Search results for "metabolic networks"
showing 10 items of 99 documents
Adaptative biochemical pathways and regulatory networks in Klebsiella oxytoca BAS-10 producing a biotechnologically relevant exopolysaccharide during…
2012
Abstract Background A bacterial strain previously isolated from pyrite mine drainage and named BAS-10 was tentatively identified as Klebsiella oxytoca. Unlikely other enterobacteria, BAS-10 is able to grow on Fe(III)-citrate as sole carbon and energy source, yielding acetic acid and CO2 coupled with Fe(III) reduction to Fe(II) and showing unusual physiological characteristics. In fact, under this growth condition, BAS-10 produces an exopolysaccharide (EPS) having a high rhamnose content and metal-binding properties, whose biotechnological applications were proven as very relevant. Results Further phylogenetic analysis, based on 16S rDNA sequence, definitively confirmed that BAS-10 belongs t…
Longevity: epigenetic and biomolecular aspects
2015
AbstractMany aging theories and their related molecular mechanisms have been proposed. Simple model organisms such as yeasts, worms, fruit flies and others have massively contributed to their clarification, and many genes and pathways have been associated with longevity regulation. Among them, insulin/IGF-1 plays a key and evolutionary conserved role. Interestingly, dietary interventions can modulate this pathway. Calorie restriction (CR), intermittent fasting, and protein and amino acid restriction prolong the lifespan of mammals by IGF-1 regulation. However, some recent findings support the hypothesis that the long-term effects of diet also involve epigenetic mechanisms. In this review, w…
Factors that influence the quality of metabolomics data in in vitro cell toxicity studies: a systematic survey
2021
Abstract REACH (Registration, Evaluation, Authorization and Restriction of Chemicals) is a global strategy and regulation policy of the EU that aims to improve the protection of human health and the environment through the better and earlier identification of the intrinsic properties of chemical substances. It entered into force on 1st June 2007 (EC 1907/2006). REACH and EU policies plead for the use of robust high-throughput "omic" techniques for the in vitro investigation of the toxicity of chemicals that can provide an estimation of their hazards as well as information regarding the underlying mechanisms of toxicity. In agreement with the 3R’s principles, cultured cells are nowadays wide…
Abscisic Acid Connects Phytohormone Signaling with RNA Metabolic Pathways and Promotes an Antiviral Response that Is Evaded by a Self-Controlled RNA …
2020
© 2020 The Authors.
Xanthine dehydrogenase processes retinol to retinoic acid in human mammary epithelial cells
2008
Retinoic acid is considered to be the active metabolite of retinol, able to control differentiation and proliferation of epithelia. Retinoic acid biosynthesis has been widely described with the implication of multiple enzymatic activities. However, our understanding of the cell biological function and regulation of this process is limited. In a recent study we evidenced that milk xanthine oxidase (E.C. 1.17.3.2.) is capable to oxidize all-trans-retinol bound to CRBP (holo-CRBP) to all-trans-retinaldehyde and then to all-trans-retinoic acid. To get further knowledge regarding this process we have evaluated the biosynthetic pathway of retinoic acid in a human mammary epithelial cell line (HME…
The YJL185C, YLR376C and YJR129C genes of Saccharomyces cerevisiae are probably involved in regulation of the glyoxylate cycle
2006
The ER24 aci (acidification) mutant of Saccharomyces cerevisiae excreting protons in the absence of glucose was transformed with a multicopy yeast DNA plasmid library. Three different DNA fragments restored the wild-type phenotype termed Aci- because it does not acidify the complete glucose medium under the tested conditions. Molecular dissection of the transforming DNA fragments identified two multicopy suppressor genes YJL185C, YJR129C and one allelic YLR376C. Disruption of either of the three genes in wild-type yeast strain resulted in acidification of the medium (Aci+ phenotype) similarly to the original ER24 mutant. These data indicate the contribution of the ER24 gene product Ylr376Cp…
BioAnalysis: A Framework for Structural and Functional Robustness Analysis of Metabolic Networks
2010
The main objective of this work is to analyze metabolic networks evolution in terms of their robustness and fault tolerance capabilities. In metabolic networks, errors can be seen as random removal of network nodes, while attacks are high-connectivity-degree node deletion aimed at compromising network activity. This paper proposes a software framework, namely BioAnalysis, used to test the robustness and the fault tolerance capabilities of real metabolic networks, when mutations and node deletions affect the network structure. The performed simulations are related to the central metabolic network of the well-known E. coli single-celled bacterium and involve either hub nodes or non-hub nodes,…
An Embedded Processor for Metabolic Networks Optimization
2011
In recent years biological processes modelling and simulation have become two key issues in analyzing complex cellular systems. The computational requirements suggest to investigate alternative solutions to the common supercomputers and clusters in order to optimize and overcome computational bottleneck. The goal of this work is the design and the realization of an embedded processor for metabolic networks optimization in order to examine their behaviour and robustness under malfunctions of one or more nodes. The embedded processor has been prototyped on the Celoxica RC203E board, equipped with programmable FPGA technologies. A case studied outlining the E. Coli bacteria metabolic network i…
Topological Information, Flux Balance Analysis, and Extreme Pathways Extraction for Metabolic Networks Behaviour Investigation
2011
In recent years biological processes modeling and simulation have become two key issues in analyzing complex cellular systems. Information about metabolic networks is often incomplete, since a large portion of available data is ignored by its probabilistic nature. The main objective of this work is to investigate metabolic networks behavior in terms of their fault tolerance capabilities as random removal of network nodes and high-connectivity-degree node deletion aimed at compromising or modifying network activity. This paper proposes a software framework, namely CEllDataLaB, containing three tasks to perform the structural and functional analysis: topological analysis, flux balance analysi…
Misinterpretation risks of global stochastic optimisation of kinetic models revealed by multiple optimisation runs
2016
Abstract One of use cases for metabolic network optimisation of biotechnologically applied microorganisms is the in silico design of new strains with an improved distribution of metabolic fluxes. Global stochastic optimisation methods (genetic algorithms, evolutionary programing, particle swarm and others) can optimise complicated nonlinear kinetic models and are friendly for unexperienced user: they can return optimisation results with default method settings (population size, number of generations and others) and without adaptation of the model. Drawbacks of these methods (stochastic behaviour, undefined duration of optimisation, possible stagnation and no guaranty of reaching optima) cau…