Density functional study of reactions of phenoxides with polycarbonate

Density functional calculations with simulated annealing have been used to study the reactions of chains of bisphenol A polycarbonate (BPA-PC) with sodium phenoxide (NaOPh), diphenyl carbonate (DPC), and tetraphenylphosphonium phenoxide (PPh4OPh). These calculations extend our work on the reactions of LiOPh, NaOPh, and phenol with the cyclic tetramer of BPA-PC. We study, in particular, chain growth catalyzed by NaOPh and PPh4OH. The energy barriers for reactions with PPh4OPh are somewhat larger than those involving LiOPh and NaOPh, but they are significantly lower than those involving phenol (HOPh), due in part to the collective rearrangement of phenyl groups in the reacting molecules. We discuss in the Appendix the bonds between alkali metal atoms (Na in the present calculations) and other atoms (here oxygen) that are analogous to the more familiar "hydrogen bonds".

From the transformation to the bancarization of the spanishsaving banks: an analysis of the results pursued

This research arises due to the current restructuring process in which is immersed the Spanish banking sector. The above mentioned process is carried out to try to reduce the doubts on the viability of the bank companies to average and long term and to be able to return again the confidence in the sector. Though the economic and financial crisis has concerned the whole banking sector, the subsector of the Spanish savings banks is the one that has experienced a major number of integrations (articulated by means of mergers, absorptions and across Institutional Protection Schemes -IPSs-), and the one that has met submitted to the bancarization process. Considering what has been said, the present paper analyses Spanish saving banks to try to discern whether thanks to that process the objectives pursued by the bank rearrangement have been fulfilled. To do this, the evolution of some important financial variables will be studied over a long period of time (1999-2012). The results suggest that not all the savings banks have seen improved their ratios of efficiency, solvency, financial gap and social work, which indicates that there is still much to be done in order to rectify the problems affecting the studied sector.

Low-frequency electrical response to microbial induced sulfide precipitation

We investigated the sensitivity of low-frequency electrical measurements to microbe-induced metal sulfide precipitation. Three identical sand-packed monitoring columns were used; a geochemical column, an electrical column and a control column. In the first experiment, continuous upward flow of nutrients and metals in solution was established in each column. Cells of Desulfovibrio vulgaris (D. vulgaris) were injected into the center of the geochemical and electrical columns. Geochemical sampling and post-experiment destructive analysis showed that microbial induced sulfate reduction led to metal precipitation on bacteria cells, forming motile biominerals. Precipitation initially occurred in the injection zone, followed by chemotactic migration of D. vulgaris and ultimate accumulation around the nutrient source at the column base. Results from this experiment conducted with metals show (1) polarization anomalies, up to 14 mrad, develop at the bacteria injection and final accumulation areas, (2) the onset of polarization increase occurs concurrently with the onset of lactate consumption, (3) polarization profiles are similar to calculated profiles of the rate of lactate consumption, and (4) temporal changes in polarization and conduction correlate with a geometrical rearrangement of metal-coated bacterial cells. In a second experiment, the same biogeochemical conditions were established except that no metals were added to the flow solution. Polarization anomalies were absent when the experiment was replicated without metals in solution. We therefore attribute the polarization increase observed in the first experiment to a metal-fluid interfacial mechanism that develops as metal sulfides precipitate onto microbial cells and form biominerals. Temporal changes in polarization and conductivity reflect changes in (1) the amount of metal-fluid interfacial area, and (2) the amount of electronic conduction resulting from microbial growth, chemotactic movement and final coagulation. This polarization is correlated with the rate of microbial activity inferred from the lactate concentration gradient, probably via a common total metal surface area effect.

Significantly improved PCR-based clonality testing in B-cell malignancies by use of multiple immunoglobulin gene targets: Report of the BIOMED-2 Concerted Action BHM4-CT98-3936.

Polymerase chain reaction (PCR) assessment of clonal immunoglobulin (Ig) and T-cell receptor (TCR) gene rearrangements is an important diagnostic tool in mature B-cell neoplasms. However, lack of standardized PCR protocols resulting in a high level of false negativity has hampered comparability of data in previous clonality studies. In order to address these problems, 22 European laboratories investigated the Ig/TCR rearrangement patterns as well as t(14;18) and t(11;14) translocations of 369 B-cell malignancies belonging to five WHO-defined entities using the standardized BIOMED-2 multiplex PCR tubes accompanied by international pathology panel review. B-cell clonality was detected by combined use of the IGH and IGK multiplex PCR assays in all 260 definitive cases of B-cell chronic lymphocytic leukemia (n¼56), mantle cell lymphoma (n¼54), marginal zone lymphoma (n¼41) and follicular lymphoma (n¼109). Two of 109 cases of diffuse large B-cell lymphoma showed no detectable clonal marker. The use of these techniques to assign cell lineage should be treated with caution as additional clonal TCR gene rearrangements were frequently detected in all disease categories. Our study indicates that the BIOMED-2 multiplex PCR assays provide a powerful strategy for clonality assessment in B-cell malignancies resulting in high Ig clonality detection rates particularly when IGH and IGK strategies are combined.

