A text mining approach for the extraction of kinetic information from literature

Systems biology has fostered interest in the use of kinetic models to better understand the dynamic behavior of metabolic networks in a wide variety of conditions. Unfortunately, in most cases, data available in different databases are not sufficient for the development of such models, since a significant part of the relevant information is still scattered in the literature. Thus, it becomes essential to develop specific and powerful text mining tools towards this aim. In this context, this work has as main objective the development of a text mining tool to extract, from scientific literature, kinetic parameters, their respective values and their relations with enzymes and metabolites. The pipeline proposed integrates the development of a novel plug-in over the text mining tool @Note2. Overall, the results validate the developed approach

Extracting kinetic information from literature with KineticRE

To better understand the dynamic behavior of metabolic networks in a wide variety of conditions, the field of Systems Biology has increased its interest in the use of kinetic models. The different databases, available these days, do not contain enough data regarding this topic. Given that a significant part of the relevant information for the development of such models is still wide spread in the literature, it becomes essential to develop specific and powerful text mining tools to collect these data. In this context, this work has as main objective the development of a text mining tool to extract, from scientific literature, kinetic parameters, their respective values and their relations with enzymes and metabolites. The approach proposed integrates the development of a novel plug-in over the text mining framework @Note2. In the end, the pipeline developed was validated with a case study on Kluyveromyces lactis, spanning the analysis and results of 20 full text documents.The work was funded by National Funds through the FCT (Portuguese Foundation for ScienceandTechnology)withinprojectref. PTDC/QUI-BIQ/119657/2010 “Finding the naturally evolved design principles of prevalent metabolic circuits”. The authors would 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. NORTE07-0124-FEDER-000028 and “PEM Metabolic Engineering Platform”, project number 23060, both co-funded by the Programa Operacional Regional do Norte (ON.2 ONovoNorte),QREN, FEDER

Role of dominant microflora of Picante cheese on proteolysis and lipolysis

Four species of bacteria (Enterococcus faecium and E. faecalis, Lactobacillus plantarum and Lb. paracasei) and three species of yeasts (Debaryomyces hansenii, Yarrowia lipolytica and Cryptococcus laurentii) isolated from Picante cheese were assayed for proteolytic and lipolytic activities. The milk type (caprine or ovine), the ripening time (0–65 d) and the concentration of NaCl (0–14% (w/v)) have been studied in terms of their effects upon in vitro curdled milk. Proteolytic and peptidolytic activities were demonstrated to be high for Y. lipolytica, and at much lower levels for the other strains. Milk type, ripening time and content of NaCl appeared to be statistically significant processing factors in terms of proteolysis. Clear lipolytic activity was detected for Y. lipolytica, but release of free fatty acids to lesser extents was observed for the other strains under study. Ripening time was statistically significant for lipolysis but milk type was not. Lipolytic activities were strongly affected by NaCl content and the extent of fat hydrolysis was affected by the increase of NaCl from 0 to 7% (w/v) more than by change from 7 to 14% (w/v). In view of the experimental results, a mixed-strain starter for Picante cheese including Lb. plantarum, E. faecium (or E. faecalis) and D. hansenii (and/or Y. lipolytica) is of potential interest

Organic acids produced by lactobacilli, enterococci and yeasts isolated from Picante cheese

Four species of bacteria (Enterococcus faecium and Enterococcus faecalis, Lactobacillus plantarum and Lactobacillus paracasei) and three species of yeasts (Debaryomyces hansenii, Yarrowia lipolytica and Cryptococcus laurentii), previously isolated from Picante cheese, were cultured in ovine and in caprine milk and assayed for sugar and organic acids metabolism for 6 days. The results indicated that both milk types can be coagulated by the four strains of lactic acid bacteria. Lb. paracasei led to a faster and greater reduction in pH. Production of lactic acid correlated to lactose degradation, and was highest for Lb. paracasei followed by E. faecium; citrate metabolism was apparent for E. faecalis and, to a lesser extent, for E. faecium, Lb. plantarum and Lb. paracasei. Relatively high contents of formic acid were found when inoculation was with Enterococcus and with Lb. plantarum

Synergistic Association of Genetic Variants with Environmental Risk Factors in Susceptibility to Essential Hypertension

Essential hypertension (EH) is a disease in which both environment and genes have an important role. This study was designed to identify the interaction model between genetic variants and environmental risk factors that most highly potentiates EH development.info:eu-repo/semantics/publishedVersio

Valorization of fish by-products: physico-chemical properties of skin gelatins

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Bioconversion of fish discards through the production of lactic acid bacteria and metabolites: sustainable application of fish peptones in nutritive fermentation media

In the current work, we study the capacity of 30 peptones obtained by enzyme proteolysis of ten discarded fish species (hake, megrim, red scorpionfish, pouting, mackerel, gurnard, blue whiting, Atlantic horse mackerel, grenadier, and boarfish) to support the growth and metabolite production of four lactic acid bacteria (LAB) of probiotic and technological importance. Batch fermentations of Lactobacillus plantarum, L. brevis, L. casei, and Leuconostoc mesenteroides in most of the media formulated with fish peptones (87% of the cases) led to similar growths (quantified as dry-weight biomass and viable cells) and metabolites (mainly lactic acid) than in commercial control broth (MRS). Comparisons among cultures were performed by means of the parameters obtained from the mathematical fittings of experimental kinetics to the logistic equation. Modelling among experimental and predicted data from each bioproduction was generally accurate. A simple economic assessment demonstrated the profitability achieved when MRS is substituted by media formulated with fish discards: a 3–4-fold reduction of costs for LAB biomass, viable cells formation, and lactic and acetic acid production. Thus, these fish peptones are promising alternatives to the expensive commercial peptones as well as a possible solution to valorize discarded fish biomasses and by-products.info:eu-repo/semantics/publishedVersio

