Protein identification pipeline for the homology-driven proteomics

Homology-driven proteomics is a major tool to characterize proteomes of organisms with unsequenced genomes. This paper addresses practical aspects of automated homology-driven protein identifications by LC-MS/MS on a hybrid LTQ orbitrap mass spectrometer. All essential software elements supporting the presented pipeline are either hosted at the publicly accessible web server, or are available for free download. (C) 2008 Elsevier B.V. All rights reserved.

Coding behavioural data for cladistic analysis: using dynamic homology without parsimony

Many of the controversies around the concept of homology rest on the subjectivity inherent to primary homology propositions. Dynamic homology partially solves this problem, but there has been up to now scant application of it outside of the molecular domain. This is probably because morphological and behavioural characters are rich in properties, connections and qualities, so that there is less space for conflicting character delimitations. Here we present a new method for the direct optimization of behavioural data, a method that relies on the richness of this database to delimit the characters, and on dynamic procedures to establish character state identity. We use between-species congruence in the data matrix and topological stability to choose the best cladogram. We test the methodology using sequences of predatory behaviour in a group of spiders that evolved the highly modified predatory technique of spitting glue onto prey. The cladogram recovered is fully compatible with previous analyses in the literature, and thus the method seems consistent. Besides the advantage of enhanced objectivity in character proposition, the new procedure allows the use of complex, context-dependent behavioural characters in an evolutionary framework, an important step towards the practical integration of the evolutionary and ecological perspectives on diversity. (C) The Willi Hennig Society 2010.

Changes in histone acetylation and methylation that are important for persistent but not transient expression of CCR4 in human CD4(+) T cells

Although regulation of CXCR3 and CCR4 is related to Th1 and Th2 differentiation, respectively, many CXCR3(+) and CCR4(+) cells do not express IFN-gamma and/or IL-4, suggesting that the chemokine receptor genes might be inducible by mechanisms that are lineage-independent. We investigated the regulation of CXCR3 versus IFNG, and CCR4 versus IL4 in human CD4(+) T cells by analyzing modifications of histone H3. In naive cord-blood cells, under nonpolarizing conditions not inducing IL4, CCR4 was induced to high levels without many of the activation-associated changes in promoter histone H3 found for both IL4 and CCR4 in Th2 cells. Importantly, CCR4 expression was stable in Th2 cells, but fell in nonpolarized cells after the cells were rested; this decline could be reversed by increasing histone acetylation using sodium butyrate. Patterns of histone H3 modifications in CXCR3(+) CCR4(-) and CXCR3(-) CCR4(+) CD4(+) T-cell subsets from adult blood matched those in cells cultured under polarizing conditions in vitro. Our data show that high-level lineage-independent induction of CCR4 can occur following T-cell activation without accessibility-associated changes in histone H3, but that without such changes expression is transient rather than persistent.

The crystal structure of the leptospiral hypothetical protein LIC12922 reveals homology with the periplasmic chaperone SurA

Leptospirosis is a world spread zoonosis caused by members of the genus Leptospira. Although leptospires were identified as the causal agent of leptospirosis almost 100 years ago, little is known about their biology, which hinders the development of new treatment and prevention strategies. One of the several aspects of the leptospiral biology not yet elucidated is the process by which outer membrane proteins (OMPs) traverse the periplasm and are inserted into the outer membrane. The crystal structure determination of the conserved hypothetical protein LIC12922 from Leptospira interrogans revealed a two domain protein homologous to the Escherichia coli periplasmic chaperone SurA. The LIC12922 NC-domain is structurally related to the chaperone modules of E. coli SurA and trigger factor, whereas the parvulin domain is devoid of peptidyl prolyl cis-trans isomerase activity. Phylogenetic analyses suggest a relationship between LIC12922 and the chaperones PrsA, PpiD and SurA. Based on our structural and evolutionary analyses, we postulate that LIC12922 is a periplasmic chaperone involved in OMPs biogenesis in Leptospira spp. Since LIC12922 homologs were identified in all spirochetal genomes sequenced to date, this assumption may have implications for the OMPs biogenesis studies not only in leptospires but in the entire Phylum Spirochaetes. (C) 2010 Elsevier Inc. All rights reserved.

