Mérnökgeofizikai szondázások elméleti modellezése = Theoretical modelling for engineering geophysical sounding

Neutron sugárzási tér és gamma sugárzási tér Monte Carlo modellezését végeztük penetrációs szonda környezetében homogén és inhomogén talajmodellek esetére. A kutatás célja penetrációs szondákkal történő neutron-porozitás meghatározás és gamma sűrűség meghatározás elméleti modellezése. A közegmodell porózus homok, amelynek porozitása 0,02 és 0,5 között változik. Termikus neutron fluxust és gamma foton intenzitást modelleztünk különböző porozitású és sűrűségű homogén modellekre, különböző sugárforrás-detektor szondahossz esetekre. Modelleztük a neutron-porozitás és sűrűség görbéket réteghatár közelében és vékony beágyazott réteggel szemben. Penetrációs elektromos szonda potenciálterét modelleztük analitikus módszerrel és véges elemes numerikus számítási módszerrel. Látszólagos fajlagos ellenállás görbéket számítottunk réteghatár közelében és véges vastagságú réteggel szemben. Terepi penetrációs mérések minőségellenőrzött inverzióját végeztük. Az egyes mérésfajtákhoz tartozó szórások (súlyok) meghatározására többféle módszert alkalmaztunk. | Neutron and gamma particle radiation was modeled by Monte Carlo method in penetration environment of homogeneous and inhomogeneous soil medium. The aim of calculations was the theoretical modeling of neutron porosity and gamma density of the soil. The soil consisted of sand (SiO2) with different porosity and of fresh water in the pore space. Thermal neutron flux and gamma photon intensity was calculated for different porosity and density values, and for different source - detector spacing. Simulated neutron porosity and density log curves were determined in the vicinity of layer boundary and finite thickness layers. Potential field of penetration electrical sonde was calculated by analytical mathematical method and by finite element numerical method. Apparent resistivity log curves were calculated for horizontally and radially layered medium. Quality controlled evaluation of penetration log complex was done in which different methods were applied for the determination of the weights of the individual logs

Internal Energy Distribution in Electrospray Ionization from the Multiple-Collision Model: The case of a Thermal-Like Distribution

In the presented study, the ion survival yields of the theoretical mass spectra simulated by the MassKinetic software are fitted with the experimental ion survival yield of substituted benzylpyridinium cations reported in a precedent paper (J. Mass Spectrom. 1999, 34, 1373-1379). A partially elastic multiple collision model is considered for describing the ion behaviour into the desolation area of the ESI source. The adjusting parameters are not the shape and the position of the P(Eint) curve but rather parameters related to the source acting, such as the pressure and the kinetic energy of ions entering the desolvation zone. In the case of a PE SCIEX ESI source interfaced with a quadrupole mass spectrometer, the energy uptake can then be well-defined by considering the case of a thermal-like distribution an average number of “effective” collisions of 29. From this model, it’s possible to correlate the voltage values applied on the orifice of the desolvation area to initial kinetic energy of ions entering into the collision zone of the ESI source. In the present case, these theoretical initial kinetic energy values range from 5.5 to 9 eV and the results of calculations shown also that the mean internal energy increases linearly with the orifice voltage. This modelling allows defining the internal energy distribution of ions in different part of the ESI source. The activation conditions occurring into the studied ESI source can be compared to a warm-up of ions. Indeed, the internal energy distributions resemble to thermal distribution of ions having a “characteristic temperature” (Tchar) parameter between 1020 to 1550 K. In addition, this study evidences a linear correlation between and Tchar. The slope value of this curve can be related to a calorimetric parameter such as the heat capacity of the activated substituted benzytlpyridinium cations

Biomolekulák szerkezetének és kölcsönhatásainak vizsgálata informatikai és tömegspektrometriai módszerek együttes alkalmazásával = Structure and interaction of biomolecules studied by a combined application of mass spectrometry and informatics

