SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology

Background The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects. Results In order to overcome this, we developed SIMBA (SImple Manager for Bacterial Assemblies), a freely available web tool that integrates several component tools for assembling and finishing bacterial genomes. SIMBA provides a friendly and intuitive user interface so bioinformaticians, even with low computational expertise, can work under a centralized administrative control system of assemblies managed by the assembly center head. SIMBA guides the users to execute assembly process through simple and interactive pages. SIMBA workflow was divided in three modules: (i) projects: allows a general vision of genome sequencing projects, in addition to data quality analysis and data format conversions; (ii) assemblies: allows de novo assemblies with the software Mira, Minia, Newbler and SPAdes, also assembly quality validations using QUAST software; and (iii) curation: presents methods to finishing assemblies through tools for scaffolding contigs and close gaps. We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM. Conclusion Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several projects in laboratories. SIMBA source code is available to download and install in local webservers at http://ufmg-simba.sourceforge.net

Antiparasitic Activity of Natural and Semi-Synthetic Tirucallane Triterpenoids from Schinus terebinthifolius (Anacardiaceae): Structure/Activity Relationships

Leishmaniasis and Chagas are diseases caused by parasitic protozoans that affect the poorest population in the World, causing a high mortality and morbidity. As a result of highly toxic and long-term treatments, the discovery of novel, safe and more efficacious drugs is essential. in this work, the in vitro antiparasitic activity and mammalian cytotoxicity of three natural tirucallane triterpenoids, isolated from leaves of Schinus terebinthifolius (Anacardiaceae), and nine semi-synthetic derivatives were investigated against Leishmania (L.) infantum and Trypanosoma cruzi. Trypomastigotes of T. cruzi were the most susceptible parasites and seven compounds demonstrated a trypanocidal activity with IC50 values in the range between 15 and 58 mu g/mL. Four compounds demonstrated selectivity towards the intracellular amastigotes of Leishmania, with IC50 values in the range between 28 and 97 mu g/mL. the complete characterization of triterpenoids was afforded after thorough analysis of nuclear magnetic resonance (NMR) data as well as electrospray ionization mass spectrometry (ESI-MS). Additionally, structure-activity relationships were performed using Decision Trees.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG)Universidade Federal de São Paulo, Inst Ciencias Ambientais Quim & Farmaceut, BR-09972270 Diadema, SP, BrazilAdolfo Lutz Inst, Ctr Parasitol, BR-01246902 São Paulo, BrazilUniv Fed Paraiba, Ctr Ciencias Aplicadas & Educ, BR-58297000 Rio Tinto, BrazilUniv Fed Uberlandia, Inst Quim, BR-38400902 Uberlandia, MG, BrazilUniversidade Federal de São Paulo, Inst Ciencias Ambientais Quim & Farmaceut, BR-09972270 Diadema, SP, BrazilCNPq: 300546/2012-2CNPq: 471458/2012-0FAPESP: 2011/51739-0FAPESP: 2012/18756-1FAPESP: 2013/16320-4Web of Scienc

In Vitro

Stryphnodendron species, popularly named “barbatimão,” are traditionally used in Brazil as anti-inflammatory agents. This study aimed to investigate the effect of barbatimão and 11 other species on the production of tumor necrosis factor-alpha (TNF-α) in lipopolysaccharide- (LPS-) stimulated THP-1 cells, as well as their anti-arthritis activity. The extracts of Stryphnodendron adstringens, Stryphnodendron obovatum, Campomanesia lineatifolia, and Terminalia glabrescens promoted a concentration-dependent inhibition of TNF-α. Mice injected with LPS in the knee joint were treated per os with fractions from the selected extracts. Both the organic (SAO) and the aqueous (SAA) fractions of S. adstringens promoted a dose-dependent reduction of leukocyte migration and neutrophil accumulation into the joint, but none of them reduced CXCL1 concentration in the periarticular tissue. In contrast, treatment with C. lineatifolia and T. glabrescens fractions did not ameliorate the inflammatory parameters. Analyses of SAO by Ultra Performance Liquid Chromatography (UPLC) coupled to electrospray ionization mass spectrometry (ESI-MS) led to the identification of gallic acid along with 11 prodelphinidins, characterized as monomers and dimers of the B-type. Our findings contribute to some extent to corroborating the traditional use of S. adstringens as an anti-inflammatory agent. This activity is probably related to a decrease of leukocyte migration into the inflammatory site. Polyphenols like gallic acid and prodelphinidins, identified in the active fraction, may contribute to the observed activity

