Genome-wide semi-automated annotation of transporter systems

Usually, transport reactions are added to genome-scale metabolic models (GSMMs) based on experimental data and literature. This approach does not allow associating specific genes with transport reactions, which impairs the ability of the model to predict effects of gene deletions. Novel methods for systematic genome-wide transporter functional annotation and their integration into GSMMs are therefore necessary. In this work, an automatic system to detect and classify all potential membrane transport proteins for a given genome and integrate the related reactions into GSMMs is proposed, based on the identification and classification of genes that encode transmembrane proteins. The Transport Reactions Annotation and Generation (TRIAGE) tool identifies the metabolites transported by each transmembrane protein and its transporter family. The localization of the carriers is also predicted and, consequently, their action is confined to a given membrane. The integration of the data provided by TRIAGE with highly curated models allowed the identification of new transport reactions. TRIAGE is included in the new release of merlin, a software tool previously developed by the authors, which expedites the GSMM reconstruction processes.This work was partially supported by a PhD grant (SFRH /BD/47307/2008) and by the ERDF—European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness), and National Funds through the FCT within the projects FCOMP-01-0124-FEDER-009707 (HeliSysBio—molecular Systems Biology in Helicobacter pylori) and PTDC/EIAEIA/115176/2009. The authors would also like to thank the FCT Strategic Project PEst-OE/EQB/LA0023/2013 and the Projects “BioInd - Biotechnology and Bioengineering for improved Industrial and Agro-Food processes”, REF. NORTE-07-0124-FEDER-000028 and “PEM – Metabolic Engineering Platform”, project number 23060 , both cofunded by the Programa Operacional Regional do Norte (ON.2 – O Novo Norte), QREN, FEDER.info:eu-repo/semantics/publishedVersio

Reutilização de águas residuais : modelação da adsorção de nutrientes no solo

O presente estudo incide na modelação da remoção de nutrientes presentes em águas residuais domésticas por adsorção no solo e na avaliação do risco de contaminação de aquíferos por parte destes. Nesse sentido, desenvolveu-se um modelo matemático e efectuou-se a determinação experimental dos parâmetros que caracterizam as isotérmicas de adsorção dos iões nitrato, fosfato e amónio. Os resultados experimentais indicaram que o solo tem principalmente carga iónica positiva, visto que os iões de carga contrária (tais como o nitrato e fosfato) foram os que principalmente adsorveram. Os resultados da simulação demonstraram que o fosfato é totalmente adsorvido e que a concentração de nitrato e amónio na água intersticial, após o período de um ano, é de 0.250 mg/L e 0.023 mg/L respectivamente, a 2 m de profundidade. Em relação ao exercício de simulação, estudouse o efeito de uma sobrecarga de nutrientes assim como a possibilidade de ocorrer saturação da coluna de solo. No caso de ocorrer uma sobrecarga de nutrientes no solo proveniente da descarga de água residual com uma concentração até quatro vezes superior ao valor médio, verificou-se que a concentração do ião amónio foi a mais afectada, aumentando de 27 % a uma profundidade de 2 m e ao fim de um ano. Finalmente, os parâmetros das isotérmicas de adsorção (segundo os modelos de Freundlich e Langmuir) foram sujeitos a uma análise de sensibilidade, tendo-se comprovado que o modelo desenvolvido é extremamente sensível à constante α da isotérmica de Freundlich

Risk of adverse events among older adults following co-prescription of clarithromycin and statins not metabolized by cytochrome P450 3A4

Background: The cytochrome P450 3A4 (CYP3A4) inhibitor clarithromycin may also inhibit liverspecific organic anion-transporting polypeptides (OATP1B1 and OATP1B3). We studied whether concurrent use of clarithromycin and a statin not metabolized by CYP3A4 was associated with an increased frequency of serious adverse events. Methods: Using large health care databases, we studied a population-based cohort of older adults (mean age 74 years) who were taking a statin not metabolized by CYP3A4 (rosuvastatin [76% of prescriptions], pravastatin [21%] or fluvastatin [3%]) between 2002 and 2013 and were newly prescribed clarithromycin (n = 51 523) or azithromycin (n = 52 518), the latter an antibiotic that inhibits neither CYP3A4 nor OATP1B1 and OATP1B3. Outcomes were hospital admission with a diagnostic code for rhabdomyolysis, acute kidney injury or hyperkalemia, and allcause mortality. All outcomes were assessed within 30 days after co-prescription. Results: Compared with the control group, patients co-prescribed clarithromycin and a statin not metabolized by CYP3A4 were at increased risk of hospital admission with acute kidney injury (adjusted relative risk [RR] 1.65, 95% confidence interval [CI] 1.31 to 2.09), admission with hyperkalemia (adjusted RR 2.17, 95% CI 1.22 to 3.86) and all-cause mortality (adjusted RR 1.43, 95% CI 1.15 to 1.76). The adjusted RR for admission with rhabdomyolysis was 2.27 (95% CI 0.86 to 5.96). The absolute increase in risk for each outcome was small and likely below 1%, even after we considered the insensitivity of some hospital database codes. Interpretation: Among older adults taking a statin not metabolized by CYP3A4, co-prescription of clarithromycin versus azithromycin was associated with a modest but statistically significant increase in the 30-day absolute risk of adverse outcomes

