Protein secondary structure conformations and associated hydrophobicity scales

We have developed conformational preference functions and a hierarchy of algorithms that can evaluate the success of each hydrophobicity scale in predicting protein secondary conformation. The results of such evaluation are shown for fiftyfive different scales with respect to their ability to predict -helix, -sheet and coil structure in three testing sets of proteins: five integral membrane proteins, twelve -class and sixteen -class soluble proteins. Our scale of conformational parameters is the best predictor of secondary structure segments in membrane proteins and -class proteins. The success rate and correlation coefficient for -helix conformation in membrane proteins are 76% and 0.46 respectively, which is superior to the performance measures attained with other prediction schemes. Evaluation of solution hydrophobicity scales, often used to predict transmembrane segments in membrane proteins, indicated absence of correlation in prediction of helix segments and experimental results for the conformation of membrane proteins. Such scales have better performance (correlation coefficient around 0.30) in predicting sheet conformation in the -class proteins.     

Quantitative pharmacokinetic analysis of DCE-MRI data without an arterial input function: a reference region model

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) can assess tumor perfusion, microvascular vessel wall permeability and extravascular-extracellular volume fraction. Analysis of DCE-MRI data is usually based on indicator dilution theory that requires knowledge of the concentration of the contrast agent in the blood plasma, the arterial input function (AIF). A method is presented that compares the tissues of interest (TOI) curve shape to that of a reference region (RR), thereby eliminating the need for direct AIF measurement. By assigning literature values for Ktrans (the blood perfusion-vessel permeability product) and v(e) (extravascular-extracellular volume fraction) in a reference tissue, it is possible to extract the Ktrans and v(e) values for a TOI without knowledge of the AIF. The operational RR equation for DCE-MRI analysis is derived, and its sensitivity to noise and incorrect assignment of the RR parameters is tested via simulations. The method is robust at noise levels of 10%, returning accurate (+/-20% in the worst case) and precise (+/-15% in the worst case) values. Errors in the TOI Ktrans and v(e) values scale approximately linearly with the errors in the assigned RR Ktrans and v(e) values. The methodology is then applied to a Lewis Lung Carcinoma mouse tumor model. A slowly enhancing TOI yielded Ktrans=0.039+/-0.002 min-1 and v(e)=0.46+/-0.01, while a rapidly enhancing region yielded Ktrans=0.35+/-0.05 min-1 and v(e)=0.31+/-0.01. Parametric Ktrans and v(e) mappings manifested a tumor periphery with elevated Ktrans (>0.30 min-1) and v(e) (>0.30) values. The main advantage of the RR approach is that it allows for quantitative assessment of tissue properties without having to obtain high temporal resolution images to characterize an AIF. This allows for acquiring images with higher spatial resolution and/or SNR, and therefore, increased ability to probe tissue heterogeneity.     

A planar tetracoordinate carbon and unusual bonding in an organodimetallic propynylidene complex arising from double C-H activation of an allene ligand

Reduction of the organoditantalum allene complex (eta-C5Me4R)2Ta2(mu-X)X3(mu-eta1,eta3-C3H4) (R = Me (Cp*), Et; X = Cl, Br) with sodium amalgam leads to the propynylidene complex (eta-C5Me4R)2Ta2(mu-H)2X2(mu-HCCCH) by a formal double 1,3-C-H activation of the allene ligand. The solid-state molecular structure contains a planar HCCCH ligand bridging, in parallel coordination mode, the two tantalum atoms, with the HCCCH and Ta atoms coplanar. Key structural features are a Ta-Ta distance of 2.8817(7) A, propynylidene C-C-C angle of 153.7(13) degrees , C-C distance of 1.370(8) A, Ta-C(central) distance of 2.194(9) A, and Ta-C(terminal) distance of 1.970(9) A. Molecular orbital calculations on the complex at the RHF/SBK(d) and B3LYP/LanL2dz levels of theory demonstrate that the propynylidene ligand is best viewed formally as an allenediylidene(4-) ligand bonded to two d0 tantalum atoms via two Ta=C(terminal) double bonds and an unusual three-center, two-electron bridge bond involving both tantalum atoms and a lone pair on the planar, tetracoordinate central carbon. There is no net Ta-Ta bonding based on the orbital analysis.     

