A database for the taxonomic and phylogenetic identification of the genus Bradyrhizobium using multilocus sequence analysis.

Biological nitrogen fixation, with an emphasis on the legume-rhizobia symbiosis, is a key process for agriculture and the environment, allowing the replacement of nitrogen fertilizers, reducing water pollution by nitrate as well as emission of greenhouse gases. Soils contain numerous strains belonging to the bacterial genus Bradyrhizobium, which establish symbioses with a variety of legumes. However, due to the high conservation of Bradyrhizobium 16S rRNA genes - considered as the backbone of the taxonomy of prokaryotes - few species have been delineated. The multilocus sequence analysis (MLSA) methodology, which includes analysis of housekeeping genes, has been shown to be promising and powerful for defining bacterial species, and, in this study, it was applied to Bradyrhizobium, species, increasing our understanding of the diversity of nitrogen-fixing bacteria. Description: Classification of bacteria of agronomic importance is relevant to biodiversity, as well as to biotechnological manipulation to improve agricultural productivity. We propose the construction of an online database that will provide information and tools using MLSA to improve phylogenetic and taxonomic characterization of Bradyrhizobium, allowing the comparison of genomic sequences with those of type and representative strains of each species. Conclusion: A database for the taxonomic and phylogenetic identification of the Bradyrhizobium, genus, using MLSA, will facilitate the use of biological data available through an intuitive web interface. Sequences stored in the on-line database can be compared with multiple sequences of other strains with simplicity and agility through multiple alignment algorithms and computational routines integrated into the database. The proposed database and software tools are available at http://mlsa.cnpso.embrapa.br, and can be used, free of charge, by researchers worldwide to classify Bradyrhizobium, strains; the database and software can be applied to replicate the experiments presented in this study as well as to generate new experiments. The next step will be expansion of the database to include other rhizobial species.Edição dos Proceedings of the 10th International Conference of the Brazilian Association for Bioinformatics and Computational Biology (X-Meeting 2014), Belo Horizonte, Oct. 2014

Theoretical site-directed mutagenesis. The Asp168Ala mutant of L-Lactate Dehydrogenase

The reduction of pyruvate to lactate catalyzed by the L-Lactate dehydrogenase has been studied in this paper by means of hybrid Quantum Mechanical / Molecular Mechanical simulations. A very flexible molecular model consisting on the full tetramer of the enzyme, together with the cofactor NADH, the substrate and solvent water molecules has allowed to theoretically mimic site directed mutagenesis studies, most of them previously experimentally performed. The potential energy surfaces obtained for every single mutation, compared with the one corresponding to the native enzyme, have been used to trace the possible reaction pathways and to locate and characterize the structures corresponding to the stationary points. The analysis of the results has been a very powerful tool to conclude about the role of key residues on the vacuole formed in the active site of the enzyme. Our results are in very good agreement with the previous conclusions derived from site directed mutagenesis. This strategy can be extrapolated to other enzyme systems thus opening the door of a very promising methodology that, in combination with the appropriate experimental technique, will enable us to describe enzyme catalysis phenomenon and the particular role of the residues that form the protein. This knowledge placed us in a privileged position to modify the activity of enzymes and to propose efficient inhibitor

Glycolipids produced by Rouxiella sp. DSM 100043 and isolation of the biosurfactants via foam-fractionation

Additional file 1. Table S1, Figure S1–Figure S3: Mass spectrometry data and plots of purified foam extracts of Rouxiella sp. DSM 100043. Figure S4: Full NMR spectra of Rouxiella sp. DMS 100043 glycolipids present in fractions 64-65

Dependence of enzyme reaction mechanism on protonation state of titratable residues and QM level description: lactate dehydrogenase