Methylenetetrahydrofolate reductase gene, homocysteine and coronary artery disease: the A1298C polymorphism does matter. Inferences from a case study (Madeira, Portugal)

Elevated levels of plasma homocysteine, an independent risk factor and a strong predictor of mortality in patients with coronary artery disease (CAD), can result from nutritional deficiencies or genetic errors, including methylenetetrahydrofolate reductase (MTHFR) C677T and A1298C polymorphisms. The contribution of these polymorphisms in the development of CAD remains controversial. We analysed the impact of MTHFR C677T and A1298C on fasting homocysteine and CAD in 298 CAD patients proved by angiography and 510 control subjects from the Island of Madeira (Portugal). After adjustment for other risk factors, plasma homocysteine remained independently correlated with CAD. Serum homocysteine was significantly higher in individuals with 677TT and 1298AA genotypes. There was no difference in the distribution of MTHFR677 genotypes between cases and controls but a significant increase in 1298AA prevalence was found in CAD patients. In spite of the clear effect of C677T mutation on elevated homocysteine levels we only found an association between 1298AA genotype and CAD in this population. The simultaneous presence of 677CT and 1298AA genotypes provides a significant risk of developing the disease, while the 1298AC genotype, combined with 677CC, shows a significant trend towards a decrease in CAD occurrence. The data shows an independent association between elevated levels of homocysteine and CAD. Both MTHFR polymorphisms are associated with increased fasting homocysteine (677TT and 1298AA genotypes), but only the 1298AA variant shows an increased prevalence in CAD group. Odds ratio seem to indicate that individuals with the MTHFR 1298AA genotype and the 677CT/1298AA compound genotype had a 1.6-fold increased risk for developing CAD suggesting a possible association of MTHFR polymorphisms with the risk of CAD in Madeira population.info:eu-repo/semantics/publishedVersio

Enhancing acetic acid and 5-hydroxymethyl furfural tolerance of C. saccharoperbutylacetonicum through adaptive laboratory evolution

Supplementary material related to this article can be found, in the online version, at doi:https://doi.org/10.1016/j.procbio.2020.11.013.In this study, adaptive laboratory evolution (ALE) was applied to isolate four strains of Clostridium saccharoperbutylacetonicum able to grow in the presence of hemicellulosic hydrolysate inhibitors unsupported by the parental strain. Among them, isolate RAC-25 presented the best fermentative performance, producing 22.1g/L of ABE and 16.7g/L of butanol. Genome sequencing revealed a deletion in the arabinose transcriptional repressor gene (araR) and a mutation in the anti-sigma factor I that promoted a downregulation of sigI. Gene expression analysis indicated high expression of genes related to H+-pumps (ATP synthases), proline biosynthesis (gamma phosphate reductase) and chaperonins (Grol), suggesting an integrated mechanism that is probably coordinated by the repression of sigI. Therefore, in addition to highlighting the power of ALE for selecting robust strains, our results suggest that sigI and araR may be interesting gene targets for increased tolerance toward inhibitor compounds relevant for lignocellulosic biofuels production.The authors would like to thank the Brazilian Center for Research in Energy and Materials (CNPEM) for providing access to the bioprocess facility of the Brazilian Biorenewables National Laboratory, and CNPq (400803/2013-5), FCT (UID/BIO/04469), BioTecNorte Operation (NORTE-01-0145-FEDER-000004) and Portuguese Biological Data Network” (ref. LISBOA-01-0145-FEDER-022231) for financial support.info:eu-repo/semantics/publishedVersio

As cerâmicas cinzentas da Sé de Lisboa

As escavações que o IPPAR promoveu no Claustro da Sé de Lisboa permitiram recolher um abundante espólio da Idade do Ferro. Entre esse espólio, de características eminentemente orientalizantes, destacava-se a cerâmica cinzenta que agora entendemos publicar. O estudo que realizámos incidiu, em primeiro lugar, sobre os aspectos estritamente formais, tendo-se definido diversos tipos e variantes. A definição tipológica originou também uma análise pormenorizada desta espécie cerâmica num contexto mais geral, concretamente peninsular, tendo-se tomado em consideração a homogeneidade e diversidade observadas em termos morfológicos, entre as diversas regiões que, durante a Idade do Ferro, produziram e consumiram cerâmicas cinzentas.The excavations that IPPAR undertook in the Cloister of the Sé Cathedral of Lisbon allowed for the recovery of abundant material from the Iron Age. Among this material, of predominantly orientalizing characteristics, stood out the grey ceramics that we now publish. The study that we carried out focused, in the first place, on those strictly formal aspects, having defined diverse types and varieties. The typological definition led also to a detailed analysis of this type of ceramic in a more general context, squarely peninsular, having taken into consideration the homogeneity and diversity observed in morphological terms, between the diverse regions that, during the Iron Age, produced and consumed gray ceramics.info:eu-repo/semantics/publishedVersio