Ethanol Production from Residual Wood Chips of Cellulose Industry: Acid Pretreatment Investigation,Hemicellulosic Hydrolysate Fermentation,and Remaining Solid Fraction Fermentation by SSF Process

Current research indicates the ethanol fuel production from lignocellulosic materials, such as residual wood chips from the cellulose industry, as new emerging technology. This work aimed at evaluating the ethanol production from hemicellulose of eucalyptus chips by diluted acid pretreatment and the subsequent fermentation of the generated hydrolysate by a flocculating strain of Pichia stipitis. The remaining solid fraction generated after pretreatment was subjected to enzymatic hydrolysis, which was carried out simultaneously with glucose fermentation [saccharification and fermentation (SSF) process] using a strain of Saccharomyces cerevisiae. The acid pretreatment was evaluated using a central composite design for sulfuric acid concentration (1.0–4.0 v/v) and solid to liquid ratio (1:2–1:4, grams to milliliter) as independent variables. A maximum xylose concentration of 50 g/L was obtained in the hemicellulosic hydrolysate. The fermentation of hemicellulosic hydrolysate and the SSF process were performed in bioreactors and the final ethanol concentrations of 15.3 g/L and 28.7 g/L were obtained, respectively.     

Photoemission study on the valence band of a β-FeSi2 thin film using synchrotron radiation

Resonant and constant-initial state photoemission spectroscopies using synchrotron radiation were applied to investigate the valence-band electronic structure of a semi-conducting β-type iron-disilicide (β-FeSi(2)) thin film. The results clearly indicated that the component elements, iron (Fe) and silicon (Si), contribute differently to the valence band features; the Fe 3d orbitals mainly concentrate in the top region of the valence band while the Si 3s and 3p orbitals spread over the wide region of the valence band. The β-FeSi(2) thin film showed a typical p-type semi-conducting nature with a work function of 4.78 eV. The β-FeSi(2) film showed the Fe M(1)VV Auger lines around the kinetic energy of 88 eV. It would be expected from these observations that there exist strong interactions between iron and silicon atoms in the β-FeSi(2) film resulting in orbital mixing and band formation.     

Shimalactone Biosynthesis Involves Spontaneous Double Bicyclo-Ring Formation with 8π-6π Electrocyclization

Shimalactones A and B are neuritogenic polyketides possessing characteristic oxabicyclo[2.2.1]heptane and bicyclo[4.2.0]octadiene ring systems that are produced by the marine fungus Emericella variecolor GF10. We identified a candidate biosynthetic gene cluster and conducted heterologous expression analysis. Expression of ShmA polyketide synthase in Aspergillus oryzae resulted in the production of preshimalactone. Aspergillus oryzae and Saccharomyces cerevisiae transformants expressing ShmA and ShmB produced shimalactones A and B, thus suggesting that the double bicyclo-ring formation reactions proceed non-enzymatically from preshimalactone epoxide. DFT calculations strongly support the idea that oxabicyclo-ring formation and 8π-6π electrocyclization proceed spontaneously after opening of the preshimalactone epoxide ring through protonation. We confirmed the formation of preshimalactone epoxide in vitro, followed by its non-enzymatic conversion to shimalactones in the dark.     

Preparation and Characterization of Carbon Nano‐Onion/PEDOT:PSS Composites

Composites of unmodified or oxidized carbon nano‐onions (CNOs/ox‐CNOs) with poly(3,4‐ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) are prepared with different compositions. By varying the ratio of PEDOT:PSS relative to CNOs, CNO/PEDOT:PSS composites with various PEDOT:PSS loadings are obtained and the corresponding film properties are studied as a function of the polymer. X‐ray photoelectron spectroscopy characterization is performed for pristine and ox‐CNO samples. The composites are characterized by scanning and transmission electron microscopy and differential scanning calorimetry studies. The electrochemical properties of the nanocomposites are determined and compared. Doping the composites with carbon nanostructures significantly increases their mechanical and electrochemical stabilities. A comparison of the results shows that CNOs dispersed in the polymer matrices increase the capacitance of the CNO/PEDOT:PSS and ox‐CNO/PEDOT:PSS composites.     

Accompanying of parameters of color,gloss and hardness on polymeric films coated with pigmented inks cured by different radiation doses of ultraviolet light

In the search for alternatives to traditional paint systems solvent-based, the curing process of polymer coatings by ultraviolet light (UV) has been widely studied and discussed, especially because of their high content of solids and null emission of VOC. In UV-curing technology, organic solvents are replaced by reactive diluents, such as monomers. This paper aims to investigate variations on color, gloss and hardness of print inks cured by different UV radiation doses. The ratio pigment/clear coating was kept constant. The clear coating presented higher average values for König hardness than pigmented ones, indicating that UV-light absorption has been reduced by the presence of pigments. Besides, they have indicated a slight variation in function of cure degree for the studied radiation doses range. The gloss loss related to UV light exposition allows inferring that some degradation occurred at the surface of print ink films.