Poisoning level of grass ruziziensis and grass brachiaria after times differents glyphosate assessment

Todos os textos, informa??es e resultados apresentados s?o de inteira responsabilidade dos autores.Parte do trabalho de Inicia??o Cientifica do primeiro autor, financiado pelo Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico (CNPq), Funda??o de Amparo ? Pesquisa do Estado de Minas Gerais (FAPEMIG), Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior (CAPES).Objetivou-se avaliar o n?vel de intoxica??o de Brachiaria ruziziensis (capim-ruziziensis) e Brachiaria decumbens (capim-braqui?ria) em diferentes ?pocas de avalia??o com a aplica??o do herbicida glyphosate. Os tratamentos foram distribu?dos no esquema fatorial (6 x 2), sendo seis doses do herbicida (0; 90; 180; 360; 540 e 720 g ha-1 de glyphosate) e duas esp?cies de Brachiaria (Brachiaria decumbens e Brachiaria ruziziensis). O delineamento experimental utilizado foi em blocos casualizados, com cinco repeti??es. Cada parcela foi constitu?da por um vaso contendo 7 L de solo e plantas de capim-ruziziensis e capim-braqui?ria. A avalia??o do n?vel de intoxica??o das plantas de capim-ruziziensis e capim-braqui?ria foi realizada aos 7, 15 e 30 dias ap?s aplica??o do herbicida ? DAA, por meio de avalia??o visual, atribuindo-se notas de 0 a 100%, sendo 0 aus?ncia de intoxica??o e 100 intoxica??o total ou controle das plantas. Com o aumento das doses de glyphosate ocorreu uma maior intoxica??o das plantas de capim-braqui?ria e capim-ruziziensis. O glyphosate proporciona intoxica??o de 100% em plantas de capim-braqui?ria e capim-ruziziensis, mesmo na menor dose de 90 g e.a. ha-1 de glyphosate, sendo observado a partir dos 15 dias ap?s a aplica??o, podendo ser utilizado com efici?ncia para o controle dessas esp?cies no in?cio de desenvolvimento

Grass brachiaria and grass ruziziensis tillering after application of glyphosate and fluazifop-p-butil

