SymGRASS: a database of sugarcane orthologous genes involved in arbuscular mycorrhiza and root nodule symbiosis : from Seventh International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, (CIBB 2010), Palermo, Italy, 16 - 18 September 2010

Background: The rationale for gathering information from plants procuring nitrogen through symbiotic interactions controlled by a common genetic program for a sustainable biofuel production is the high energy demanding application of synthetic nitrogen fertilizers. We curated sequence information publicly available for the biofuel plant sugarcane, performed an analysis of the common SYM pathway known to control symbiosis in other plants, and provide results, sequences and literature links as an online database. Methods: Sugarcane sequences and informations were downloaded from the nucEST database, cleaned and trimmed with seqclean, assembled with TGICL plus translating mapping method, and annotated. The annotation is based on BLAST searches against a local formatted plant Uniprot90 generated with CD-HIT for functional assignment, rpsBLAST to CDD database for conserved domain analysis, and BLAST search to sorghum's for Gene Ontology (GO) assignment. Gene expression was normalized according the Unigene standard, presented as ESTs/100 kb. Protein sequences known in the SYM pathway were used as queries to search the SymGRASS sequence database. Additionally, antimicrobial peptides described in the PhytAMP database served as queries to retrieve and generate expression profiles of these defense genes in the libraries compared to the libraries obtained under symbiotic interactions. Results: We describe the SymGRASS, a database of sugarcane orthologous genes involved in arbuscular mycorrhiza (AM) and root nodule (RN) symbiosis. The database aggregates knowledge about sequences, tissues, organ, developmental stages and experimental conditions, and provides annotation and level of gene expression for sugarcane transcripts and SYM orthologous genes in sugarcane through a web interface. Several candidate genes were found for all nodes in the pathway, and interestingly a set of symbiosis specific genes was found. Conclusions: The knowledge integrated in SymGRASS may guide studies on molecular, cellular and physiological mechanisms by which sugarcane controls the establishment and efficiency of endophytic associations. We believe that the candidate sequences for the SYM pathway together with the pool of exclusively expressed tentative consensus (TC) sequences are crucial for the design of molecular studies to unravel the mechanisms controlling the establishment of symbioses in sugarcane, ultimately serving as a basis for the improvement of grass crops

Modeling the impacts of climate extremes and multiple water uses to support water management in the Icó-Mandantes Bay, Northeast Brazil

The hydropower production, water supply and aquaculture services of the Itaparica Reservoir are of immense importance for the Brazilian Northeast. Uncontrolled water resources consumption (e.g. irrigation, water supply), climate and land use change effects deteriorated the water quantity and quality in the reservoir, leading to socio-economic and environmental problems. In this work, a depth-averaged shallow water model was set up for the Icó-Mandantes Bay, one major branch of the reservoir, using the open TELEMAC-MASCARET system. The aim was to assess the impacts of the newly built water diversion channel, as well as the effects of a flood and tracer transport from an intermittent tributary, both located in the bay. An alternative approach to estimate the water retention times was additionally implemented. The simulations showed that though the diversion channel did not significantly influence the hydrodynamics of the bay, it is necessary to continuously monitor water quality parameters in the withdrawal, especially during rainy periods after droughts, because of the nutrient inputs from the tributary and the overflows of the nearby drainage systems. Management measures adapting to the continuously changing natural conditions and anthropogenic impacts are thus indispensable and the model presented can be a valuable supporting tool for this purpose.BMBF, 01LL0904A, Verbundvorhaben INNOVATE: Nachhaltige Nutzung von Stauseen durch innovative Kopplung von aquatischen und terrestrischen Ökosystemfunktionen - Teilvorhaben 1: Verbundkoordination, Grüne Leber und Ökonomi

Identidade!

Negritude chegou! Mas o que é?Peter t. NashQual deve ser o perfil de um/a estudante de Teologia?Lurdiene da SilvaEl Salvador: O País da Alegria!!Günter Bayerl PadilhaExistem duas BahiasFrancisco R. SantosUma experiência do Espírito Santo na religiosidade Cristã negraAdriano OttoUm dia na vida de um intercambistaJosé Alencar Lhulhier Júnio

Crystal structure and mechanism of human lysine-specific demethylase-1

The reversible methylation of specific lysine residues in histone tails is crucial in epigenetic gene regulation. LSD1, the first known lysine-specific demethylase, selectively removes monomethyl and dimethyl, but not trimethyl modifications of Lys4 or Lys9 of histone-3. Here, we present the crystal structure of LSD1 at 2.9-Å resolution. LSD1 forms a highly asymmetric, closely packed domain structure from which a long helical 'tower' domain protrudes. The active site cavity is spacious enough to accommodate several residues of the histone tail substrate, but does not appear capable of recognizing the different methylation states of the substrate lysine. This supports the hypothesis that trimethylated lysine is chemically rather than sterically discriminated. We present a biochemical analysis of LSD1 mutants that identifies crucial residues in the active site cavity and shows the importance of the SWIRM and tower domains for catalysis

Structure of a double ubiquitin-like domain in the talin head: a role in integrin activation

Talin is a 270-kDa protein that activates integrins and couples them to cytoskeletal actin. Talin contains an N-terminal FERM domain comprised of F1, F2 and F3 domains, but it is atypical in that F1 contains a large insert and is preceded by an extra domain F0. Although F3 contains the binding site for β-integrin tails, F0 and F1 are also required for activation of β1-integrins. Here, we report the solution structures of F0, F1 and of the F0F1 double domain. Both F0 and F1 have ubiquitin-like folds joined in a novel fixed orientation by an extensive charged interface. The F1 insert forms a loop with helical propensity, and basic residues predicted to reside on one surface of the helix are required for binding to acidic phospholipids and for talin-mediated activation of β1-integrins. This and the fact that basic residues on F2 and F3 are also essential for integrin activation suggest that extensive interactions between the talin FERM domain and acidic membrane phospholipids are required to orientate the FERM domain such that it can activate integrins