Differences in Trace Element Concentrations between the Right and Left Hemispheres of Human Brain Using INAA

Very few publications have quoted differences between the same regions in both the right and left hemispheres of the human brain. It may be possible that that the two hemispheres have different trace elemental concentrations, since it is known that they both have different functions. In this study, three brain regions from both the right and left hemispheres of the cortex have been sampled from five elderly individuals (three 'normal' and two Alzheimer's disease) and their elemental concentrations have been determined by instrumental neutron activation analysis (INAA).     

Matrix-assisted laser desorption/ionisation mass spectrometry imaging of lipids in rat brain tissue with integrated unsupervised and supervised multivariant statistical analysis

To date matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) analysis has been largely concerned with mapping the distribution of known analytes in tissues. An important step in the progression of its applications is the determination of unknown variants for metabolite and protein profiling in both clinical studies and studies of disease. Principal component analysis (PCA) is a statistical approach which can be used as a means of determining latent variables in multivariate data sets. In the work reported here, PCA, in both unsupervised and supervised modes, has been used to differentiate brain regions based on their lipid composition determined by MALDI-MSI. PCA has been shown to be useful in the determination of hidden variables between spectra taken from six regions of brain tissue. It is possible to identify ions of interest from the loadings plot which are likely to be more prominent in the different regions of the brain and thus differentiating between white and grey matter. It is also possible to distinguish between the grey Cerebellar Cortex and the Hippocampal formation, due to the grey Cerebellar Cortex having a positive PC2 and the Hippocampal formation having a negative PC2 score; this is only possible in supervised PCA with this data set because with unsupervised PCA the two regions overlap.     

Determination of the geographical origin of Brazilian wines by isotope and mineral analysis

In the present research, we studied wines from three different south Brazilian winemaking regions with the purpose of differentiating them by geographical origin of the grapes. Brazil's wide territory and climate diversity allow grape cultivation and winemaking in many regions of different and unique characteristics. The wine grape cultivation for winemaking concentrates in the South Region, mainly in the Serra Gaúcha, the mountain area of the state of Rio Grande do Sul, which is responsible for 90% of the domestic wine production. However, in recent years, two new production regions have developed: the Campanha, the plains to the south and the Serra do Sudeste, the hills to the southeast of the state. Analysis of isotopic ratios of ¹⁸O/¹⁶O of wine water, ¹³C/¹²C of ethanol, and of minerals were used to characterize wines from different regions. The isotope analysis of δ¹⁸O of wine water and minerals Mg and Rb were the most efficient to differentiate the regions. By using isotope and mineral analysis, and discrimination analysis, it was possible to classify the wines from south Brazil.     

Mass spectrometry strategies applied to the characterization of proline-rich peptides from secretory parotid granules of pig (Sus scrofa)

Basic proline-rich proteins (bPRPs) are a class of proteins widely present in saliva of humans and other mammals. They are synthesized as preproproteins and enzymatically cleaved into small peptides before secretion from the salivary glands. Recently, we characterized two proline-rich peptides (SP-A and SP-B) in parotid secretory granules of pig (Sus Scrofa) that are derived from three isoforms of a PRP proprotein (Swiss-Prot data bank: Q95JC9-1, Q95JC9-2 and Q95JC9-3). Together the coding regions for SP-A and SP-B, which are repeated many times, account for 52-70% of the coding regions of the PRP proproteins. This study was undertaken to identify peptides encoded by unassigned regions of the PRP proproteins. RP-HPLC-ESI-IT-MS analysis of enriched granule preparations from pig parotid glands by two different analytical strategies identified ten new proline-rich peptides derived from the three proproteins. Together with the coding regions for SP-A and SP-B already identified it was possible to assign 68-75% of the proproteins coding regions. The peptide sequences indicated a number of unusual proteolytic cleavage sites suggesting the presence of unknown proprotein convertases.     

The effects of coupling on chemical wave propagation in quadratic and cubic autocatalysis with decay

The initiation of reaction-diffusion travelling waves in two regions coupled together by the linear diffusive interchange of an autocatalytic species is considered. In one region a purely autocatalytic production process (either quadratic or cubic) is assumed, while in the other region there are both autocatalytic and decay processes (either linear or quadratic). A perturbation analysis based on small initial inputs of the autocatalyst is presented. This indicates conditions under which travelling wave formation is possible as well as identifying two special cases which need further consideration, namely cubic autocatalysis in both regions with quadratic or linear decay in one region. The former case gives rise to a zero eigenvalue and the perturbation method has to be extended to include the higher order terms to resolve this case. The latter case requires a threshold on the initial input of autocatalyst and further information about this threshold is gained from a solution for strong coupling.     

