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)

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

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

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

A Genomic Signature and the Identification of New Sporulation Genes

Bacterial endospores are the most resistant cell type known to humans, as they are able to withstand extremes of temperature, pressure, chemical injury, and time. They are also of interest because the endospore is the infective particle in a variety of human and livestock diseases. Endosporulation is characterized by the morphogenesis of an endospore within a mother cell. Based on the genes known to be involved in endosporulation in the model organism Bacillus subtilis, a conserved core of about 100 genes was derived, representing the minimal machinery for endosporulation. The core was used to define a genomic signature of about 50 genes that are able to distinguish endospore-forming organisms, based on complete genome sequences, and we show this 50-gene signature is robust against phylogenetic proximity and other artifacts. This signature includes previously uncharacterized genes that we can now show are important for sporulation in B. subtilis and/or are under developmental control, thus further validating this genomic signature. We also predict that a series of polyextremophylic organisms, as well as several gut bacteria, are able to form endospores, and we identified 3 new loci essential for sporulation in B. subtilis: ytaF, ylmC, and ylzA. In all, the results support the view that endosporulation likely evolved once, at the base of the Firmicutes phylum, and is unrelated to other bacterial cell differentiation programs and that this involved the evolution of new genes and functions, as well as the cooption of ancestral, housekeeping functions.FCT grant: (PEst-OE/EQB/LA0004/2011), FCT Ph.D. fellowship: (SFRH/BPD/36328/2007), FCT postdoc fellowship: (SFRH/BPD/65605/2009), Instituto Gulbenkian de Ciência research fellowship

Contribution of remote sensing to the evidence and location of granite hosted pegmatites – Ponte da Barca (Minho)

"I Congresso Internacional de Geociências na CPLP"Em contexto de prospecção de bolsadas pegmatíticas hospedadas em granitos da região de Ponte da Barca, procurou‑se, combinando técnicas de análise distanciada e levantamento de campo, detectar interfaces litológicas com as quais se pudesse relacionar a organização espacial e estrutural dos pegmatitos aí aflorantes. A evidência de alinhamentos curvilíneos em imagens do Landsat, sobretudo bem marcados nas imagens que resultam da aplicação de algoritmos de classificação Maxver, são compatíveis com a existência de fluidalidades planares ou plano‑‑lineares concêntricas, possivelmente herdadas de plumas de “ballooning”, verificando‑‑se uma correlação espacial entre a localização dos pegmatitos e as suas periferias, que separam domínios diferenciados de “clustering” de fenocristais.Within the context of prospecting operations of pegmatite bodies hosted in granites in the Ponte da Barca region, we sought to detect lithologic interfaces from which the relationship between the spatial and structural organization of the outcropping pegmatite bodies could be established, by combining field work and remotely sensed data analysis. The evidence of curvilinear alignments in LANDSAT imagery, especially well‑marked in the images obtained from the application of classification algorithms, are compatible with the existence of concentric planar or plan‑linear fluidalities, possibly inherited from ballooning plumes. We thus verified a spatial correlation between the pegmatite outcrops and ballooning plumes peripheries, which separate different domains of phenocristaline clustering

inTB - a data integration platform for molecular and clinical epidemiological analysis of tuberculosis

This deposit is composed by the main article plus the supplementary materials of the publication.Tuberculosis is currently the second highest cause of death from infectious diseases worldwide. The emergence of multi and extensive drug resistance is threatening to make tuberculosis incurable. There is growing evidence that the genetic diversity of Mycobacterium tuberculosis may have important clinical consequences. Therefore, combining genetic, clinical and socio-demographic data is critical to understand the epidemiology of this infectious disease, and how virulence and other phenotypic traits evolve over time. This requires dedicated bioinformatics platforms, capable of integrating and enabling analyses of this heterogeneous data.Instituto Gulbenkian de Ciência, Programa Nacional de Luta contra a Tuberculose, Instituto Nacional de Saúde Ricardo Jorge, Administração Regional de Saúde de Lisboa e Vale do Tejo

Protective effects of Amburoside A, a phenol glucoside from Amburana cearensis, against CCl4-induced hepatotoxicity in rats.

The aim of this study was to investigate the possible beneficial effects of amburoside A, AMB [4-(0-b-d-glycopyranosyl) benzyl protocatechoate], against carbon tetrachloride (CCl) toxicity in rats

Network Archaeology: Uncovering Ancient Networks from Present-day Interactions

Often questions arise about old or extinct networks. What proteins interacted in a long-extinct ancestor species of yeast? Who were the central players in the Last.fm social network 3 years ago? Our ability to answer such questions has been limited by the unavailability of past versions of networks. To overcome these limitations, we propose several algorithms for reconstructing a network's history of growth given only the network as it exists today and a generative model by which the network is believed to have evolved. Our likelihood-based method finds a probable previous state of the network by reversing the forward growth model. This approach retains node identities so that the history of individual nodes can be tracked. We apply these algorithms to uncover older, non-extant biological and social networks believed to have grown via several models, including duplication-mutation with complementarity, forest fire, and preferential attachment. Through experiments on both synthetic and real-world data, we find that our algorithms can estimate node arrival times, identify anchor nodes from which new nodes copy links, and can reveal significant features of networks that have long since disappeared.Comment: 16 pages, 10 figure