An integrated network visualization framework towards metabolic engineering applications

Background Over the last years, several methods for the phenotype simulation of microorganisms, under specified genetic and environmental conditions have been proposed, in the context of Metabolic Engineering (ME). These methods provided insight on the functioning of microbial metabolism and played a key role in the design of genetic modifications that can lead to strains of industrial interest. On the other hand, in the context of Systems Biology research, biological network visualization has reinforced its role as a core tool in understanding biological processes. However, it has been scarcely used to foster ME related methods, in spite of the acknowledged potential. Results In this work, an open-source software that aims to fill the gap between ME and metabolic network visualization is proposed, in the form of a plugin to the OptFlux ME platform. The framework is based on an abstract layer, where the network is represented as a bipartite graph containing minimal information about the underlying entities and their desired relative placement. The framework provides input/output support for networks specified in standard formats, such as XGMML, SBGN or SBML, providing a connection to genome-scale metabolic models. An user-interface makes it possible to edit, manipulate and query nodes in the network, providing tools to visualize diverse effects, including visual filters and aspect changing (e.g. colors, shapes and sizes). These tools are particularly interesting for ME, since they allow overlaying phenotype simulation results or elementary flux modes over the networks. Conclusions The framework and its source code are freely available, together with documentation and other resources, being illustrated with well documented case studies.This work is partially funded by ERDF - European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness) and by National Funds through the FCT (Portuguese Foundation for Science and Technology) within project ref. COMPETE FCOMP-01-0124-FEDER-015079 and the FCT Strategic Project PEst-OE/EQB/LA0023/2013. The work of PV is funded by PhD grant ref. SFRH/BDE/51442/2011

New Multicomponent Forms of the Antiretroviral Nevirapine with Improved Dissolution Performance

In the pharmaceutical area, some drugs exhibit physicochemical properties that adversely affect the formulation processes for bioavailability and effectiveness. Nevirapine (NVP) is an antiretroviral drug that presents low aqueous solubility, which directly impacts its bioavailability. Among all possible modifications, multicomponent crystals, such as cocrystals and eutectic compositions, have been successfully used to improve the solubility of drugs. In this work, the propensity of the formation of multicomponent systems of NVP with seven possible coformers were predicted and tested: salicylic acid (SA), 3-hydroxybenzoic acid (3HBZC), 4-hydroxybenzoic acid (4HBZC), saccharin (SAC), theophylline (THEO), caffeine (CAF), and urea (URE). Results indicate that NVP-SA, NVP-SAC, NVP-3HBZC, and NVP-4HBZC are cocrystals, whereas NVP-THEO and NVP-CAF are eutectic materials, and NVP-URE is a solid physical mixture. A temperature-dependent disorder behavior was identified for NVP-SA cocrystal. Dissolution studies for the eutectic materials are reported, evidencing that these materials exhibit a significant increase in NVP dissolution kinetics.Fil: Costa, Rogeria Nunes. Universidade Federal de Sao Paulo; BrasilFil: Reviglio, Ana Lucía. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Física Enrique Gaviola. Universidad Nacional de Córdoba. Instituto de Física Enrique Gaviola; Argentina. Universidad Nacional de Córdoba. Facultad de Matemática, Astronomía y Física; ArgentinaFil: Siedler, Sana. Universidade Federal de Santa Catarina; BrasilFil: Cardoso, Simone G.. Universidade Federal de Santa Catarina; BrasilFil: Garro Linck, Yamila. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Física Enrique Gaviola. Universidad Nacional de Córdoba. Instituto de Física Enrique Gaviola; Argentina. Universidad Nacional de Córdoba. Facultad de Matemática, Astronomía y Física; ArgentinaFil: Monti, Gustavo Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Física Enrique Gaviola. Universidad Nacional de Córdoba. Instituto de Física Enrique Gaviola; Argentina. Universidad Nacional de Córdoba. Facultad de Matemática, Astronomía y Física; ArgentinaFil: Carvalho, Alexandre Magnus G.. Centro Nacional de Pesquisa em Energia e Materiais; BrasilFil: Resende, Jackson A. L. C.. Universidade Federal do Mato Grosso do Sul; BrasilFil: Chaves, Marcelo H. C.. Fundación Oswaldo Cruz; BrasilFil: Rocha, Helvético Vinícius Antunes. Fundación Oswaldo Cruz; BrasilFil: Choquesillo Lazarte, Duane. Consejo Superior de Investigaciones Científicas; España. Universidad de Granada; EspañaFil: Infantes, Lourdes. Consejo Superior de Investigaciones Científicas; España. Instituto de Química Física Rocasolano; EspañaFil: Cuffini, Silvia Lucia. Universidade de Sao Paulo; Brasi

