An optimization model for metabolic pathways

This article is available open access through the publisher’s website through the link below. Copyright @ The Author 2009.Motivation: Different mathematical methods have emerged in the post-genomic era to determine metabolic pathways. These methods can be divided into stoichiometric methods and path finding methods. In this paper we detail a novel optimization model, based upon integer linear programming, to determine metabolic pathways. Our model links reaction stoichiometry with path finding in a single approach. We test the ability of our model to determine 40 annotated Escherichia coli metabolic pathways. We show that our model is able to determine 36 of these 40 pathways in a computationally effective manner. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online (http://bioinformatics.oxfordjournals.org/cgi/content/full/btp441/DC1)

Microwave-assisted synthesis and electrochemical evaluation of VO2 (B) nanostructures

Understanding how intercalation materials change during electrochemical operation is paramount to optimizing their behaviour and function and in situ characterization methods allow us to observe these changes without sample destruction. Here we first report the improved intercalation properties of bronze phase vanadium dioxide VO2 (B) prepared by a microwave-assisted route which exhibits a larger electrochemical capacity (232 mAh g-1) compared with VO2 (B) prepared by a solvothermal route (197 mAh g-1). These electrochemical differences have also been followed using in situ X-ray absorption spectroscopy allowing us to follow oxidation state changes as they occur during battery operation

Transforming LiTMP lithiation of challenging diazines via gallium alkyl trans-metal-trapping

This study establishes a new trans-metal-trapping (TMT) protocol based on a mixture of LiTMP (the base) and tris(trimethylsilylmethyl)gallium [Ga(CH2SiMe3)3, GaR3] (the trap) that, operating in a tandem manner, is effective for the regioselective deprotonation of sensitive diazines in hydrocarbon solution as illustrated through reactions of pyrazine, pyridazine and pyrimidine, as well as through the N-S heterocycle benzothiazole, the metallo-activated complexes of all of which have been isolated and structurally defined

Tratamiento quirúrgico en las cifosis congénitas: Revisión de 14 pacientes

Los autores efectúan una revisión de 14 pacientes con cifosis congénita, intervenidos entre los años 1979-1989, con un seguimiento medio de 7 años. La edad media preoperatoria fue de 11 años (todos ellos mayores de 5 años), con una cifosis media de 7 9 . En 6 casos se realizó una artrodesis posterior y en 8 una anterior combinada con una fusión posterior. Inicialmente obtuvieron una corrección media de la curva de 18° con la artrodesis posterior y 20° con la artrodesis combinada. La pérdida postoperatoria final fue de 10° y 8° respectivamente. En un caso, se produjo una pseudoartrosis por fusión corta. Como complicaciones postoperatorias en 5 pacientes, una radiculopatía, una infección superficial y cuatro protusiones de material que requirieron su extracción. Los autores analizan los factores que han podido influir en los resultados obtenidos, comparándolos posteriormente con los conseguidos por otros centros hospitalarios importantes.Fourteen patients with congenital kyphosis treated surgically between 1979- 1989 were reviewed. All had a follow-up of 2 years or more, with an average follow-up of 7 years. The average age at surgery was 11 and the average kyphosis was 79°. Six cases had posterior fusion only and eigth had combined anterior and posterior fusion. The results showed an average correction of the curve at surgery of 18° with posterior arthrodesis and 20° with combined arthrodesis. There was thus an average loss of 10° and 8° respectively from the time of surgery in both types of treatment. Pseudoarthrosis by short fusion ocurred in one case. Other complications after surgery were 1 radiculopathy, one wound infection and four rod protusion (six patients). The factors that have influence in this results were analysed. A comparison from the results of treatment at other medical centers was also carried out

Organozinc pivalate reagents : segregation, solubility, stabilisation and structural insights

The pivalates RZnOPiv⋅Mg(OPiv)X⋅n LiCl (OPiv=pivalate; R=aryl; X=Cl, Br, I) stand out amongst salt-supported organometallic reagents, because apart from their effectiveness in Negishi cross-coupling reactions, they show more resistance to attack by moist air than conventional organometallic compounds. Herein a combination of synthesis, coupling applications, X-ray crystallographic studies, NMR (including DOSY) studies, and ESI mass spectrometric studies provide details of these pivalate reagents in their own right. A p-tolyl case system shows that in [D8]THF solution these reagents exist as separated Me(p-C6H4)ZnCl and Mg(OPiv)2 species. Air exposure tests and X-ray crystallographic studies indicate that Mg(OPiv)2 enhances the air stability of aryl zinc species by sequestering H2O contaminants. Coupling reactions of Me(p-C6H4)ZnX (where X=different salts) with 4-bromoanisole highlight the importance of the presence of Mg(OPiv)2. Insight into the role of LiCl in these multicomponent mixtures is provided by the molecular structure of [(THF)2Li2(Cl)2(OPiv)2Zn]