Identification of candidate genes for yeast engineering to improve bioethanol production in very high gravity and lignocellulosic biomass industrial fermentations

<p>Abstract</p> <p>Background</p> <p>The optimization of industrial bioethanol production will depend on the rational design and manipulation of industrial strains to improve their robustness against the many stress factors affecting their performance during very high gravity (VHG) or lignocellulosic fermentations. In this study, a set of <it>Saccharomyces cerevisiae </it>genes found, through genome-wide screenings, to confer resistance to the simultaneous presence of different relevant stresses were identified as required for maximal fermentation performance under industrial conditions.</p> <p>Results</p> <p>Chemogenomics data were used to identify eight genes whose expression confers simultaneous resistance to high concentrations of glucose, acetic acid and ethanol, chemical stresses relevant for VHG fermentations; and eleven genes conferring simultaneous resistance to stresses relevant during lignocellulosic fermentations. These eleven genes were identified based on two different sets: one with five genes granting simultaneous resistance to ethanol, acetic acid and furfural, and the other with six genes providing simultaneous resistance to ethanol, acetic acid and vanillin. The expression of <it>Bud31 </it>and <it>Hpr1 </it>was found to lead to the increase of both ethanol yield and fermentation rate, while <it>Pho85</it>, <it>Vrp1 </it>and <it>Ygl024w </it>expression is required for maximal ethanol production in VHG fermentations. Five genes, <it>Erg2</it>, <it>Prs3</it>, <it>Rav1</it>, <it>Rpb4 </it>and <it>Vma8</it>, were found to contribute to the maintenance of cell viability in wheat straw hydrolysate and/or the maximal fermentation rate of this substrate.</p> <p>Conclusions</p> <p>The identified genes stand as preferential targets for genetic engineering manipulation in order to generate more robust industrial strains, able to cope with the most significant fermentation stresses and, thus, to increase ethanol production rate and final ethanol titers.</p

Crescimento e desempenho de espécies nativas de campo rupestre em áreas degradadas quartzíticas

The rupestrian grasslands stand out for their exceptional biodiversity and high proportion of endemic species. Ecological restoration studies on this ecosystem are urgently needed in view of its extremely low resilience and special vulnerability to soil degradation. We experimentally investigated the performance of survival, height growth, and reproductive phenology of eight rupestrian grassland native species, planted in quartzitic degraded areas. Planting took place in 2011 and the saplings were monitored for 12 to 18 months. All species presented high survival (90-100%) during the sampled time interval, with significant height growth, which suggested the successful establishment and adaptation to the harsh conditions found in these degraded areas. In addition, four shrubs completed the reproductive cycle, reaching seed dispersion at approximately two years age. The results indicate that planting saplings of native species should be considered an important tool for the restoration of quartzitic degraded areas in rupestrian grasslands.Keywords: Cerrado, ecological restoration, facilitation, quartzitic soils, sapling growth, Serra do Cipó.Os campos rupestres da Cadeia do Espinhaço destacam-se por sua grande biodiversidade e alta proporção de espécies endêmicas. Estudos sobre a restauração ecológica desse ecossistema são urgentemente necessários, tendo em vista sua resiliência extremamente baixa e especial vulnerabilidade frente à degradação do solo. Investigamos experimentalmente o desempenho de sobrevivência, crescimento em altura e fenologia reprodutiva de mudas de oito espécies nativas de campo rupestre plantadas em áreas degradadas quartzíticas. O plantio foi feito em 2011, e as mudas foram monitoradas por 12 a 18 meses. Todas as espécies apresentaram elevada sobrevivência (90-100%) durante o período considerado e crescimento significativo em altura, o que indicou o estabelecimento bem-sucedido e adaptação às condições rigorosas encontradas nessas áreas degradadas. Além disso, quatro espécies arbustivas completaram o ciclo reprodutivo, atingindo a dispersão de sementes com aproximadamente dois anos de idade. Os resultados indicam que o plantio de mudas de espécies nativas deve ser considerado como uma importante ferramenta na restauração de áreas degradadas quartzíticas em campos rupestres.Palavras-chave: Cerrado, crescimento de mudas, facilitação, restauração ecológica, Serra do Cipó, solos quartzíticos

Is there still room to explore cyclodextrin glycosyltransferase-producers in Brazilian biodiversity?

