Peptidomic Analysis of Human Cell Lines

Peptides have been proposed to function in intracellular signaling within the cytosol. Although cytosolic peptides are considered to be highly unstable, a large number of peptides have been detected in mouse brain and other biological samples. In the present study, we evaluated the peptidome of three diverse cell lines: SH-SY5Y, MCF7, and HEIC293 cells. A comparison of the peptidomes revealed considerable overlap in the identity of the peptides found in each cell line. The majority of the observed peptides are not derived from the most abundant or least stable proteins in the cell, and approximately half of the cellular peptides correspond to the N- or C- termini of the precursor proteins. Cleavage site analysis revealed a preference for hydrophobic residues in the PI position. Quantitative peptidomic analysis indicated that the levels of most cellular peptides are not altered in response to elevated intracellular calcium, suggesting that calpain is not responsible for their production. The similarity of the peptidomes of the three cell lines and the lack of correlation with the predicted cellular degradome implies the selective formation or retention of these peptides, consistent with the hypothesis that they are functional in the cells.

The non-twist standard map with robust tori

The non-twist standard map occurs frequently in many fields of science specially in modelling the dynamics of the magnetic field lines in tokamaks. Robust tori, dynamical barriers that impede the radial transport among different regions of the phase space, are introduced in the non-twist standard map in a conservative fashion. The resulting non-twist standard map with robust tori is an improved model to study transport barriers in plasmas confined in tokamaks.

Plasma confinement in tokamaks with robust torus

We present a non-linear symplectic map that describes the alterations of the magnetic field lines inside the tokamak plasma due to the presence of a robust torus (RT) at the plasma edge. This RT prevents the magnetic field lines from reaching the tokamak wall and reduces, in its vicinity, the islands and invariant curve destruction due to resonant perturbations. The map describes the equilibrium magnetic field lines perturbed by resonances created by ergodic magnetic limiters (EMLs). We present the results obtained for twist and non-twist mappings derived for monotonic and non-monotonic plasma current density radial profiles, respectively. Our results indicate that the RT implementation would decrease the field line transport at the tokamak plasma edge. (C) 2010 Elsevier B.V. All rights reserved.

2-(4,5,6,7-tetrafluorobenzimidazol-2-yl)-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazole-3-oxide-1-oxyl, a hydrogen-bonded organic quasi-1D ferromagnet

The title radical (F4BlmNN) is a stable nitronylnitroxide that forms hydrogen-bonded NH center dot center dot center dot ON chains in the solid state. The chains assemble the F4BlmNN molecules to form stacked contacts between the radical groups, in a geometry that is expected to exhibit ferromagnetic (FM) exchange based on spin polarization (SP) models. The experimental magnetic susceptibility of F4BlmNN confirms the expectation, showing 1-D Heisenberg chain FM exchange behavior over 1.8-300 K with an intrachain exchange constant Of J(chain)/k = +22 K. At lower temperatures, ac magnetic susceptibility and variable field heat capacity measurements show that F4BlmNN acts as a quasi-1-D ferromagnet. The dominant ferromagnetic exchange interaction is attributable to overlap between spin orbitals of molecules within the hydrogen-bonded chains, consistent with the SP model expectations. The chains appear to be antiferromagnetically exchange coupled, giving cusps in the ac susceptibility and zero field heat capacity at lower temperatures. The results indicate that the sample orders magnetically at about 0.7 K. The magnetic heat capacity ordering cusp shifts to lower temperatures as external magnetic field increases, consistent with forming a bulk antiferromagnetic phase below a Neel temperature of T-N(0) = 0.72 K, with a critical field of H-c approximate to 1800 Oe. The interchain exchange is estimated to be zJ/k congruent to (-)0.1 K.