T-cell-rich histiocyte-rich B-cell lymphoma of parotid gland

We describe a malignant lymphoma of the parotid gland arising in a patient with Sjögren's syndrome. Diagnosis was established on needle biopsy which showed a mixed population of lymphoid cells. Immunohistochemistry revealed B-lymphoid cells, T-lymphoid cells and histiocytes. Clonal immunoglobulin heavy chain gene rearrangement was demonstrated using the polymerase chain reaction. Within the confines of the small biopsy, the lesion qualifies for the designation T-cell-rich histiocyte-rich B-cell lymphoma. The value of molecular techniques in the diagnosis of malignant lymphoma on limited tissue samples is highlighted by this case.

Site specificity of glycation and carboxymethylation of bovine serum albumin by fructose

We report an investigation of the site specificity, extent and nature of modification of bovine serum albumin (BSA) incubated with fructose or glucose at physiological temperature and pH. Sites of early glycation (Heyns rearrangement products (HRP) from fructose; fructoselysine (FL) from glucose) as well as advanced glycation (N-epsilon-(carboxymethyl)lysine; CML) wereanalyzed by liquid chromatography-mass spectrometry. The major site of modification by fructose, like glucose, is Lysine-524 and this results in, respectively, 31 and 76% loss of the corresponding unmodified tryptic peptide, Gln525-Lys533. In addition, total lysine, HRP, FL, CML and N-epsilon-(carboxyethyl)lysine in the incubations, was quantified. Almost all of the loss of lysine in the fructose-modified BSA was attributed to the formation of CML, with the yield of CML being up to 17-fold higher than glucose-modified BSA. A mechanism for the formation of CML from the HRP is proposed.

Foot-and-mouth disease virus, but not bovine enterovirus, targets the host cell cytoskeleton via the nonstructural protein 3Cpro.

Foot-and-mouth disease virus (FMDV), a member of the Picornaviridae, is a pathogen of cloven-hoofed animals and causes a disease of major economic importance. Picornavirus-infected cells show changes in cell morphology and rearrangement of cytoplasmic membranes, which are a consequence of virus replication. We show here, by confocal immunofluorescence and electron microscopy, that the changes in morphology of FMDV-infected cells involve changes in the distribution of microtubule and intermediate filament components during infection. Despite the continued presence of centrosomes in infected cells, there is a loss of tethering of microtubules to the microtubule organizing center (MTOC) region. Loss of labeling for -tubulin, but not pericentrin, from the MTOC suggests a targeting of -tubulin (or associated proteins) rather than a total breakdown in MTOC structure. The identity of the FMDV protein(s) responsible was determined by the expression of individual viral nonstructural proteins and their precursors in uninfected cells. We report that the only viral nonstructural protein able to reproduce the loss of -tubulin from the MTOC and the loss of integrity of the microtubule system is FMDV 3Cpro. In contrast, infection of cells with another picornavirus, bovine enterovirus, did not affect -tubulin distribution, and the microtubule network remained relatively unaffected.

FACT facilitates chromatin transcription by RNA polymerases I and III

Efficient transcription elongation from a chromatin template requires RNA polymerases (Pols) to negotiate nucleosomes. Our biochemical analyses demonstrate that RNA Pol I can transcribe through nucleosome templates and that this requires structural rearrangement of the nucleosomal core particle. The subunits of the histone chaperone FACT (facilitates chromatin transcription), SSRP1 and Spt16, co-purify and co-immunoprecipitate with mammalian Pol I complexes. In cells, SSRP1 is detectable at the rRNA gene repeats. Crucially, siRNA-mediated repression of FACT subunit expression in cells results in a significant reduction in 47S pre-rRNA levels, whereas synthesis of the first 40 nt of the rRNA is not affected, implying that FACT is important for Pol I transcription elongation through chromatin. FACT also associates with RNA Pol III complexes, is present at the chromatin of genes transcribed by Pol III and facilitates their transcription in cells. Our findings indicate that, beyond the established role in Pol II transcription, FACT has physiological functions in chromatin transcription by all three nuclear RNA Pols. Our data also imply that local chromatin dynamics influence transcription of the active rRNA genes by Pol I and of Pol III-transcribed genes.

