Multi-level dynamic modeling in biological systems : application of hybrid Petri nets to network simulation

The recent progress in the high-throughput experimental technologies allows the reconstruction of many biological networks and to evaluate changes in proteins, genes and metabolites levels in different conditions. On the other hand, computational models, when complemented with regulatory information, can be used to predict the phenotype of an organism under different genetic and environmental conditions. These computational methods can be used for example to identify molecular targets capable of inactivating a bacterium and to understand its virulence factors. This work proposes a hybrid metabolic-regulatory Petri net approach that is based on the combination of approximate enzyme-kinetic rate laws and Petri nets. A prototypic network model is used as a test-case to illustrate the application of these concepts in Systems Biology.This work was partially supported by post-doctoral grant by Fundacao para a Ciencia e a Tecnologia (FCT) (SFRH/BPD/80784/2011), project PneumoSyS - A Systems Biology approach to the role of pneumococcal carbon metabolism in colonization and invasive disease (FCT contract: PTDC/SAU-MII/100964/2008) and by FCT (INESC-ID multiannual funding) through the PIDDAC program funds

High-resolution structure of an atypical α-phosphoglucomutase related to eukaryotic phosphomannomutases

The first structure of a bacterial α-phosphoglucomutase with an overall fold similar to eukaryotic phosphomannomutases is reported. Unlike most α-phosphoglucomutases within the α-D-phosphohexomutase superfamily, it belongs to subclass IIb of the haloacid dehalogenase superfamily (HADSF). It catalyzes the reversible conversion of α-glucose 1-phosphate to glucose 6-phosphate. The crystal structure of α-phosphoglucomutase from Lactococcus lactis (APGM) was determined at 1.5 Å resolution and contains a sulfate and a glycerol bound at the enzyme active site that partially mimic the substrate. A dimeric form of APGM is present in the crystal and in solution, an arrangement that may be functionally relevant. The catalytic mechanism of APGM and its strict specificity towards α-glucose 1-phosphate are discussed.Diamond Light Source

Overview on sugar metabolism and its control in Lactococcus lactis - The input from in vivo NMR

The wide application of lactic acid bacteria in the production of fermented foods depends to a great extent on the unique features of sugar metabolism in these organisms. The relative metabolic simplicity and the availability of genetic tools made Lactococcus lactis the organism of choice to gain insight into metabolic and regulatory networks. In vivo nuclear magnetic resonance has proven a very useful technique to monitor non-invasively the dynamics of intracellular metabolite and co-factor pools following a glucose pulse. Examples of the application of this methodology to identify metabolic bottlenecks and regulatory sites are presented. The use of this information to direct metabolic engineering strategies is illustrated. (c) 2005 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved

O Educador como Prático Reflexivo

p. 129-142De forma a contribuir para a partilha de experiências no âmbito da avaliação dos estágios profissionalizantes, e promovendo o desenvolvimento de estratégias inovadoras para os cursos de ensino, pretende-se com este artigo abordar a visão do aluno-estagiário sobre a sua prática e o seu processo formativo em geral. A apresentação de registos de algumas reflexões retiradas dos portfólios reflexivos, construídos pelos alunos, reveste-se de importância, não só para os mais diversos cursos de ensino mas, igualmente, como um exemplo para os profissionais que pretendem reflectir sobre a sua prática. Assim, desenvolvemos, inicialmente, uma abordagem teórica relativa à importância da reflexão na prática pedagógica do Educador de Infância, neste caso em particular, do estagiário finalista. Neste contexto, procedemos a uma selecção das reflexões mais significativas desenvolvidas por um grupo de alunas ao longo do estágio profissionalizante do curso em Educação de Infância no ano lectivo de 2006/07. Neste artigo pretendemos suscitar uma reflexão sobre as práticas educativas junto dos profissionais de educação

Green polymers toward nanobiotechnology(I): synthesis of glycopolypeptides and their analogues

Harnessing natural-based renewable molecular resources to construct functional synthetic green polymers is a promising research frontier at the interface of sustainable/green chemistry, polymer chemistry and nanobiotechnology. As natural glycoprotein mimics/analogues and biocompatible building blocks of nanobio- materials, synthetic functional glycopolypeptides and their structural/functional analogues have attracted great attentions in recent years. This mini-perspective article reviewed current synthetic strategies and methods of glycopolypeptides and their analogues. The pros and cons of the synthesis protocols were discussed, moreover, possible future perspectives in this field were also stated.info:eu-repo/semantics/publishedVersio

Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling

Although bifidobacteria are widely used as probiotics, their metabolism and physiology remain to be explored in depth. In this work, strain-specific genome-scale metabolic models were developed for two industrially and clinically relevant bifidobacteria, Bifidobacterium animalis subsp. lactis BB-12\uae and B. longum subsp. longum BB-46, and subjected to iterative cycles of manual curation and experimental validation. A constraint-based modeling framework was used to probe the metabolic landscape of the strains and identify their essential nutritional requirements. Both strains showed an absolute requirement for pantethine as a precursor for coenzyme A biosynthesis. Menaquinone-4 was found to be essential only for BB-46 growth, whereas nicotinic acid was only required by BB-12\uae. The model-generated insights were used to formulate a chemically defined medium that supports the growth of both strains to the same extent as a complex culture medium. Carbohydrate utilization profiles predicted by the models were experimentally validated. Furthermore, model predictions were quantitatively validated in the newly formulated medium in lab-scale batch fermentations. The models and the formulated medium represent valuable tools to further explore the metabolism and physiology of the two species, investigate the mechanisms underlying their health-promoting effects and guide the optimization of their industrial production processes

Poly(Ethylene glycol) diacrylate iongel membranes reinforced with nanoclays for co2 separation

Despite the fact that iongels are very attractive materials for gas separation membranes, they often show mechanical stability issues mainly due to the high ionic liquid (IL) content (≥60 wt%) needed to achieve high gas separation performances. This work investigates a strategy to improve the mechanical properties of iongel membranes, which consists in the incorporation of montmorillonite (MMT) nanoclay, from 0.2 to 7.5 wt%, into a cross-linked poly(ethylene glycol) diacrylate (PEGDA) network containing 60 wt% of the IL 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([C2mim][TFSI]). The iongels were prepared by a simple one-pot method using ultraviolet (UV) initiated polymerization of poly(ethylene glycol) diacrylate (PEGDA) and characterized by several techniques to assess their physico-chemical properties. The thermal stability of the iongels was influenced by the addition of higher MMT contents (>5 wt%). It was possible to improve both puncture strength and elongation at break with MMT contents up to 1 wt%. Furthermore, the highest ideal gas selectivities were achieved for iongels containing 0.5 wt% MMT, while the highest CO2 permeability was observed at 7.5 wt% MMT content, due to an increase in diffusivity. Remarkably, this strategy allowed for the preparation and gas permeation of self-standing iongel containing 80 wt% IL, which had not been possible up until now.publishersversionpublishe