We have studied the dependence of the chemical reaction mechanism of L-lactate dehydrogenase (LDH) on the protonation state of titratable residues and on the level of the quantum mechanical (QM) description by means of hybrid quantum-mechanical/molecular-mechanical (QM/MM) methods; this methodology has allowed clarification of the timing of the hydride transfer and proton transfer components that hitherto had not been possible to state definitively.Ferrer Castillo, Silvia, [email protected], Silla Santos, Estanislao, [email protected] ; Tuñon Garcia de Vicuña, Ignacio Nilo, [email protected]

Canonicalizing Knowledge Base Literals

Ontology-based knowledge bases (KBs) like DBpedia are very valuable resources, but their usefulness and usability is limited by various quality issues. One such issue is the use of string literals instead of semantically typed entities. In this paper we study the automated canonicalization of such literals, i.e., replacing the literal with an existing entity from the KB or with a new entity that is typed using classes from the KB. We propose a framework that combines both reasoning and machine learning in order to predict the relevant entities and types, and we evaluate this framework against state-of-the-art baselines for both semantic typing and entity matching

Machine-assisted cultivation and analysis of biofilms

Biofilms are the natural form of life of the majority of microorganisms. These multispecies consortia are intensively studied not only for their effects on health and environment but also because they have an enormous potential as tools for biotechnological processes. Further exploration and exploitation of these complex systems will benefit from technical solutions that enable integrated, machine-assisted cultivation and analysis. We here introduce a microfluidic platform, where readily available microfluidic chips are connected by automated liquid handling with analysis instrumentation, such as fluorescence detection, microscopy, chromatography and optical coherence tomography. The system is operable under oxic and anoxic conditions, allowing for different gases and nutrients as feeding sources and it offers high spatiotemporal resolution in the analysis of metabolites and biofilm composition. We demonstrate the platform’s performance by monitoring the productivity of biofilms as well as the spatial organization of two bacterial species in a co-culture, which is driven by chemical gradients along the microfluidic channel

Ontology of core data mining entities

In this article, we present OntoDM-core, an ontology of core data mining entities. OntoDM-core defines themost essential datamining entities in a three-layered ontological structure comprising of a specification, an implementation and an application layer. It provides a representational framework for the description of mining structured data, and in addition provides taxonomies of datasets, data mining tasks, generalizations, data mining algorithms and constraints, based on the type of data. OntoDM-core is designed to support a wide range of applications/use cases, such as semantic annotation of data mining algorithms, datasets and results; annotation of QSAR studies in the context of drug discovery investigations; and disambiguation of terms in text mining. The ontology has been thoroughly assessed following the practices in ontology engineering, is fully interoperable with many domain resources and is easy to extend

Human hippocampal neurogenesis drops sharply in children to undetectable levels in adults.

New neurons continue to be generated in the subgranular zone of the dentate gyrus of the adult mammalian hippocampus. This process has been linked to learning and memory, stress and exercise, and is thought to be altered in neurological disease. In humans, some studies have suggested that hundreds of new neurons are added to the adult dentate gyrus every day, whereas other studies find many fewer putative new neurons. Despite these discrepancies, it is generally believed that the adult human hippocampus continues to generate new neurons. Here we show that a defined population of progenitor cells does not coalesce in the subgranular zone during human fetal or postnatal development. We also find that the number of proliferating progenitors and young neurons in the dentate gyrus declines sharply during the first year of life and only a few isolated young neurons are observed by 7 and 13 years of age. In adult patients with epilepsy and healthy adults (18-77 years; n = 17 post-mortem samples from controls; n = 12 surgical resection samples from patients with epilepsy), young neurons were not detected in the dentate gyrus. In the monkey (Macaca mulatta) hippocampus, proliferation of neurons in the subgranular zone was found in early postnatal life, but this diminished during juvenile development as neurogenesis decreased. We conclude that recruitment of young neurons to the primate hippocampus decreases rapidly during the first years of life, and that neurogenesis in the dentate gyrus does not continue, or is extremely rare, in adult humans. The early decline in hippocampal neurogenesis raises questions about how the function of the dentate gyrus differs between humans and other species in which adult hippocampal neurogenesis is preserved