δ34S for tracing the origin of cheese and detecting its authenticity

Casein δ³⁴S of 725 samples of cheese from all over the world were measured using IRMS. δ³⁴S alone made it possible to establish characteristic ranges of values for two types of Italian cheese (Grana Padano PDO and Parmigiano Reggiano PDO) and for the different regions and provinces of both the Grana Padano PDO and the Parmigiano Reggiano PDO zones. Moreover, δ³⁴S of PDO Italian samples were compared to both Italian (not PDO) and foreign competitive cheese samples. In all the cases, sulfur isotopic ratio analysis was a powerful tool to fix characteristic ranges of values for cheeses coming from different countries and to improve the information given by other isotopic parameters.     

Neutron activation analysis of Cuban soils

Thirty elements were determined by INAA in Cuban soil samples collected in 17 zones from western regions of Cuba, which were affected by neuropathy epidemic in 1992. The presence of toxic elements was evaluated to provide data for the analysis of possible paths of intoxication through local agriculture product consumption. The results obtained for As, Th and U are compared with similar data reported on literature.     

Gene mapping study for constitutive skin color in an isolated Mongolian population

To elucidate the genes responsible for constitutive human skin color, we measured the extent of skin pigmentation in the buttock, representative of lifelong non-sun-exposed skin, and conducted a gene mapping study on skin color in an isolated Mongolian population composed of 344 individuals from 59 families who lived in Dashbalbar, Mongolia. The heritability of constitutive skin color was 0.82, indicating significant genetic association on this trait. Through the linkage analysis using 1,039 short tandem repeat (STR) microsatellite markers, we identified a novel genomic region regulating constitutive skin color on 11q24.2 with an logarithm of odds (LOD) score of 3.39. In addition, we also found other candidate regions on 17q23.2, 6q25.1, and 13q33.2 (LOD ≥ 2). Family-based association tests on these regions with suggestive linkage peaks revealed ten and two significant single nucleotide polymorphisms (SNPs) on the linkage regions of chromosome 11 and 17, respectively. We were able to discover four possible candidate genes that would be implicated to regulate human skin color: ETS1, UBASH3B, ASAM, and CLTC.     

Geographical classification of some Australian wines by discriminant analysis using HPLC with UV and chemiluminescence detection

HPLC with UV and acidified potassium permanganate chemiluminescence detection, combined with multivariate data analysis techniques, were used for the geographical classification of some Australian red (Cabernet Sauvignon) and white (Chardonnay) wines from two regions (Coonawarra and Geelong). Identification of the wine constituents prominent in the chromatography was performed by mass spectrometry. Principal components analysis and linear discriminant analysis were used to classify the wines according to region of production. Separation between regions was achieved with both detection systems and key components leading to discrimination of the wines were identified. Using two principal components, linear discriminant analysis with UV detection correctly classified 100% of the Chardonnay wines and, overall 91% of the Cabernet Sauvignon wines. With acidified potassium permanganate chemiluminescence detection, 75% of the Chardonnay wines and 94% of the Cabernet Sauvignon wines were correctly classified using two factors.     

Temperature weighted histogram analysis method, replica exchange, and transition paths

We analyzed the data from a replica exchange molecular dynamics simulation using the weighted histogram analysis method to combine data from all of the temperature replicas (T-WHAM) to obtain the room-temperature potential of mean force of the G-peptide (the C-terminal beta-hairpin of the B1 domain of protein G) in regions of conformational space not sampled at room temperature. We were able to determine the potential of mean force in the transition region between a minor alpha-helical population and the major beta-hairpin population and identify a possible transition path between them along which the peptide retains a significant amount of secondary structure. This observation provides new insights into a possible mechanism of formation of beta-sheet secondary structures in proteins. We developed a novel Bayesian statistical uncertainty estimation method for any quantity derived from WHAM and used it to validate the calculated potential of mean force. The feasibility of estimating regions of the potential of mean force with unfavorable free energy at room temperature by T-WHAM analysis of replica exchange simulations was further tested on a system that can be solved analytically and presented some of the same challenges found in more complex chemical systems.     

