TDPS - Turnover dependent phenotypic simulation: a quantitative constraint-based simulation method that accommodates all main strain design strategies

Constraint-based modelling methodologies can expedite the strain engineering process by helping in the search for interesting genetic modification targets. Although the search for gene knock-outs is fairly established with in silico methodologies, most computational strain design methods still model gene up/down-regulations by forcing the corresponding flux values to pre-calculated levels without considering the availability of resources. We have developed a new simulation method, Turnover Dependent Phenotypic Simulation (TDPS), which was designed with the goal of simulating quantitatively the phenotype of strains with diverse genetic modifications in a resource conscious manner. Besides gene deletions and down-regulations, TDPS can also simulate the up-regulation of metabolic reactions as well as the introduction of heterologous genes or the activation of dormant reactions. In TDPS the flux values through modified metabolic reactions are modelled by taking into consideration the availability of precursor metabolites in the network, which is accomplished by assuming that the production turnover of a metabolite can be used as an indication of its abundance. The developed method is based on a MILP formulation that manipulates the fractions of metabolite turnovers consumed by the modified reactions. Furthermore, TDPS also integrates a new objective function that promotes network rigidity in order to predict the flux phenotype of modified strains. TDPS was validated using metabolically engineered S. cerevisiae strains available in the literature by comparing the simulated and experimental production yields of the target metabolite

Tumors of skin appendages – A 10-year review

Introdução: Os tumores dos anexos cutâneos representam um grupo heterogéneo de neoplasias benignas e malignas com diferentes diferenciações morfológicas. Material e Métodos: Foi efectuado o estudo retrospectivo dos tumores dos anexos cutâneos diagnosticados na consulta externa do Serviço de Dermatologia do Centro Hospitalar do Porto, EPE-HSA entre 2000 a 2009. Resultados: Foram diagnosticados 404 tumores dos anexos cutâneos. Apenas 3% dos tumores eram malignos. A maioria apresentou uma diferenciação (62,6 %) folicular. Discussão: A revisão da literatura mostrou uma escassez de dados relativos a estudos retrospectivos dos tumores dos anexos cutâneos. Mais estudos são necessários para uma melhor caracterização epidemiológica destas entidades

Film thickness in a ball-on-disc contact lubricated with greases, bleed oils and base oils

Three different lubricating greases and their bleed and base oils were compared in terms of film thickness in a ball-on-disc test rig through optical interferometry. The theoretical values calculated according to Hamrock's equation are in close agreement with the base oil film thickness measurements, which validates the selected experimental methodology. The grease and bleed oil film thickness under fully flooded lubrication conditions presented quite similar behaviour and levels. Therefore, the grease film thickness under full film conditions might be predicted using their bleed oil properties, namely the viscosity and pressure-viscosity coefficient. The base and bleed oil lubricant parameter LP are proportional to the measured film thickness. A relationship between grease and the corresponding bleed oil film thickness was evidenced

Discovery and implementation of a novel pathway for n-butanol production via 2-oxoglutarate

Background One of the European Union directives indicates that 10% of all fuels must be bio-synthesized by 2020. In this regard, biobutanolnatively produced by clostridial strainsposes as a promising alternative biofuel. One possible approach to overcome the difficulties of the industrial exploration of the native producers is the expression of more suitable pathways in robust microorganisms such as Escherichia coli. The enumeration of novel pathways is a powerful tool, allowing to identify non-obvious combinations of enzymes to produce a target compound. Results This work describes the in silico driven design of E. coli strains able to produce butanol via 2-oxoglutarate by a novel pathway. This butanol pathway was generated by a hypergraph algorithm and selected from an initial set of 105,954 different routes by successively applying different filters, such as stoichiometric feasibility, size and novelty. The implementation of this pathway involved seven catalytic steps and required the insertion of nine heterologous genes from various sources in E. coli distributed in three plasmids. Expressing butanol genes in E. coli K12 and cultivation in High-Density Medium formulation seem to favor butanol accumulation via the 2-oxoglutarate pathway. The maximum butanol titer obtained was 85±1 mg L1 by cultivating the cells in bioreactors. Conclusions In this work, we were able to successfully translate the computational analysis into in vivo applications, designing novel strains of E. coli able to produce n-butanol via an innovative pathway. Our results demonstrate that enumeration algorithms can broad the spectrum of butanol producing pathways. This validation encourages further research to other target compounds.This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of a Ph.D. Grant (PD/BD/52366/2013) from MIT Portugal Program and the strategic funding of UID/BIO/04469 unit. Additional support was received by COMPETE 2020 (POCI-01-0145-FEDER-006684) and BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020-Programa Operacional Regional do Norte. The authors also thank the Times New Roman project “Dynamics”, Ref. ERA-IB-2/0002/2014, funded by national funds through FCT/MCTES. The genes thl, hbd, crt and adhE1 were kindly provided by Kristala L. Jones Prather from MIT. The authors thank the project DDDeCaF - Bioinformatics Services for Data-Driven Design of Cell Factories and Communities, Ref. H2020-LEIT-BIO-2015-1 686070–1, funded by the European Commission and the Project LISBOA010145 FEDER007660 (Microbiologia Molecular, Estrutural e Celular) funded by FEDER funds through COMPETE2020 Programa Operacional Competitividade e Internacionalização (POCI) and by national funds through FCT Fundacao para a Ciencia e a Tecnologiainfo:eu-repo/semantics/publishedVersio