Todos os textos, informa??es e resultados apresentados s?o de inteira responsabilidade dos autores.Parte do trabalho de Inicia??o Cientifica do primeiro autor, financiado pelo Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico (CNPq), Funda??o de Amparo ? Pesquisa do Estado de Minas Gerais (FAPEMIG), Coordenac?o de Aperfei?oamento de Pessoal de N?vel Superior (CAPES).Objetivou-se avaliar o n?mero de perfilhos de Brachiaria decumbens (capim-braqui?ria) e Brachiaria ruziziensis (capim-ruziziensis) 30 dias ap?s a aplica??o dos herbicidas glyphosate e fluazifop-p-butil. Os tratamentos foram distribu?dos no esquema fatorial (6 x 2), sendo seis doses equivalentes dos herbicidas glyphosate e fluazifop-p-butil (0; 0,25; 0,5; 1; 1,5 e 2 L ha-1 vezes a dose comercial indicada pelos fabricantes para controle de gram?neas do g?nero Brachiaria e duas esp?cies (Brachiaria decumbens e Brachiaria ruziziensis). O delineamento experimental utilizado foi em blocos casualizados, com cinco repeti??es. Cada parcela foi constitu?da por um vaso contendo 7 L de solo com duas plantas de capim-ruziziensis e capim-braqui?ria. Aos 30 DAA, as plantas de ambas as esp?cies foram colhidas ao n?vel do solo, e quantificou-se o n?mero de perfilhos vivos totais de cada esp?cie por vaso, para determina??o da taxa de perfilhamento. O glyphosate e fluazifop-p-butil reduzem a taxa de perfilhamento de capim-braqui?ria e capim-ruziziensis, com maior redu??o para as plantas de capim-ruziziensis submetidas ao glyphosate. O capim-ruziziensis ? mais suscept?vel aos herbicidas glyphosate e fluazifop-p-butil, em compara??o ao capim-braqui?ria.The aim of this study was to evaluate the number of Brachiaria decumbens (grass brachiaria) and Brachiaria ruziziensis (grass ruziziensis) tillers, 30 days after the application of herbicides glyphosate and fluazifop-p-butil. The treatments were distributed in a factorial design (6 x 2), being six equivalent doses of herbicides glyphosate and fluazifop-p-butil (0; 0,25; 0,5; 1; 1,5 and 2 L ha-1 times the commercial dose indicated by fabricators to control grasses of the genus Brachiaria and two species (Brachiaria decumbens and Brachiaria ruziziensis). The experimental design was a randomized block with five repetitions. Each plot was composed of a vase containing 7 L of soil with two plants of grass ruziziensis and grass brachiaria. On 30 DAA, the plants of both species were harvested at ground level, and quantified the number of total alive tillers for each species per vase, to determinate the rate of tillering. The glyphosate and fluazifop-p-butil reduces the rate of grass brachiaria and grass ruziziensis tillering, with a bigger reduction for the plants of grass ruziziensis submitted to glyphosate. The grass ruziziensis is more susceptible to herbicides glyphosate and fluazifop-p-butil, compared to grass brachiaria

Grass brachiaria and grass ruziziensis tillering after application of glyphosate and fluazifop-p-butil

Todos os textos, informa??es e resultados apresentados s?o de inteira responsabilidade dos autores.Parte do trabalho de Inicia??o Cientifica do primeiro autor, financiado pelo Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico (CNPq), Funda??o de Amparo ? Pesquisa do Estado de Minas Gerais (FAPEMIG), Coordenac?o de Aperfei?oamento de Pessoal de N?vel Superior (CAPES).Objetivou-se avaliar o n?mero de perfilhos de Brachiaria decumbens (capim-braqui?ria) e Brachiaria ruziziensis (capim-ruziziensis) 30 dias ap?s a aplica??o dos herbicidas glyphosate e fluazifop-p-butil. Os tratamentos foram distribu?dos no esquema fatorial (6 x 2), sendo seis doses equivalentes dos herbicidas glyphosate e fluazifop-p-butil (0; 0,25; 0,5; 1; 1,5 e 2 L ha-1 vezes a dose comercial indicada pelos fabricantes para controle de gram?neas do g?nero Brachiaria e duas esp?cies (Brachiaria decumbens e Brachiaria ruziziensis). O delineamento experimental utilizado foi em blocos casualizados, com cinco repeti??es. Cada parcela foi constitu?da por um vaso contendo 7 L de solo com duas plantas de capim-ruziziensis e capim-braqui?ria. Aos 30 DAA, as plantas de ambas as esp?cies foram colhidas ao n?vel do solo, e quantificou-se o n?mero de perfilhos vivos totais de cada esp?cie por vaso, para determina??o da taxa de perfilhamento. O glyphosate e fluazifop-p-butil reduzem a taxa de perfilhamento de capim-braqui?ria e capim-ruziziensis, com maior redu??o para as plantas de capim-ruziziensis submetidas ao glyphosate. O capim-ruziziensis ? mais suscept?vel aos herbicidas glyphosate e fluazifop-p-butil, em compara??o ao capim-braqui?ria.The aim of this study was to evaluate the number of Brachiaria decumbens (grass brachiaria) and Brachiaria ruziziensis (grass ruziziensis) tillers, 30 days after the application of herbicides glyphosate and fluazifop-p-butil. The treatments were distributed in a factorial design (6 x 2), being six equivalent doses of herbicides glyphosate and fluazifop-p-butil (0; 0,25; 0,5; 1; 1,5 and 2 L ha-1 times the commercial dose indicated by fabricators to control grasses of the genus Brachiaria and two species (Brachiaria decumbens and Brachiaria ruziziensis). The experimental design was a randomized block with five repetitions. Each plot was composed of a vase containing 7 L of soil with two plants of grass ruziziensis and grass brachiaria. On 30 DAA, the plants of both species were harvested at ground level, and quantified the number of total alive tillers for each species per vase, to determinate the rate of tillering. The glyphosate and fluazifop-p-butil reduces the rate of grass brachiaria and grass ruziziensis tillering, with a bigger reduction for the plants of grass ruziziensis submitted to glyphosate. The grass ruziziensis is more susceptible to herbicides glyphosate and fluazifop-p-butil, compared to grass brachiaria