In the present work, different Brazilian biomes aiming to identify and select cyclodextrin glycosyltransferase-producer bacteria are explored. This enzyme is responsible for converting starch to cyclodextrin, which are interesting molecules to carry other substances of economic interest applied by textile, pharmaceutical, food, and other industries. Based on the enzymatic index, 12 bacteria were selected and evaluated, considering their capacity to produce the enzyme in culture media containing different starch sources. It was observed that the highest yields were presented by the bacteria when grown in cornstarch. These bacteria were also characterized by sequencing of the 16S rRNA region and were classified as Bacillus, Paenibacillus, Gracilibacillus and Solibacillus.publishersversionpublishe

The Stability and Chloride Entrapping Capacity of ZnAl-NO2 LDH in High-Alkaline/Cementitious Environment

In this work, the ZnAl-NO2 LDH (layered double hydroxide) is investigated as a possible additive for mitigating the chloride-induced corrosion of steel in reinforced concrete. The investigation focused on the stability and chloride binding capacity of this LDH in the pH range typical of cementitious materials. Until pH = 12.5 the material was stable and effective in capturing chloride ions from the surrounding aqueous environment. For higher pH, precisely that of hydrated cement, the LDH was partially dissolved and OH− preferentially entrapped instead of Cl−. These results suggested that ZnAl-NO2 has excellent chloride entrapping capability at neutral pH, but this is reduced with increasing pH. However, when the LDH was incorporated into mortars, the chloride ingress was delayed, signifying that the dissolution of LDH leads to a secondary mechanism responsible for chloride capture

Enhancing the enzymatic saccharification of whole slurry from autohydrolyzed Eucalyptus globulus wood by supplementation with a recombinant carbohydrate-binding module

Microbiotec'17 - Congress of Microbiology and Biotechnology 2017Background: Lignocellulosic biomass has a recognised potential as a sustainable platform for the production of biofuels and other biochemicals. However, lignin residues and other inhibitory compounds resulting from lignocellulosics pretreatment affect the digestibility of resulting whole slurries. The addition of synergistic proteins that can cooperate with cellulases is an emerging strategy for enhanced lignocellulosics hydrolysis. Carbohydrate-binding modules (CBMs) have been shown to improve the enzymatic hydrolysis of pure cellulose models but their effect on the enzymatic hydrolysis of lignocellulosic materials has not yet been evaluated. Thus, in this work, the potential synergistic effect of a family 3 CBM on the enzymatic saccharification of a pretreated lignocellulosic biomass was studied for the first time. [...]C. Oliveira and D. Gomes acknowledge support from Fundação para a Ciência e a Tecnologia (FCT), Portugal (grants SFRH/BPD/110640/2015 and SFRH/BD/88623/2012, respectively). This study was supported by the FCT under the scope of the GlycoCBMs Project PTDC/AGR-FOR/3090/2012–FCOMP-01-0124-FEDER-027948 and the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684) and BioTecNorte operation (NORTE-010145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020 - Programa Operacional Regional do Norte.info:eu-repo/semantics/publishedVersio

Strong relationships between soil and vegetation in reference ecosystems of a riparian atlantic rainforest in the upper Doce River watershed, southeastern Brazil

Habitat loss and fragmentation have been impacting ecosystem services essential for human survival. The Brazilian Atlantic rainforest, a biodiversity hotspot, has suffered from historical deforestation and, more recently, from an environmental disaster caused by the Fundão dam collapse that released ore tailings drastically affecting a large territory in the Doce River watershed. This work aims to assess the relationships between soil properties and vegetation in a reference ecosystem to provide guidelines for restoration projects in areas affected by the dam collapse. We conducted phytosociological (vegetation characteristic) and soil quality studies in three distinct natural sites and studied different vegetation strata to better understand plant species composition in reference sites along the impacted Doce River and their potential role in community structuring and functioning. We recorded 140 species, 78 in the tree stratum, and 90 in the sapling stratum. Furthermore, our results highlight the influence of soil on floristic composition in the Atlantic rainforest. Smallscale edaphic variation influenced species composition in both sapling and tree strata. We also identified species of the same genus with strong association with the extremes of the edaphic gradient. Therefore, we highlight that studies in various regions along the Doce River watershed are of utmost importance to evaluate the association between species and soils. The particularities of the species are crucial to the effectiveness of restoration processes since this plant-soil correlation should not be extrapolated even within the same genus. This knowledge is of strategic relevance to provide scientificbased guidance for restoring these environments, aiming at the recovery of biodiversity and ecosystem services.Fil: Ramos, Letícia. Universidade Federal de Minas Gerais; BrasilFil: Negreiros, Daniel. Universidade Federal de Minas Gerais; BrasilFil: Ferreira, Bárbara S. Silva. Universidade Federal de Minas Gerais; BrasilFil: Figueiredo, João Carlos Gomes. Universidade Estadual de Montes Claros; BrasilFil: Paiva, Dario C.. Florida International University; Estados UnidosFil: Oki, Yumi. Universidade Federal de Minas Gerais; BrasilFil: De Souza Justino, Wénita. Universidade Federal de Minas Gerais; BrasilFil: Dos Santos, Rubens Manoel. Universidade Federal de Lavras; BrasilFil: Aguilar, Ramiro. Universidade Federal de Minas Gerais; Brasil. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Nunes, Yule Roberta Ferreira. Universidade Estadual de Montes Claros; BrasilFil: Fernandes, G Wilson. Universidade Federal de Minas Gerais; Brasi