Late Bronze Age Hoard studied by PIXE

The hoards of metallic objects belonging to the Late European Bronze Age can be interpreted differently depending on the type, number and composition of the artefacts. PIXE analysis has been performed in nine items from the Hoard of Freixanda in Portugal comprising 4 socket axes, a palstave axe, a ring, a chisel, a dagger, and a casting debris. Besides the composition of the main matrix elements, that is Cu and Sn, the amount of trace elements of interest like, As, Pb, Ni and Ag has been determined using this ion beam technique. The high tin content alloy and the high purity of the metals from the Freixanda hoard are characteristic of the Portuguese and Spanish Late Bronze Age metallurgy, supporting the idea of a regional production

Energetic and biomechanical contributions for longitudinal performance in master swimmers

The current study aimed to verify the changes in performance, physiological and biomechanical variables throughout a season in master swimmers. Methods: Twenty-three master swimmers (34.9 ± 7.4 years) were assessed three times during a season (December: M1, March: M2, June: M3), in indoor 25 m swimming pools. An incremental 5 × 200 m test was used to evaluate the speed at 4 mmol·L−1 of blood lactate concentration (sLT), maximal oxygen uptake (VO2max), peak blood lactate ([La-]peak) after the test, stroke frequency (SF), stroke length (SL), stroke index (SI) and propelling efficiency (ηp). The performance was assessed in the 200 m front crawl during competition. Results: Swimming performance improved between M1, M2 (2%, p = 0.03), and M3 (4%, p < 0.001). Both sLT and VO2max increased throughout the season (4% and 18%, p < 0.001, respectively) but not [La-]peak. While SF decreased 5%, SL, SI and ηp increased 5%, 7%, and 6% (p < 0.001) from M1 to M3. Conclusions: Master swimmers improved significantly in their 200 m front crawl performance over a season, with decreased SF, and increased SL, ηp and SI. Despite the improvement in energetic variables, the change in performance seemed to be more dependent on technical than energetic factorsThis work is supported by national funding through the Portuguese Foundation for Science and Technology, I.P., under project UIDB/04045/2020info:eu-repo/semantics/publishedVersio

Natural organic matter fractionation along the treatment of water for human consumption

The main objective of this study was to characterize the organic matter present in raw water and along the treatment process, as well as its seasonal variation. A natural organic matter fractionation approach has been applied to Lever water treatment plant located in Douro River, in Oporto (Portugal). The process used was based on the sorption of dissolved organic matter in different types of ion exchange resins, DAX-8, DAX-4 and IRA-958, allowing its separation into four fractions: very hydrophobic acids (VHA), slightly hydrophobic acids (SHA), charged hydrophilic (CHA) and hydrophilic neutral (NEU). The dissolved organic carbon (DOC) determination was used to quantify dissolved organic matter. Samples were collected monthly, during approximately one year, from raw water captured at the surface and under the bed of the river, and after each step of the treatment: pre-filtration in sand/anthracite filters, ozonation, coagulation/flocculation, counter current dissolved air flotation and filtration (CoCoDAFF) and chlorination. The NEU fraction showed a seasonal variation, with maximum values in autumn for the sampling points corresponding to raw water captured at the surface and under the bed of the river. It was usually the predominating fraction and did not show a significant decrease throughout the treatment. Nevertheless their low concentration, the same occurred for the CHA and VHA fractions. There was an overall decrease in the SHA fraction throughout the water treatment (especially after CoCoDAFF and ozonation) as well as in the DOC. The TSUVA254 values obtained for raw water generally varied between 2.0 and 4.0 L mgC-1 m-1 and between 0.75 and 1.78 L mgC-1 m-1 for treated water. It was observed a decrease of TSUVA values along the treatment, especially after ozonation. These results may contribute to a further optimization in the process of treating water for human consumption