Observation of persistent photoconductivity in vanadyl phthalocyanine

Persistent photoconductivity (PPC) in vanadyl phthalocyanine (VOPc) organic light-emitting diodes was investigated using photoconductive time response, photocurrent-voltage characteristics and charge extraction in linearly increasing voltage (CELIV) measurements. The experiments were performed in phase 1 (amorphous) and in phase 2 (crystalline) samples obtained by the physical vapour deposition (PVD) technique over ITO/glass electrodes with an Al covering electrode. The results indicated a photoconductivity with a long decay time in phase 1 VOPc described by a stretched exponential relaxation. The device showed a rectifying behaviour and the mobility of holes was measured by CELIV, following a dispersive model. In crystalline samples the PPC effect was not observed and the dominant mechanism of transport of holes was hopping in a Gaussian density of states.

The first group (co)homology of a group G with coefficients in some G-modules

Let G be a group. We give some formulas for the first group homology and cohomology of a group G with coefficients in an arbitrary G-module (Z) over tilde. More explicit calculations are done in the special cases of free groups, abelian groups and nilpotent groups. We also perform calculations for certain G-module M, by reducing it to the case where the coefficient is a G-module (Z) over tilde. As a result of the well known equalities H-1(X, M) = H-1(pi(1)(X), M) and H-1(X, M) = H-1(pi(1) (X), M), for any G-module M, we are able to calculate the first homology and cohomology groups of topological spaces with certain local system of coefficients.

Thermoluminescence and synchrotron radiation studies on the persistent luminescence of BaAl(2)O(4)/Eu(2+),Dy(3+)

The persistent luminescence materials, barium aluminates doped with Eu(2+) and Dy(3+) (BaAl(2)O(4): Eu(2+),Dy(3+)), were prepared with the combustion synthesis at temperatures between 400 and 600 degrees C as well as with the solid state reaction at 1500 degrees C. The concentrations of Eu(2+)/Dy(3+) (in mol% of the Ba amount) ranged from 0.1/0.1 to 1.0/3.0. The electronic and defect energy level structures were studied with thermoluminescence (TL) and synchrotron radiation (SR) spectroscopies: UV-VUV excitation and emission, as well as with X-ray absorption near-edge structure (XANES) methods. Theoretical calculations using the density functional theory (DFT) were carried out in order to compare with the experimental data. (C) 2010 Elsevier Inc. All rights reserved.

Optical energy storage properties of Sr(2)MgSi(2)O(7):Eu(2+),R(3+) persistent luminescence materials

The details of the mechanism of persistent luminescence were probed by investigating the trap level structure of Sr(2)MgSi(2)O(7):Eu(2+),R(3+) materials (R: Y, La-Lu, excluding Pm and Eu) with thermoluminescence (TL) measurements and Density Functional Theory (DFT) calculations. The TL results indicated that the shallowest traps for each Sr(2)MgSi(2)O(7):Eu(2+),R(3+) material above room temperature were always ca. 0.7 eV corresponding to a strong TL maximum at ca. 90 A degrees C. This main trap energy was only slightly modified by the different co-dopants, which, in contrast, had a significant effect on the depths of the deeper traps. The combined results of the trap level energies obtained from the experimental data and DFT calculations suggest that the main trap responsible for the persistent luminescence of the Sr(2)MgSi(2)O(7):Eu(2+),R(3+) materials is created by charge compensation lattice defects, identified tentatively as oxygen vacancies, induced by the R(3+) co-dopants.

Persistent luminescence of Eu(2+) and Dy(3+) doped barium aluminate (BaAl(2)O(4):Eu(2+),Dy(3+)) materials

Polycrystalline Eu(2+) and Dy(3+) doped barium aluminate materials, BaAl(2)O(4):Eu(2+),Dy(3+), were prepared with solid state reactions at temperatures between 700 and 1500 degrees C. The influence of the thermal treatments on the stability, homogeneity and structure as well as to the UV-excited and persistent luminescence of the materials was investigated by X-ray powder diffraction, SEM imaging and infrared spectroscopies as well as by steady state luminescence spectroscopy and persistent luminescence decay curves, respectively. The IR spectra of the materials prepared at 250, 700, and 1500 degrees C follow the formation of BaAl(2)O(4) composition whereas the X-ray powder diffraction of compounds revealed how the hexagonal structure was obtained. The morphology of the materials at high temperatures indicated important aggregation due to sintering. The luminescence decay of the quite narrow Eu(2+) band at ca. 500 nm shows the presence of persistent luminescence after UV irradiation. The dopant (Eu(2+)) and co-clopant (Dy(3+)) concentrations affect the crystallinity and luminescence properties of the materials. (C) 2009 Elsevier B.V. All rights reserved.