A kutatás legfontosabb eredménye peptidek, glikopeptidek és fehérjék tömegspektrometriás viselkedésének tapasztalati és elméleti leírása. Ezen eredmények alapján olyan, nemzetközi összehasonlításban is sikeres módszereket és szoftvereket fejlesztettünk ki, mely a szerkezetkutatás lehetőségeit és a tömegspektrometria alkalmazhatóságát jelentősen bővítik. Meghatároztuk az ütközési energia optimális értéke és a molekulatömeg közötti összefüggést; mely elősegíti a kísérletek automatizálását. Sikeresen leírtuk peptidek és glikopeptidek fragmentációjának szabályait, mely a spektrumok automatikus értelmezésének alapjául szolgál. Ezen eredményeink alapján olyan szoftvert dolgoztunk ki, mely lehetővé teszi a glikoziláció mintázatának meghatározását, ill. amely ezt a rendkívül munkaigényes értékelést automatizálja. Alapkutatási eredményeinket felhasználtuk a glikozilációs mintázat meghatározására, valamint kapcsolatot mutattunk ki egyes betegségek és fehérjék glikozilációja között. | The most significant result of the research project is experimental and theoretical description of the mass spectrometric behaviour of peptides, glycopeptides and proteins. Based on these results we have introduced successful new methodologies and software tools to improve applicability of mass spectrometry for structure analysis and for proteomics. A correlation between the optimal collision energy and molecular mass has been established; which facilitates the design of automatic operation protocols for mass spectrometry. Fragmentation behaviour of peptides and glycopeptides has been described; which is the basis of automatic spectra evaluation. Based on these results a new algorithm and software have been developed, which allows automatic determination of glycosylation patterns. This can substitute the very time consuming manual interpretation; which has been a major obstacle for studying glycosylation. The results described above have been used to determine glycosylation patterns and to observe correlations between protein glycosylation and various illnesses

Microwave-assisted solid-liquid phase alkylation of naphthols

Abstract: The microwave promoted alkylation of 1- and 2-naphthols with benzyl, butyl, ethyl and isopropyl halides in the presence of an alkali carbonate may result in O- and C-alkylated products. The alkylations were O-selective in the presence of K2CO3 in acetonitrile as the solvent and in the absence of phase transfer catalyst. The alkylations utilizing butyl and ethyl halides were also O-selective in solventless accomplishment and in the presence of triethylbenzylammonium chlorid

Degrees of freedom effect on fragmentation in tandem mass spectrometry of singly charged supramolecular aggregates of sodium sulfonates

The characteristic collision energy (CCE) to obtain 50% fragmentation of positively and negatively single charged non-covalent clusters has been measured. CCE was found to increase linearly with the degrees of freedom (DoF) of the precursor ion, analogously to that observed for synthetic polymers. This suggests that fragmentation behavior (e.g. energy randomization) in covalent molecules and clusters are similar. Analysis of the slope of CCE with molecular size (DoF) indicates that activation energy of fragmentation of these clusters (loss of a monomer unit) is similar to that of the lowest energy fragmentation of protonated leucine-enkephalin. Positively and negatively charged aggregates behave similarly, but the slope of the CCE vs DoF plot is steeper for positive ions, suggesting that these are more stable than their negative counterparts

Salt and solvent effects in the microscale chromatographic separation of heparan sulfate disaccharides

The analysis of heparan sulfate disaccharides poses a real challenge both from chromatographic and mass spectrometric point of view. This necessitates the constant improvement of their analytical methodology. In the present study, the chromatographic effects of solvent composition, salt concentration, and salt type were systematically investigated in isocratic HILIC-WAX separations of heparan sulfate disaccharides. The combined use of 75% acetonitrile with ammonium formate had overall benefits regarding intensity, detection limits, and peak shape for all salt concentrations investigated. Results obtained with the isocratic measurements suggested the potential use of a salt gradient method in order to maximize separation efficiency. A 3-step gradient from 14 mM to 65 mM ammonium formate concentration proved to be ideal for separation and quantitation. The LOD of the resulting method was 0.8-1.5 fmol for the individual disaccharides and the LOQ was between 2.5-5 fmol. Outstanding linearity could be observed up to 2 pmol. This novel combination provided sufficient sensitivity for disaccharide analysis, which was demonstrated by the analysis of heparan sulfate samples from porcine and bovine origin

Deciphering Salt and Solvent Effects in the Chromatographic Separation of Heparan Sulfate Disaccharides

Heparan sulfate (HS) belongs to the class of glycosaminoglycans, it is a polysaccharide consisting of repeating disaccharide units of hexuronic acid and N-acetylglucosamine. The saccharide units can be sulfated at various positions and epimerization may also occur along the chain. These modifications influence interactions of the HS chain with effector proteins such as cytokines and chemokines. Determining the ratio of these different structures is important in understanding the mechanisms underlying several diseases. Analysis of intact HS chains is practically impossible by instrumental analytical tools due to their large size (up to 70 kDa). Characterization of the average sulfation pattern is usually performed after enzymatic hydrolysis of the polymeric chain into the constituent disaccharide units. However, HPLC-MS analysis of HS disaccharides poses a challenge from both chromatography and mass spectrometry sides, due to their diverse polarity and unfavorable ionization characteristics. The aim of our work was to systematically investigate the chromatographic effects of solvent composition, salt concentration, and salt type in isocratic HILIC-WAX separations of HS disaccharides building on our previous results [1]. Acetonitrile-water ratio of the solvent highly influenced both the elution characteristics and ionization efficiency. Altering the salt concentration improved elution characteristics and did not cause ion suppression. Based on these results, we developed a salt gradient operating with self-packed HILIC-WAX µHPLC columns coupled to ESI mass spectrometry working in negative ion mode. Using the salt gradient improved sensitivity and repeatability could be achieved, compared to previous methods using the same resin. It was possible to separate and quantify the unsaturated HS disaccharides down to a few femtomoles, using a relatively short, 20-minute long gradient. Application of the described method was demonstrated in case of biological examples. Sulfation patterns of heparan sulfates determined using the present method enabled HS structural characterization from limited sample amount