Signatures of arithmetic simplicity in metabolic network architecture

Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their evolutionary history and complex wiring constitutes one of the most fascinating open questions in biology, intimately related to the enigma of life's origin itself. Is the evolution of metabolism subject to general principles, beyond the unpredictable accumulation of multiple historical accidents? Here we search for such principles by applying to an artificial chemical universe some of the methodologies developed for the study of genome scale models of cellular metabolism. In particular, we use metabolic flux constraint-based models to exhaustively search for artificial chemistry pathways that can optimally perform an array of elementary metabolic functions. Despite the simplicity of the model employed, we find that the ensuing pathways display a surprisingly rich set of properties, including the existence of autocatalytic cycles and hierarchical modules, the appearance of universally preferable metabolites and reactions, and a logarithmic trend of pathway length as a function of input/output molecule size. Some of these properties can be derived analytically, borrowing methods previously used in cryptography. In addition, by mapping biochemical networks onto a simplified carbon atom reaction backbone, we find that several of the properties predicted by the artificial chemistry model hold for real metabolic networks. These findings suggest that optimality principles and arithmetic simplicity might lie beneath some aspects of biochemical complexity

Scale-free Networks from Optimal Design

A large number of complex networks, both natural and artificial, share the presence of highly heterogeneous, scale-free degree distributions. A few mechanisms for the emergence of such patterns have been suggested, optimization not being one of them. In this letter we present the first evidence for the emergence of scaling (and smallworldness) in software architecture graphs from a well-defined local optimization process. Although the rules that define the strategies involved in software engineering should lead to a tree-like structure, the final net is scale-free, perhaps reflecting the presence of conflicting constraints unavoidable in a multidimensional optimization process. The consequences for other complex networks are outlined.Comment: 6 pages, 2 figures. Submitted to Europhysics Letters. Additional material is available at http://complex.upc.es/~sergi/software.ht

Computing the shortest elementary flux modes in genome-scale metabolic networks

This article is available open access through the publisher’s website through the link below. Copyright @ The Author 2009.Motivation: Elementary flux modes (EFMs) represent a key concept to analyze metabolic networks from a pathway-oriented perspective. In spite of considerable work in this field, the computation of the full set of elementary flux modes in large-scale metabolic networks still constitutes a challenging issue due to its underlying combinatorial complexity. Results: In this article, we illustrate that the full set of EFMs can be enumerated in increasing order of number of reactions via integer linear programming. In this light, we present a novel procedure to efficiently determine the K-shortest EFMs in large-scale metabolic networks. Our method was applied to find the K-shortest EFMs that produce lysine in the genome-scale metabolic networks of Escherichia coli and Corynebacterium glutamicum. A detailed analysis of the biological significance of the K-shortest EFMs was conducted, finding that glucose catabolism, ammonium assimilation, lysine anabolism and cofactor balancing were correctly predicted. The work presented here represents an important step forward in the analysis and computation of EFMs for large-scale metabolic networks, where traditional methods fail for networks of even moderate size. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online (http://bioinformatics.oxfordjournals.org/cgi/content/full/btp564/DC1).Fundação Calouste Gulbenkian, Fundação para a Ciência e a Tecnologia (FCT) and Siemens SA Portugal

The solvation and dissociation of 4-benzylaniline hydrochloride in chlorobenzene

A reaction scheme is proposed to account for the liberation of 4-benzylaniline from 4-benzylaniline hydrochloride, using chlorobenzene as a solvent at a temperature of 373 K. Two operational regimes are explored: “closed” reaction conditions correspond to the retention of evolved hydrogen chloride gas within the reaction medium, whereas an “open” system permits gaseous hydrogen chloride to be released from the reaction medium. The solution phase chemistry is analyzed by 1H NMR spectroscopy. Complete liberation of solvated 4-benzylaniline from solid 4-benzylaniline hydrochloride is possible under “open” conditions, with the entropically favored conversion of solvated hydrogen chloride to the gaseous phase thought to be the thermodynamic driver that effectively controls a series of interconnecting equilibria. A kinetic model is proposed to account for the observations of the open system