Atomistic Insights into Rhodopsin Activation from a Dynamic Model

Rhodopsin, the light sensitive receptor responsible for blue-green vision, serves as a prototypical G protein-coupled receptor (GPCR). Upon light absorption, it undergoes a series of conformational changes that lead to the active form, metarhodopsin II (META II), initiating a signaling cascade through binding to the G protein transducin (G(t)). Here, we first develop a structural model of META II by applying experimental distance restraints to the structure of lumi-rhodopsin (LUMI), an earlier intermediate. The restraints are imposed by using a combination of biased molecular dynamics simulations and perturbations to an elastic network model. We characterize the motions of the transmembrane helices in the LUMI-to-META II transition and the rearrangement of interhelical hydrogen bonds. We then simulate rhodopsin activation in a dynamic model to study the path leading from LUMI to our META II model for wild-type rhodopsin and a series of mutants. The simulations show a strong correlation between the transition dynamics and the pharmacological phenotypes of the mutants. These results help identify the molecular mechanisms of activation in both wild type and mutant rhodopsin. While static models can provide insights into the mechanisms of ligand recognition and predict ligand affinity, a dynamic model of activation could be applicable to study the pharmacology of other GPCRs and their ligands, offering a key to predictions of basal activity and ligand efficacy.

Comparative genomic analysis reveals species-dependent complexities that explain difficulties with microsatellite marker development in molluscs

Reliable population DNA molecular markers are difficult to develop for molluscs, the reasons for which are largely unknown. Identical protocols for microsatellite marker development were implemented in three gastropods. Success rates were lower for Gibbula cineraria compared to Littorina littorea and L. saxatilis. Comparative genomic analysis of 47.2?kb of microsatellite containing sequences (MCS) revealed a high incidence of cryptic repetitive DNA in their flanking regions. The majority of these were novel, and could be grouped into DNA families based upon sequence similarities. Significant inter-specific variation in abundance of cryptic repetitive DNA and DNA families was observed. Repbase scans show that a large proportion of cryptic repetitive DNA was identified as transposable elements (TEs). We argue that a large number of TEs and their transpositional activity may be linked to differential rates of DNA multiplication and recombination. This is likely to be an important factor explaining inter-specific variation in genome stability and hence microsatellite marker development success rates. Gastropods also differed significantly in the type of TEs classes (autonomous vs non-autonomous) observed. We propose that dissimilar transpositional mechanisms differentiate the TE classes in terms of their propensity for transposition, fixation and/or silencing. Consequently, the phylogenetic conservation of non-autonomous TEs, such as CvA, suggests that dispersal of these elements may have behaved as microsatellite-inducing elements. Results seem to indicate that, compared to autonomous, non-autonomous TEs maybe have a more active role in genome rearrangement processes. The implications of the findings for genomic rearrangement, stability and marker development are discussed.

Anomalous fluorinations of 3-aryl-2-hydroxypropanoic esters by diethylaminosulfur trifluoride (DAST).

Anomalous fluorinations of 3-aryl-2-hydroxypropanoic esters by diethylaminosulfur trifluoride (DAST). Haigh, David; Jefcott, Lee J.; Magee, Katherkine; McNab, Hamish. Dep. Med. chem., SmithKline Beecham Pharmaceuticals, Epsom, UK. Journal of the Chemical Society, Perkin Transactions 1: Organic and Bio-Organic Chemistry (1996), (24), 2895-2900. Publisher: Royal Society of Chemistry, CODEN: JCPRB4 ISSN: 0300-922X. Journal written in English. CAN 126:143928 AN 1997:56534 CAPLUS (Copyright (C) 2009 ACS on SciFinder (R)) Abstract Treatment of 3-aryl-2-hydroxypropanoic esters with diethylaminosulfur trifluoride (DAST) gives considerable amts. of rearranged 2-aryl-3-fluoropropanoic esters, together with the expected products. The extent of rearrangement is dependent on solvent and on the substitution pattern of the aryl ring; the mechanism of rearrangement probably involves anchimeric assistance by the aryl group in the SN1 component of the reaction pathway. Reaction of the isomeric 3-hydroxy-2-phenylpropanoic ester shows much less rearrangement under similar conditions, and an elimination product is also obtained.