Localized Amyloidosis of the Upper Aerodigestive Tract : Complex Analysis of the Cellular Infiltrate and the Amyloid Mass

The aim of this study was to analyse the composition of amyloid mass and the plasmacytic infiltrate of localized amyloidosis of the upper aerodigestive tract.Biopsy materials were studied by light microscopy, immunohistochemistry (IHC), and mRNA in situ hybridization (mRNA-ISH). The amyloid mass was also analysed with high-performance liquid chromatography mass spectrometry- (HPLC-MS-) based proteomics.Nodular and diffuse forms of amyloid deposition were detected. IHC analysis revealed λ-light chain (LC) in two cases, κ-LC in one case. The remaining two were positive with both. Proteins, well known from other amyloidoses like amyloid A (AA), prealbumin/transthyretin (PA), apolipoprotein A-I (ApoAI), and amyloid P component (APC), and also keratin were found with variable intensities in the cases. HPLC-MS revealed dozens of proteins with both LCs in all the lesions but sometimes with surprisingly small intensities. mRNA-ISH analysis revealed identical λ and κ dominance and only one normal κ/λ cell ratio.Cellular infiltrate and protein components in the amyloid showed congruent results in all but one case. The only exception with normal cell ratio and λ-dominant amyloid could be originated from the different protein-secreting activity of plasma cell clones. HPLC-MS analysis explored both LCs in all the amyloid in variable amount, but other proteins with much higher intensities like keratins, apolipoprotein A-IV (ApoAIV), were also detected. Proteins like AA, PA, ApoAI, and APC, previously known about amyloid-forming capability, also appeared. This indicates that localized amyloid in the upper aerodigestive tract is not a homogenous immunoglobulin mass but a mixture of proteins. The sometimes very low light chain intensities might also suggest that not all the localized amyloidosis cases of the upper aerodigestive tract are of convincingly AL type, and the analysis of the cellular infiltrate might indicate that not all are monoclonal

Simple correction improving long-term reproducibility of HPLC-MS

Summary Signal intensities in long series of HPLC-MS experiments often vary, which decrease reproducibility and may cause bias in the results. It was found that the sensitivity of various components change differently; in our case variability is in the order of 20-40%; and it is most likely due to changing conditions in ESI ionization. The most often used intensity correction methods do not take this effect into account. The change in signal intensities (peak areas) can be well described by a polynomial function; we found that a 4th order polynomial is most often suitable. We suggest a simple correction algorithm based on polynomial fitting. When the experiments were inherently well reproducible, this correction improved reproducibility from 12% to 3% (on average for various components). When random errors were larger, this improvement was less significant (15% to 12% in nano-ESI), but nevertheless essential in order to avoid possible bias in the results

Changes in the proteome of sea urchin Paracentrotus lividus coelomocytes in response to LPS injection into the body cavity

The immune system of echinoderm sea urchins is characterised by a high degree of complexity that is not completely understood. The Mediterranean sea urchin Paracentrotus lividus coelomocytes mediate immune responses through phagocytosis, encapsulation of non-self particles, and production of diffusible factors including antimicrobial molecules. Details of these processes, and molecular pathways driving these mechanisms, are still to be fully elucidated.In the present study we treated the sea urchin P. lividus with the bacterial lipopolysaccharide (LPS) and collected coelomocytes at different time-points (1, 3, 6 and 24 hours). We have shown, using label-free quantitative mass spectrometry, how LPS is able to modulate the coelomocyte proteome and to effect cellular pathways, such as endocytosis and phagocytosis, as soon as the immunomodulating agent is injected. The present study has also shown that treatment can modulate various cellular processes such as cytoskeleton reorganisation, and stress and energetic homeostasis.Our data demonstrates, through mass spectrometry and the following functional annotation bioinformatics analysis, how the bacterial wall constituent is sufficient to set off an immune response inducing cytoskeleton reorganisation, the appearance of clusters of heat shock proteins (Hsp) and histone proteins and the activation of the endocytic and phagocytic pathways