frequency while the tangent of phase did not change and was approximately δ = 40°.     

Use of Br and Se in peat to reconstruct the natural and anthropogenic fluxes of atmospheric Hg: A 10000-year record from Caribou Bog, Maine

Using Br and Se as reference elements, the natural and anthropogenic fluxes of atmospheric Hg were reconstructed for the past 10,000 years using peat cores from Caribou Bog, ME. In the ombrotrophic peat layers, the average background Hg accumulation rate (AR) was 1.7 +/- 1.3 microg m(-2) year(-1) which is comparable with the natural rate of atmospheric Hg accumulation reported in other retrospective studies. The average Hg AR determined using all peat samples dating from preindustrial times, including minerotrophic peat, was slightly greater (3.1 +/- 2.3 microg m(-2) year(-1)) which may reflect differences in canopy interception due to the changes in plant communities, aquatic inputs, or possibly climatic factors. The maximum Hg AR (32 microg m(-2) year(-1)) occurred ca. 1961 A.D. In samples predating the settlement by Europeans, there is a linear correlation between the AR of Hg and those of Br and Se; this relationship allows both Br and Se to be used to calculate the natural AR of Hg (Hgnat). The difference between Hg AR and Hg(nat) is the Hg AR in excess of background (Hg(ex)). Because Hg(ex) was positive only after ca. 1840 A.D., it is assumed to represent the anthropogenic Hg component. By the late 19th century, Hg(ex) deposition was equal to the natural flux. At the peak in Hg deposition in 1961 A.D., Hgex made up >90% of total atmospheric Hg deposition. The AR in the uppermost peat decreased to 25% of peak values by 2000 A.D.     

X-ray absorption of gold nanoparticles with thin silica shell

Silica-coated gold (Au) nanoparticles were prepared and their morphological and X-ray absorption properties were investigated. These core-shell type nanoparticles are very stable in aqueous media and may be suitable for an X-ray contrast agent in biological systems. Transmission electron micrographs confirmed well-separated and relatively homogeneous morphology of the nanoparticles in highly concentrated colloids. Peak position for Au plasmon resonance was red-shifted with increasing shell thickness. X-ray absorption by the colloids of silica-coated Au nanoparticles was stronger than that by those of silica-coated Agl nanoparticles, a recently investigated X-ray contrast agent, at similar experimental conditions.     

Myoglobin–Pyruvate Interactions: Binding Thermodynamics,Structure–Function Relationships,and Impact on Oxygen Release Kinetics

Myoglobin (Mb), besides its roles as an oxygen (O₂) carrier/storage protein and nitric oxide NO scavenger/producer, may participate in lipid trafficking and metabolite binding. Our recent findings have shown that O₂ is released from oxy-Mb upon interaction with lactate (LAC, anerobic glycolysis end-product). Since pyruvate (PYR) is structurally similar and metabolically related to LAC, we investigated the effects of PYR (aerobic glycolysis end-product) on Mb using isothermal titration calorimetry, circular dichroism, and O₂-kinetic studies to evaluate PYR affinity toward Mb and to compare the effects of PYR and LAC on O₂ release kinetics of oxy-Mb. Similar to LAC, PYR interacts with both oxy- and deoxy-Mb with a 1:1 stoichiometry. Time-resolved circular dichroism spectra revealed that there are no major conformational changes in the secondary structures of oxy- or deoxy-Mb during interactions with PYR or LAC. However, we found contrasting results with respect to binding affinities and substrate preference, where PYR has higher affinity toward deoxy-Mb when compared with LAC (which prefers oxy-Mb). Furthermore, PYR interaction with oxy-Mb releases a significantly lower amount of O₂ than LAC. Taken together, our findings support the hypothesis that glycolytic end-products play a distinctive role in the Mb-rich tissues by serving as novel regulators of O₂ availability, and/or by impacting other activities related to oxy-/deoxy-Mb toggling in resting vs. exercised or metabolically activated conditions.     

Probing matrix/filler interphase with ultrasonic waves

Journal of Materials Science - Sound propagation velocities in rod-shaped samples of epoxy-graphene nanocomposites with varying concentrations of multi-layered graphene fillers are measured...