Copepod diversity along the Congo River Basin: a first approach

peer reviewedThe free-living copepods of the Congo River Basin in Africa, the second largest in the world just after the Amazonas River Basin, are still insufficiently known because of problematic accessibility and complex logistics related to sampling. We analyzed samples from 82 sites obtained during expeditions in 2010 and 2013. The Congo River main channel and its main mouth tributaries (1700km; between Kisangani and Kinshasa), and the Kasai River and its main mouth tributaries (600km) were visited. A Schindler-Patallas trap was used in the open waters, with five samplings at each site. Twenty-five taxa were found, with dominance of immature forms (nauplii and copepodites). We recognized three undescribed species of Cyclopoida. The most speciose genera were: Microcyclops (five species), Mesocyclops, , and (three species each). The most frequent species were: Microcyclops varicans (27,6% of the samples) and Cryptocyclops sp. (10,6%). Few presumably cosmopolitan species were found, like pocyclops prasinus, , and Microcyclops varicans. Few diaptomid calanoids were found. Rarefaction and extrapolation curves revealed that the diversity found is about half that estimated considering just the open water species here studied. Spatially, the highest species richness was found in the main channel of the Congo River (23) compared to Kasai (20) and other tributaries (14, 9 from the Congo tributaries, 6 from the Kasai). The abundance of adult individuals was low, with an average of 2,36 individuals per sample when considering all water bodies. A distance-based redundancy analysis based on abundance and Bray Curtis dissimilarity index revealed two large groups of copepod species in the sites of the Congo main channel, plus two minor groups with mixed sites among Congo and Kasai main channels, and tributaries of both rivers, the latter being represented by small groups correlated with nitrogen forms, total phosphorus, and oxygen concentrations. Concerning the two large Congo´s channel groups of species, one was associated with water transparency, chlorophyll, and phytoplankton dominated by Dinophyceae, Chlorophyceae, Cryptophyceae, and diatoms. The other was correlated with conductivity, chlorophyll-a and Cyanophyceae. Kasai main channel sampling sites were dispersed among the four groups resulting from our analysis. Our results indicate that the copepod species in the area are separated into two large groups associated with black and white waters, with low and high primary productivity, respectively. The results showed a high copepod diversity along the Congo Basin as expected for large tropical rivers, and a low abundance for the adult copepods, as in other lotic environments. More species are expected to be discovered in this basin with the continuation of this investigation

Standalone vertex finding in the ATLAS muon spectrometer

A dedicated reconstruction algorithm to find decay vertices in the ATLAS muon spectrometer is presented. The algorithm searches the region just upstream of or inside the muon spectrometer volume for multi-particle vertices that originate from the decay of particles with long decay paths. The performance of the algorithm is evaluated using both a sample of simulated Higgs boson events, in which the Higgs boson decays to long-lived neutral particles that in turn decay to bbar b final states, and pp collision data at √s = 7 TeV collected with the ATLAS detector at the LHC during 2011

Measurements of Higgs boson production and couplings in diboson final states with the ATLAS detector at the LHC

Measurements are presented of production properties and couplings of the recently discovered Higgs boson using the decays into boson pairs, H →γ γ, H → Z Z∗ →4l and H →W W∗ →lνlν. The results are based on the complete pp collision data sample recorded by the ATLAS experiment at the CERN Large Hadron Collider at centre-of-mass energies of √s = 7 TeV and √s = 8 TeV, corresponding to an integrated luminosity of about 25 fb−1. Evidence for Higgs boson production through vector-boson fusion is reported. Results of combined fits probing Higgs boson couplings to fermions and bosons, as well as anomalous contributions to loop-induced production and decay modes, are presented. All measurements are consistent with expectations for the Standard Model Higgs boson

Abnormal NK cell lymphocytosis detected after splenectomy: association with repeated infections, relapsing neutropenia, and persistent polyclonal B-cell proliferation

Abnormal NK cell lymphocytosis detected after splenectomy: association with repeated infections, relapsing neutropenia, and persistent polyclonal B-cell proliferation. Granjo E, Lima M, Fraga M, Santos F, Magalhães C, Queirós ML, Moreira I, Rocha S, Silva AS, Rebelo I, Quintanilha A, Ribeiro ML, Candeias J, Orfão A. Department of Hematology, Hospital S. João, Porto, Portugal. [email protected] Abstract We report the case of a boy with hereditary spherocytosis who presented with mild microcytic hypochromic anemia and recurrent leg ulcers that had been present since childhood. Chronic natural killer (NK) cell and B-cell lymphocytosis was detected 1 year after therapeutic splenectomy during investigation of recurrent episodes of neutropenia and persistent lymphocytosis. NK cells proved to be abnormal at immunophenotyping studies, and B-cells were polyclonal and displayed a normal immunophenotype. Genotypic analysis of T-cell receptor (TCR)-beta and TCR-gamma genes showed a germ-line pattern. The clinical course of this patient was characterized by multiple pulmonary infections and amygdalitis. We discuss the potential roles of persistent immune stimulation due to chronic hemolysis and severe leg ulcers and of splenectomy in the origin of NK cell lymphocytosis and the relationship between NK cells and recurrent infections, relapsing neutropenia, and polyclonal B-cell response

Measurement of the top quark pair cross section with ATLAS in pp collisions at √s=7 TeV using final states with an electron or a muon and a hadronically decaying τ lepton

A measurement of the cross section of top quark pair production in proton-proton collisions recorded with the ATLAS detector at the Large Hadron Collider at a centre-of-mass energy of 7 TeV is reported. The data sample used corresponds to an integrated luminosity of 2.05 fb -1. Events with an isolated electron or muon and a τ lepton decaying hadronically are used. In addition, a large missing transverse momentum and two or more energetic jets are required. At least one of the jets must be identified as originating from a b quark. The measured cross section, σtt-=186±13(stat.)±20(syst.)±7(lumi.) pb, is in good agreement with the Standard Model prediction