Evolutionary Patterns in Coiled-Coils

Models of protein evolution are used to describe evolutionary processes, for phylogenetic analyses and homology detection. Widely used general models of protein evolution are biased toward globular domains and lack resolution to describe evolutionary processes for other protein types. As three-dimensional structure is a major constraint to protein evolution, specific models have been proposed for other types of proteins. Here, we consider evolutionary patterns in coiled-coil forming proteins. Coiled-coils are widespread structural domains, formed by a repeated motif of seven amino acids (heptad repeat). Coiled-coil forming proteins are frequently rods and spacers, structuring both the intracellular and the extracellular spaces that often form protein interaction interfaces. We tested the hypothesis that due to their specific structure the associated evolutionary constraints differ from those of globular proteins. We showed that substitution patterns in coiled-coil regions are different than those observed in globular regions, beyond the simple heptad repeat. Based on these substitution patterns we developed a coiled-coil specific (CC) model that in the context of phylogenetic reconstruction outperforms general models in tree likelihood, often leading to different topologies. For multidomain proteins containing both a coiled-coil region and a globular domain, we showed that a combination of the CC model and a general one gives higher likelihoods than a single model. Finally, we showed that the model can be used for homology detection to increase search sensitivity for coiled-coil proteins. The CC model, software, and other supplementary materials are available at http://www.evocell.org/cgl/resources (last accessed January 29, 2015).FCT fellowship: (SFRH/BD/51880/2012)

Rabifier2: an improved bioinformatic classifier of Rab GTPases

SUMMARY: The Rab family of small GTPases regulates and provides specificity to the endomembrane trafficking system; each Rab subfamily is associated with specific pathways. Thus, characterization of Rab repertoires provides functional information about organisms and evolution of the eukaryotic cell. Yet, the complex structure of the Rab family limits the application of existing methods for protein classification. Here, we present a major redesign of the Rabifier, a bioinformatic pipeline for detection and classification of Rab GTPases. It is more accurate, significantly faster than the original version and is now open source, both the code and the data, allowing for community participation. AVAILABILITY AND IMPLEMENTATION: Rabifier and RabDB are freely available through the web at http://rabdb.org. The Rabifier package can be downloaded from the Python Package Index at https://pypi.python.org/pypi/rabifier, the source code is available at Github https://github.com/evocell/rabifier

Aurora at the pole and equator: overlapping functions of Aurora kinases in the mitotic spindle

The correct assembly and timely disassembly of the mitotic spindle is crucial for the propagation of the genome during cell division. Aurora kinases play a central role in orchestrating bipolar spindle establishment, chromosome alignment and segregation. In most eukaryotes, ranging from amoebas to humans, Aurora activity appears to be required both at the spindle pole and the kinetochore, and these activities are often split between two different Aurora paralogues, termed Aurora A and B. Polar and equatorial functions of Aurora kinases have generally been considered separately, with Aurora A being mostly involved in centrosome dynamics, whereas Aurora B coordinates kinetochore attachment and cytokinesis. However, double inactivation of both Aurora A and B results in a dramatic synergy that abolishes chromosome segregation. This suggests that these two activities jointly coordinate mitotic progression. Accordingly, recent evidence suggests that Aurora A and B work together in both spindle assembly in metaphase and disassembly in anaphase. Here, we provide an outlook on these shared functions of the Auroras, discuss the evolution of this family of mitotic kinases and speculate why Aurora kinase activity may be required at both ends of the spindle microtubules

Within-tree and between-tree variation of wood density components in cork oak trees in two sites in Portugal

The axial and radial variation of wood density was studied using microdensitometry in cork oaks ( Quercus suber ) in two sites in Portugal. The observations were made in mature trees under cork production and in juvenile trees before the fi rst cork extraction, at three height levels (stem base, 1.3 m and before stem bifurcation). The cork oak wood revealed a very high mean density (0.884 – 1.068 g cm 3 ). Differences between earlywood and latewood were small (0.866 and 1.061 g cm 3 , respectively). Latewood corresponded on average to 61 per cent of the total. The variation of density between trees was statistically highly signifi cant, but no differences were found between the two sites. The within-tree axial variation was negligible but the radial direction within a cross-section was one of the main origins of variation of the density components (18 per cent of the total variation). The density decreased from pith to cambium and this radial variation corresponded to 19 – 24 per cent of the total variation of wood density. Overall, the magnitude of density variations between and within cork oaks was small and an advantageous factor for their use for quality wood productsinfo:eu-repo/semantics/publishedVersio

Melhor Suporte Nutricional — «Melhor» Composição Corporal? Uma Análise em Recém-Nascidos de Baixo Peso

Objectivo: Avaliar o impacto de diferentes estratégias de suporte nutricional na composição corporal de recém-nascidos de baixo peso (RNBP), por intermédio não só do peso, mas também das áreas muscular braquial (AMB) e adiposa braquial (AAB). Indivíduos e métodos: Comparou-se a média do dia de recuperação do peso, da AMB e da AAB entre dois grupos de RNBP assistidos em períodos distintos, com suportes nutricionais diferentes — grupo I (n=10): 1991 versus grupo II (n=24): 1995/96. Os recém-nascidos foram incluidos de modo consecutivo e avaliados prospectivamente sob o ponto de vista antropométrico. Resultados: Não houve diferenças significativas da média das idades gestacionais e dos pesos de nascimento entre os dois grupos. Os recém-nascidos do grupo II, comparativamente com os do grupo I, receberam provisões mais precoces de energia, lípidos e proteínas através da alimentação parentérica. Não se observaram diferenças significativas no dia de recuperação do peso e da AMB entre os grupos. No entanto, os RN do grupo II recuperaram mais precocemente a AAB (dia 6,9 ± 2,5 vs dia 12,6 ± 5,1) (p<0,01), após um período inicial de declínio dos respectivos valores. Conclusões: O atraso na adequada provisão de energia e proteínas pode ter um impacto negativo na reserva lipídica, não detectada pela observação isolada da evolução ponderai. A medição das áreas braquiais representa um método simples e não invasivo de avaliação indirecta da composição corporal dos RNBP