Determination of the chemical composition and Raman characterization of barite samples from Denizli and Akdamadeni,Turkey, using Energy Dispersive X-ray fluorescence and Raman microscopy

Accurate analysis of samples is very important for scientists working in many fields. XRF device is used very frequently especially in mine analysis. However, researchers are trying to reach accurate results with many different analysis methods. In addition to the known analysis methods, alternative research methods also guide the studies. In this study, two barite ore samples, collected from two regions of different nature (Denizli and Akda?madeni) by following specified sampling methods, were analyzed using Confocal Raman Spectroscopy (CRS) and Polarized Energy Dispersive X-Ray Fluorescence (PEDXRF) spectrometer. The first sample was from a metamorphic basement, and the second was from an alkali syenite rock unit. The main objective of this paper is to compare the optical characteristics of these two different barite samples collected from different regions under a polarized microscope, using CRS and PEDXRF. The results of polarized microscopy analysis showed that the barite taken from Denizli is associated with calcite. On the other hand, the barite taken from Akda?madeni is associated with galena, celestite, and quartz. Two different colors were observed in the barite samples. CRS and PEDXRF results showed that the barites collected from two regions differed in mineral association, chemical composition, and physical properties. The accuracy of the chemical analysis technique was ensured by following USGS standards, GBW 7109, and GBW-7309 Sediment. Barite ores were analyzed using HR-800 (HORIBA-Jobin Yvon) CRS and a polarized microscope (Leica DMLP). Thanks to this study, it has been shown that mineral analyzes can be performed with an accuracy close to XRF with Confocal Raman spectroscopy. Confocal Raman spectroscopy will also guide researchers for mineral analysis.     

Separation and analysis of nitroarenes from airborne particulate organic matter by HPLC and capillary GC-MS methods

Normal-phase HPLC has been applied to the separation of nitroarenes from dichloromethane extracts from airborne particulate matter samples collected in urban regions of Upper Silesia. GC-MS and capillary gas chromatography with NP detector analysis of the nitroarene fraction made it possible to identify and determine quantitatively those compounds which dominate in the organic matter emitted to the atmosphere in highly industrialized regions (2-nitrofluorene, isomeric nitroarenes of MW = 247, i.e. nitropyrene/nitrofluoranthene/nitroacephenanthrylene).     

Bimodal Complexations of Steroids with Cyclodextrins by a Flexible Docking Algorithm

A flexible docking algorithm was developed for studying the inclusion complexes of cyclodextrins with steroids in aqueous solution by an optimization method and an empirical function. The function is used to estimate the binding free energy including intermolecular interaction energy, the conformational energy change, and the solvation energy. The bimodal complexations of twelve steroids in β- and γ-CD cavities were studied by the algorithm. For the two orientations of the guests in the cavity, the possible binding regions were investigated, and the lowest energies for the inclusion complexes in the binding regions were obtained. The stability constant for each orientation was estimated from the optimized energy components by a quantitative model. Therefore, the preferential orientations of the guests were found out from the results finally.     

Bimodal Complexations of Steroids with Cyclodextrins by a Flexible Docking Algorithm

A flexible docking algorithm was developed for studying the inclusion complexes of cyclodextrins with steroids in aqueous solution by an optimization method and an empirical function. The function is used to estimate the binding free energy including intermolecular interaction energy, the conformational energy change, and the solvation energy. The bimodal complexations of twelve steroids in β- and γ-CD cavities were studied by the algorithm. For the two orientations of the guests in the cavity, the possible binding regions were investigated, and the lowest energies for the inclusion complexes in the binding regions were obtained. The stability constant for each orientation was estimated from the optimized energy components by a quantitative model. Therefore, the preferential orientations of the guests were found out from the results finally.This revised version was published online in July 2005 with a corrected issue number.     

Blotting efficiency investigated by using two-dimensional electrophoresis, hydrophobic membranes and proteins from different sources

Purification and chemical characterization of proteins may be achieved by combining two-dimensional electrophoresis (2-DE) and microsequencing or amino acid analysis. To enable this combination, the protein has to be transferred as completely as possible from the gel into the sequencer. In this study hydrophobic membranes were used as support for the transfer and proteins were transferred from the gels onto the membranes by semidry blotting. Blotting conditions were optimized to obtain high blotting efficiencies for as many proteins of a complex 2-DE pattern as possible. Under optimized conditions, blotting efficiencies between 60% and 100% were obtained for five marker proteins; the mean values from four regions of a 2-DE pattern from 29 unknown proteins of a complex protein mixture from mouse brain were between 60% and 79%. The four commercially available hydrophobic membranes that were compared showed only slight differences in protein amount on the membranes after blotting for whole protein patterns, whereas single proteins occurred with higher amounts on either one or the other membrane. The results of the blotting optimization allowed us to suggest a blotting mechanism with which systematic improvement of the blotting conditions is possible for problematic proteins.     