Electrical transport in disordered and ordered magnetic domains under pressures and magnetic fields

Magnetic M( T, H, P) and electrical transport.( T, H, P) measurements in a strong spin-lattice-charge coupled La(0.7)Ca(0.3)MnO(3) system have been conducted. The application of H and P leads to the formation of different magnetic domain structures in the vicinity and below the polaronic-to-ferromagnetic transition temperature. The charge mobility is more sensitive to the variation of the spatial wave function overlap between Mn(3+) eg and O(2-) 2p orbitals due to the applied compacting pressure rather than the relative spin orientation between neighbouring Mn ions when the magnetic field is applied. In spite of the presence of different magnetic domain structures due to the sample history, the effect of magnetic field and pressure is less pronounced at lower temperatures on electrical transport properties.

Large Changes of Static Electric Properties Induced by Hydrogen Bonding: An ab Initio Study of Linear HCN Oligomers

We report the partitioning of the interaction-induced static electronic dipole (hyper)polarizabilities for linear hydrogen cyanide complexes into contributions arising from various interaction energy terms. We analyzed the nonadditivities of the studied properties and used these data to predict the electric properties of an infinite chain. The interaction-induced static electric dipole properties and their nonadditivities were analyzed using an approach based on numerical differentiation of the interaction energy components estimated in an external electric field. These were obtained using the hybrid variational-perturbational interaction energy decomposition scheme, augmented with coupled-cluster calculations, with singles, doubles, and noniterative triples. Our results indicate that the interaction-induced dipole moments and polarizabilities are primarily electrostatic in nature; however, the composition of the interaction hyperpolarizabilities is much more complex. The overlap effects substantially quench the contributions due to electrostatic interactions, and therefore, the major components are due to the induction and exchange induction terms, as well as the intramolecular electron-correlation corrections. A particularly intriguing observation is that the interaction first hyperpolarizability in the studied systems not only is much larger than the corresponding sum of monomer properties, but also has the opposite sign. We show that this effect can be viewed as a direct consequence of hydrogen-bonding interactions that lead to a decrease of the hyperpolarizability of the proton acceptor and an increase of the hyperpolarizability of the proton donor. In the case of the first hyperpolarizability, we also observed the largest nonadditivity of interaction properties (nearly 17%) which further enhances the effects of pairwise interactions.

Langmuir-Blodgett films of diazobenzene molecules

Langmuir-Blodgett (LB) films from diazobenzene Sudan III have been investigated using surface potential measurements as a function of number of layers and deposition pressures, with the surface potential data being related to molecular dipole moments obtained from theoretical electronic structure calculations. The surface potential increased with the number of layers for SIII LB films, and then tended to saturate. Results from density functional theory (DIFT) and UV-vis spectroscopy indicated that the increase is due to addition of layers with oriented molecular dipoles, with the saturation tendency being attributed to a decrease in the amount of material deposited in each layer. The surface potential increased with the surface pressure used for deposition, probably owing to a higher contribution from the vertical component of the dipole moment as a closer molecular packing, which is associated with decreasing conformational entropy, was reached. (C) 2008 Elsevier Inc. All rights reserved.

Epidemics in networks of spatially correlated three-dimensional root-branching structures

Using digitized images of the three-dimensional, branching structures for root systems of bean seedlings, together with analytical and numerical methods that map a common susceptible-infected- recovered (`SIR`) epidemiological model onto the bond percolation problem, we show how the spatially correlated branching structures of plant roots affect transmission efficiencies, and hence the invasion criterion, for a soil-borne pathogen as it spreads through ensembles of morphologically complex hosts. We conclude that the inherent heterogeneities in transmissibilities arising from correlations in the degrees of overlap between neighbouring plants render a population of root systems less susceptible to epidemic invasion than a corresponding homogeneous system. Several components of morphological complexity are analysed that contribute to disorder and heterogeneities in the transmissibility of infection. Anisotropy in root shape is shown to increase resilience to epidemic invasion, while increasing the degree of branching enhances the spread of epidemics in the population of roots. Some extension of the methods for other epidemiological systems are discussed.