Reversible Photorheology in Solutions of Cetyltrimethylammonium Bromide, Salicylic Acid, and trans-2,4,4 '-Trihydroxychalcone

We show photorheology in aqueous solutions of weakly entangled wormlike micelles prepared with cetyltrimethylammonium bromide (CTAB), salicylic acid (HSal), and dilute amounts of the photochromic multistate compound trans-2,4,4'-trihydroxychalcone (Ct). Different chemical species of Ct are associated with different colorations and propensities to reside within or outside CTAB micelles. A light-induced transfer between the intra- and intermicellar space is used to alter the mean length of wormlike micelles and hence the rheological properties of the fluid, studied in steady-state shear Bow and in dynamic rheological measurements. Light-induced changes of fluid rheology are reversible by a the relaxation process. at relaxation rates which depend on pH and which are consistent with photochromic reversion rates measured by UV-vis absorption spectroscopy. Parameterizing viscoelostic rheological states by their effective relaxation time tau(c) and corresponding response modulus G(c), we find the light and dark states of the system to fall onto a characteristic state curve defined by comparable experiments conducted without photosensitive components. These reference experiments were prepared with the same concentration of CTAB, but different concentrations of HSal or sodium salicylote (NaSal), and tested at different temperatures

Pegmatite productive terrains in the Variscan Granite hosts from Northern and Central Portugal

The detection of suboutcropping pegmatite deposits in regions recognizably fertile regarding the occurrence of pegmatites depends upon the optimization of conceptual models which support the interpretation of the regional distribution of pegmatites and the structure of their assemblies. In intra-granitic context is at concern the more conventional cartographic expression of pegmatites in connection with the structuring of granitic cupolas. The establishment of occurrence situations linked to certain lithological units or structural alignments is a pathway for the delimitation of productive research areas. Some productivity situations deduced from geological mapping include: accommodation in preferred structural directions, proximity to mixing-mingling corridors, certain petrographic structuring units that reflect irregularities in terms of flow and fractionation processes, and trends of hydrothermal and supergene alteration of host granitic masses. The detection of these aspects, to regard as exploration guides, can avail itself of remote sensing, as they represent contrasting chromatic lithotypes with sufficient surface continuity.(undefined

Tratamientos de consolidación aplicados en materiales cerámicos: ¿Son homogéneos?

The mass consolidation treatment of azulejos is necessary when ceramic biscuits show signs of disaggregation. Such treatment is often used as a complementary conservation technique to the reestablishment of weakened glaze-ceramic bonds. In this research, two commonly used consolidants (ethyl silicate and acrylic resin) were tested on artisanal ceramic tiles via mass consolidation and the resulting impregnation profiles were evaluated. The results indicated that after consolidation, hard zones frequently formed due to localized consolidant concentration after the polymerization and curing processes. These inhomogeneous hard zones subsequently influenced the results obtained through conventional mechanical strength testing (i.e. flexural and compression), creating a false impression of success. This research demonstrated that by using the Drilling Resistance Measuring System, impregnation characteristics such as penetration depth and distribution of consolidant could be observed that otherwise could not be discerned through the more common testing methods. As such, a more extensive evaluation of consolidation effects was achieved.En la conservación de los azulejos alterados se utilizan productos con acción consolidante a fin de recuperar la cohesión del cuerpo cerámico disgregado. En este trabajo se investiga el efecto de la consolidación de dos productos muy utilizados en la práctica de la conservación de los azulejos (un silicato de etilo comercial y una resina acrílica), aplicados en un material cerámico artesanal. Los resultados obtenidos indican que pueden producirse zonas con resistencias mayores debido a la concentración local del producto y, a la vez de un material consolidado homogéneo, resulta un material heterogéneo. Por otro lado, la existencia de estas zonas puede conducir a falsos resultados en los ensayos destructivos (resistencia mecánica a la flexión y compresión) utilizados frecuentemente en la evaluación de la acción de consolidación. Se demuestra que mediante el uso de la resistencia a la perforación (DRMS) es posible definir las características, la distribución y el patrón de impregnación, los cuales no pueden ser observadas por los métodos comúnmente utilizados

Contributions to pegmatite exploration within granitic plutons in Central and Northern Portugal

Exploration programs for granitic pegmatites face the lack of detectable contrasts, either geophysical or geochemical, between pegmatites and their granitic host-rocks. The known productive sectors bearing pegmatites located inside granitic plutons, with economic interest for quartz and feldspar provide adequate field testing for alternative research, dealing with the peculiarities of lithological diversity and the arrangement of structural elements, around pegmatite swarms at suitable granite cupolas. The most efficient assessment for pegmatite positioning in tactical stages of exploration is the use of geological factors analyzed through raw or specifically treated remote imagery, enhancing the favorable lineaments and the most productive granite-host matrixes. The identification of targets using this approach led to a reasonable success tested by experimental drilling in some selected sites