Structure-Specific Ribonucleases for MS-Based Elucidation of Higher-Order RNA Structure

Supported by high-throughput sequencing technologies, structure-specific nucleases are experiencing a renaissance as biochemical probes for genome-wide mapping of nucleic acid structure. This report explores the benefits and pitfalls of the application of Mung bean (Mb) and V1 nuclease, which attack specifically single- and double-stranded regions of nucleic acids, as possible structural probes to be employed in combination with MS detection. Both enzymes were found capable of operating in ammonium-based solutions that are preferred for high-resolution analysis by direct infusion electrospray ionization (ESI). Sequence analysis by tandem mass spectrometry (MS/MS) was performed to confirm mapping assignments and to resolve possible ambiguities arising from the concomitant formation of isobaric products with identical base composition and different sequences. The observed products grouped together into ladder-type series that facilitated their assignment to unique regions of the substrate, but revealed also a certain level of uncertainty in identifying the boundaries between paired and unpaired regions. Various experimental factors that are known to stabilize nucleic acid structure, such as higher ionic strength, presence of Mg(II), etc., increased the accuracy of cleavage information, but did not completely eliminate deviations from expected results. These observations suggest extreme caution in interpreting the results afforded by these types of reagents. Regardless of the analytical platform of choice, the results highlighted the need to repeat probing experiments under the most diverse possible conditions to recognize potential artifacts and to increase the level of confidence in the observed structural information.

Homopairing possibilities of the DNA base adenine

Using calculations based on the ab initio density functional theory, we for the first time report all possible planar DNA base adenine homodimers. Two density functionals and both localized and plane wave basis sets were used, and the results are compared with previous quantum chemical and semiempirical calculations available for a few pairs. We find that there are 21 possible planar adenine pairs with variable binding energies ranging from -0.03 to -0.86 eV. More stable pairs are associated with two strong hydrogen bonds formed between the monomers, while the least stable pairs are characterized by two or one relatively weak bonds. We find that stable hydrogen bonds can be characterized by the difference charge density that shows well-developed regions of alternating excess and depletion of the electron charge similar to a "kebab" structure. The presented detailed information on all planar adenine pairs can be utilized, for example, in considering possible adenine monolayers seen on various surfaces.     

Proton NMR relaxation studies on several nitroxyl-water systems

Proton spin-lattice and spin-spin relaxation times of several nitroxyl radicals in aqueous solutions have been measured between 10 kHz and 90 MHz. There are two regions where the relaxation times of the solvent water protons are frequency dependent. It is possible to extract from these experimental data structural and dynamical parameters such as the number of solvated water protons and/or their mean lifetime in the first hydration sphere around the paramagnetic center. These results were found to differ considerably from corresponding data reported in the literature which have been deduced mainly from chemical shift measurements. To whom correspondence should be addressed.     

Structural inhomogeneity in cotton cellulose upon its interaction with water

Comparative analysis of the characteristics of supramolecular structures of dry and swollen cotton fibers makes it possible to differentiate structural regions accessible to water. The revealed features of water desorption from cotton cellulose (exceptionally low rates at the final stages, presence of residual moisture) are related to the removal of water, which is localized in the regions of the crystalline phase disorganized upon drying. The fact of incomplete moisture removal from cotton fibers at < 325 K is interpreted from the stand-point of the frozen molecular mobility in the microsurroundings of sorption sites, which are located at the defects of crystallites, at the final stage of the desorption process. A marked contribution from the recrystallization of disorganized regions in the surface layer of crystallites to the thermal effect of the interaction between water and cotton cellulose at low water content is established.     

Metal distribution patterns in the mussel Mytilus edulis cytosols using size-exclusion chromatography and double focusing ICP-MS detection

In order to estimate metal distribution patterns in biomolecules of different sizes and their possible relationship with environmental heavy metal contamination, multi-elemental distributions in different fractions of the cytosols of mussels were studied. To do so, samples were collected from natural populations of two coastal regions in Spain: a wild (uncontaminated) coast and an industrialised (contaminated) area in Asturias. Moreover, some commercial mussels from the Galicia coast were also investigated for comparison. Aliquots of the mussel cytosol extracts from each sample were applied to a calibrated Sephadex G-75 column (100 x 1 cm) and forty 3 ml fractions were obtained. After suitable dilution, 18 trace metals were determined by double focusing inductively coupled plasma mass spectrometry (DF-ICP-MS). The use of DF-ICP-MS detection allowed the resolution of several spectral interferences that cannot be resolved by quadrupole ICP-MS. Accurate results for ultratrace elements at basal levels are possible even after sample dilution to prevent matrix effects. After biomolecule-metal association pattern has been established, quantitative analysis of mussel cytosols from the three coastal areas was carried out, using external aqueous calibration plus standard additions to correct for possible matrix effects. Results showed that total metal contents increased following the expected order: wild coast < Galicia coast < industrial area coast. Speciation of Cu, Zn, Ca, U, Ni, Mo, Mn, Cr, V, Cd, Al and Sb showed a similar distribution pattern among cytosolic ligands for all the studied samples. Conversely, Fe, Pb, Sn, Co, Hg and Ag were found to exhibit different speciation patterns when samples from industrialised (contaminated) and non-industrialised areas were compared.