The CATH Hierarchy Revisited-Structural Divergence in Domain Superfamilies and the Continuity of Fold Space

This paper explores the structural continuum in CATH and the extent to which superfamilies adopt distinct folds. Although most superfamilies are structurally conserved, in some of the most highly populated superfamilies (4% of all superfamilies) there is considerable structural divergence. While relatives share a similar fold in the evolutionary conserved core, diverse elaborations to this core can result in significant differences in the global structures. Applying similar protocols to examine the extent to which structural overlaps occur between different fold groups, it appears this effect is confined to just a few architectures and is largely due to small, recurring super-secondary motifs (e.g., alpha beta-motifs, alpha-hairpins). Although 24% of superfamilies overlap with superfamilies having different folds, only 14% of nonredundant structures in CATH are involved in overlaps. Nevertheless, the existence of these overlaps suggests that, in some regions of structure space, the fold universe should be seen as more continuous.

The CATH classification revisited-architectures reviewed and new ways to characterize structural divergence in superfamilies

The latest version of CATH (class, architecture, topology, homology) (version 3.2), released in July 2008 (http://www.cathdb.info), contains 1 14215 domains, 2178 Homologous superfamilies and 1110 fold groups. We have assigned 20 330 new domains, 87 new homologous superfamilies and 26 new folds since CATH release version 3.1. A total of 28 064 new domains have been assigned since our NAR 2007 database publication (CATH version 3.0). The CATH website has been completely redesigned and includes more comprehensive documentation. We have revisited the CATH architecture level as part of the development of a `Protein Chart` and present information on the population of each architecture. The CATHEDRAL structure comparison algorithm has been improved and used to characterize structural diversity in CATH superfamilies and structural overlaps between superfamilies. Although the majority of superfamilies in CATH are not structurally diverse and do not overlap significantly with other superfamilies, similar to 4% of superfamilies are very diverse and these are the superfamilies that are most highly populated in both the PDB and in the genomes. Information on the degree of structural diversity in each superfamily and structural overlaps between superfamilies can now be downloaded from the CATH website.

gamma-zein secondary structure in solution by circular dichroism

The proline-rich N-terminal domain of gamma-zein has been reported in relevant process, which include its ability to cross the cell membranes. Evidences indicate that synthetic hexapeptide (PPPVHL), naturally found in N-terminal portion of gamma-zein, can adopt the polyproline II (PPII) conformation in aqueous solution. The secondary structure of gamma-zein in maize protein bodies had been analyzed by solid state Fourier transform infrared and nuclear magnetic resonance spectroscopies. However, it was not possible to measure PPII content in physiological environment since the beta-sheet and PPII signals overlap in both solid state techniques. Here, the secondary structure of gamma-zein has been analyzed by circular dichroism in SDS aqueous solution with and without ditiothreitol (DTT), and in 60% of 2-propanol and water with DTT The results show that gamma-zein has high helical content in all solutions. The PPII conformation was present at about 7% only in water/DTT solution. (c) 2007 Wiley Periodicals, Inc.

Mice and larvae tracking using a particle filter with an auto-adjustable observation model

This paper proposes a novel way to combine different observation models in a particle filter framework. This, so called, auto-adjustable observation model, enhance the particle filter accuracy when the tracked objects overlap without infringing a great runtime penalty to the whole tracking system. The approach has been tested under two important real world situations related to animal behavior: mice and larvae tracking. The proposal was compared to some state-of-art approaches and the results show, under the datasets tested, that a good trade-off between accuracy and runtime can be achieved using an auto-adjustable observation model. (C) 2009 Elsevier B.V. All rights reserved.

Cordierite-bearing lavas from Jaguarao, southern Brazil: Petrological evidence for crustal melts during early rifting of Gondwana

The Jaguarao stratoid dacites (Rio Grande do Sul, Brazil) are limited in areal extent, are comprised of about 3.2 km(3) of preserved erupted material, and outcrop only in areas of the region underlain by mylonitic and ultramylonitic rocks. They are S-type volcanic rocks containing cordierite, orthopyroxene, plagioclase, and ilmenite as liquidus phases, and partially melted granite, gneiss, and migmatite enclaves that are very similar to the Precambrian basement rocks. The Jaguarao lavas have distinct geochemical signatures and Sr-Nd isotopes with respect to other volcanic rocks of the region. Available geochronological data for Jaguarao dacites range between 157 +/- 5 Ma and 139.6 +/- 7.4 Ma. Considering the errors, the younger ages obtained for Jaguarao lavas overlap the 138-128 Ma age of rocks of the Serra Geral Group, and thus indicate that the dacites were erupted prior to the break-up of Gondwana in this region. Petrographic, mineralogical, and petrochemical data, as well as the tectonic context of the Jaguarao lavas, suggest that magma genesis was linked, at least in part, to friction melts. The dacitic magma was generated by partial melting reactions involving biotite breakdown in a dominantly quartz-feldspathic source terrane, leaving a granulite facies residue in subsurface. These melts were probably generated as a consequence of crustal thinning linked to simple shear extension just prior to Gondwana break-up and rifting of the southern Atlantic Ocean. (C) 2009 International Association for Gondwana Research. Published by Elsevier B.V. All rights reserved.