Erratum to: The study of cardiovascular risk in adolescents – ERICA: rationale, design and sample characteristics of a national survey examining cardiovascular risk factor profile in Brazilian adolescents

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Prediabetes Induces More Severe Acute COVID-19 Associated With IL-6 Production Without Worsening Long-Term Symptoms.

Aims: Pre-existing conditions, such as age, hypertension, obesity, and diabetes, constitute known risk factors for severe COVID-19. However, the impact of prediabetes mellitus (PDM) on COVID-19 severity is less clear. This study aimed to evaluate the influence of PDM in the acute and long-term phases of COVID-19. Materials and methods: We compared inflammatory mediators, laboratory and clinical parameters and symptoms in COVID-19 patients with prediabetes (PDM) and without diabetes (NDM) during the acute phase of infection and at three months post-hospitalization. Results: Patients with PDM had longer hospital stays and required intensive care unit admission more frequently than NDM. Upon hospitalization, PDM patients exhibited higher serum levels of interleukin 6 (IL-6), which is related to reduced partial pressure of oxygen (PaO2) in arterial blood, oxygen saturation (SpO2) and increased COVID-19 severity. However, at three months after discharge, those with PDM did not exhibit significant alterations in laboratory parameters or residual symptoms; however, PDM was observed to influence the profile of reported symptoms. Conclusions: PDM seems to be associated with increased risk of severe COVID-19, as well as higher serum levels of IL-6, which may constitute a potential biomarker of severe COVID-19 risk in affected patients. Furthermore, while PDM correlated with more severe acute-phase COVID-19, no long-term worsening of sequelae was observed

Rarity of monodominance in hyperdiverse Amazonian forests.

Tropical forests are known for their high diversity. Yet, forest patches do occur in the tropics where a single tree species is dominant. Such "monodominant" forests are known from all of the main tropical regions. For Amazonia, we sampled the occurrence of monodominance in a massive, basin-wide database of forest-inventory plots from the Amazon Tree Diversity Network (ATDN). Utilizing a simple defining metric of at least half of the trees ≥ 10 cm diameter belonging to one species, we found only a few occurrences of monodominance in Amazonia, and the phenomenon was not significantly linked to previously hypothesized life history traits such wood density, seed mass, ectomycorrhizal associations, or Rhizobium nodulation. In our analysis, coppicing (the formation of sprouts at the base of the tree or on roots) was the only trait significantly linked to monodominance. While at specific locales coppicing or ectomycorrhizal associations may confer a considerable advantage to a tree species and lead to its monodominance, very few species have these traits. Mining of the ATDN dataset suggests that monodominance is quite rare in Amazonia, and may be linked primarily to edaphic factors