Lymphocytic gastritis-like T cell lymphoma: molecular evidence of an unusual recurrence

This report describes a patient with a gastric biopsy specimen showing histomorphological and immunohistochemical appearances indistinguishable from those usually present in lymphocytic gastritis, a rare condition of unknown aetiology with a distinctive phenotype. The patient had a history of a biopsy confirmed T cell non-Hodgkin lymphoma at two anatomical sites ( bladder and stomach), which was subsequently treated. Molecular analysis of the T cell receptor (TCR) gamma chain gene rearrangements showed a distinct monoclonal T cell population in the bladder and gastric biopsies. The same analysis in the lymphocytic gastritis-like biopsy sample showed a monoclonal population with identical base pair size to that identified in the other specimens. This report highlights the importance of TCR gene rearrangement analysis in the diagnosis of unusual gastric inflammation, and the use of capillary electrophoresis based polymerase chain reaction in the follow up of lymphoproliferative disorders.

Metastable anions of dinitrobenzene: Resonances for electron attachment and kinetic energy release

Attachment of free, low-energy electrons to dinitrobenzene (DNB) in the gas phase leads to DNB as well as several fragment anions. DNB, (DNB-H), (DNB-NO), (DNB-2NO), and (DNB-NO2) are found to undergo metastable (unimolecular) dissociation. A rich pattern of resonances in the yield of these metastable reactions versus electron energy is observed; some resonances are highly isomer-specific. Most metastable reactions are accompanied by large average kinetic energy releases (KER) that range from 0.5 to 1.32 eV, typical of complex rearrangement reactions, but (1,3-DNB-H)(-) features a resonance with a KER of only 0.06 eV for loss of NO. (1,3-DNB-NO)(-) offers a rare example of a sequential metastable reaction, namely, loss of NO followed by loss of CO to yield C5H4O- with a large KER of 1.32 eV. The G4(MP2) method is applied to compute adiabatic electron affinities and reaction energies for several of the observed metastable channels. (C) 2010 American Institute of Physics. [doi:10.1063/1.3514931]

Thermodynamical studies of irreversible sorption of CO2 by Wyodak coal

Differential scanning calorimetry (DSC), temperature programmed desorption mass spectrometry (TPD-MS) and small angle neutron scattering (SANS) were used to investigate CO2 uptake by the Wyodak coal. The adsorption of carbon dioxide on Wyodak coal was studied by DSC. The exotherms evident at low temperatures are associated with the uptake of CO2 suggesting that carbon dioxide interacts strongly with the coal surface. The reduction in the value of the exotherms between the first and second runs for the Wyodak coal suggests that some CO2 is irreversibly bound to the structure even after heating to 200 °C DSC results also showed that adsorption of CO2 on the coal surface is an activated process and presumably at the temperature of the exotherms there is enough thermal energy to overcome the activation energy for adsorption. The adsorption process is instantly pursued by much slower diffusion of the gas molecules into the coal matrix (absorption). Structural rearrangement in coal by CO2 is examined by change in the glass transition temperature of coal after CO2 uptake at different pressures. The amount of gas dissolved in the coal increases with increasing CO2 pressure. TPD-MS showed that CO2 desorption from the Wyodak coal follows a first order kinetic model. Increase in the activation energy for desorption with pre-adsorbed CO2 pressure suggests that higher pressures facilitate the transport of CO2 molecules through the barriers therefore the amount of CO2 uptake by the coal is greater at higher pressures and more attempts are required to desorb CO2 molecules sorbed at elevated pressures. These conclusions were further confirmed by examining the Wyodak coal structure in high pressure CO 2 by SANS.

Study of structural change in Wyodak coal in high pressure CO2 by small-angle neutron scattering

Small angle neutron scattering (SANS) has been applied to examine the effect of high pressure CO2 on the structure of Wyodak coal. Significant decrease in the scattering intensities upon exposure of the coal to high pressure CO2 showed that high pressure CO2 rapidly adsorbs on the coal and reaches to all pores in the structure. This is confirmed by strong and steep exothermic peaks observed on DSC scans during coal/ CO2 interactions. In situ small angle neutron scattering on coal at high pressure CO2 atmosphere showed an increase in scattering intensities with time suggesting that after adsorption, high pressure CO2 immediately begins to diffuse into the coal matrix, changes the macromolecular structure of the coal, swells the matrix and probably creates microporosity in coal structure by extraction of volatile components from coal. Significant decrease in the glass transition temperature of coal caused by high pressure CO2 also confirms that CO2 at elevated pressures dissolve in the coal matrix, results in significant plasticization and physical rearrangement of the coal’s macromolecular structure.