Early Onset Obsessive-Compulsive Disorder With and Without Tics

Introduction: Research suggests that obsessive-compulsive disorder (OCD) is not a unitary entity, but rather a highly heterogeneous condition, with complex and variable clinical manifestations. Objective: The aims of this study were to compare clinical and demographic characteristics of OCD patients with early and late age of onset of obsessive-compulsive symptoms (OCS); and to compare the same features in early onset OCD with and without tics. The independent impact of age at onset and presence of tics on comorbidity patterns was investigated. Methods: Three hundred and thirty consecutive outpatients meeting Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition criteria for OCD were evaluated: 160 patients belonged to the ""early onset"" group (EOG): before 11 years of age, 75 patients had an ""intermediate onset"" (IOG), and 95 patients were from the ""late onset"" group (LOG): after 18 years of age. From the 160 EOG, 60 had comorbidity with tic disorders. The diagnostic instruments used were: the Yale-Brown Obsessive Compulsive Scale and the Dimensional Yale-Brown Obsessive Compulsive Scale (DY-BOCS), Yale Global Tics Severity Scale; and Structured Clinical Interview for DSM-IV Axis I Disorders-patient edition. Statistical tests used were: Mann-Whitney, full Bayesian significance test, and logistic regression. Results: The EOG had a predominance of males, higher frequency of family history of OCS, higher mean scores on the ""aggression/violence"" and ""miscellaneous"" dimensions, and higher mean global DY-BOCS scores. Patients with EOG without tic disorders presented higher mean global DY-BOCS scores and higher mean scores in the ""contamination/cleaning"" dimension. Conclusion: The current results disentangle some of the clinical overlap between early onset OCD with and without tics. CNS Spectr. 2009; 14(7):362-370

Photoluminescence study of new lanthanide complexes with benzeneseleninic acids

New lanthanide complexes with benzeneseleninic (ABSe) and 4-chloro-benzeneseleninic (ABSeCl) acids have been synthesized and characterized by elemental analysis, infrared and UV-visible spectroscopies. The emission spectra of the trivalent europium complexes presented the typical electronic (5)D(0) -> (7)F(j) transitions of the ion (J = 0-4). The ground-state geometries of the europium complexes have been calculated by using the Sparkle/AM1 model. From these results, the 4f-4f intensity parameters and energies of the ligand singlet and triplet excited states have been obtained. The lower emission quantum yield for the [Eu(ABSe)(3)(H(2)O)(2)](H(2)O)(2) compound, as compared to the [Eu(Al(3)SeCl)(3)(H(2)O)(2)] one, can be associated to the higher numbers of water molecules, in the first and second coordination spheres, that contribute to the luminescence quenching. The [Eu(Al(3)Se)(3)(H(2)O)(2)](H(2)O)(2) complex presents an intermediate state whose energy difference with respect to the first excited singlet state is resonant with three phonons from the water molecules, favouring a multiphonon relaxation process from the singlet state followed by a fast internal conversion process; this effect is less pronounced in the complex with the ABSeCl ligand. The luminescence decay curves of the gadolinium complexes indicate that the level responsible for the intramolecular energy transfer process has a triplet character for both compounds. The nephelauxetic effect in these compounds was investigated under the light of a recently proposed covalency scale based on the concept of overlap polarizability of the chemical bond. (C) 2009 Elsevier B.V. All rights reserved.