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)

Características generales de las subcuencas del margen peninsular meditarráneo ("Rift" del Surco de Valencia)

This paper describes the general characteristics, namely the geometry and the sedimentary infill, of several troughs of Tertiary age present in the off-shore eastem Mediterranean margin of Spain. Al1 of them are included within the Valencia Trough, a rift basin developed during Paleogene and early Miocene times between the Balearic archipelago and mainland Spain. Although some authors (Soler et al., 1983; Fontboté et al., 1990; Roca and Desegaulx, 1992; Watts and Torné, 1992; Martínez del Olmo, 1994) have recently described the Valencia Trough as a foredeep basin of the Betics, we think that the referred foredeep does not extend as far as to the westernmost area of the Mediterranean. This is based on the evidence provided by the interpretation of numerous seismic surveys and nearly two hundred wells drilled without finding a single repetition or a clear evidence of compression in the area of this study. This rift is tbe southemmost branch of the European rift, which crosses most of western Europe from the Rhine graben through the westem Alps southwards into Morocco along the eastem coast of Spain (Sanz de Galdeano, 1990; Fontboté et al., 1990). The substratum of the basin is basically formed by Mesozoic (mainly carbonates) and pre-Mesozoic sediments (mainly clastics and metamorphics), folded and deformed during the Pyrenean orogeny and later fractured as horsts and grabens during the rift stage. The carbonates were severely fractured and intensively karsted during subaerial exposure following the deformation of the region. These processes have enhanced tbeir reservoir cbaracteristics (porosity and permeability) thus allowing the accumulation of hydrocarbons. Aborted during middle Miocene times, this rift started its development in the north during Paleogene times (Rosas and Barcelona troughs) and the sediments of this age constitute the bulk of the infill. On the contrary, in the southern sub-basins (Tarragona and Castellón troughs) the formation of the rift was younger, dunng early middle Miocene times, and the bulk of sediments infilling the troughs are of this age. This change in the age of the sedimentary infill, younger towards the south paralells the southwards development of the main rift. The sediments were filling the rift troughs, and by middle Miocene times al1 reliefs (horsts and grahens) had been leveled off. During early Miocene times the sedimentation in the troughs (mainly starved basins) took place under restricted marine conditions that favored the accumulation and preservation of the organic matter and the subsequent development of hydrocarhon source beds in some of them (Demaison and Bourgeois, 1984). The high thermal gradient, typical of rift hasins, favored the early maturation of the organic matter. The migration of the newly generated hydrocarbons into the neighbour paleoreliefs, mostly formed by karsted carbonates (Martínez del Olmo and Esteban, 1983), brought about severa1 oil fields that have been actively explored and exploited. So far only in the Tarragona trough commercial accumulations have been found (Amposta, Casablanca, Dorada and Tarraco) but other troughs (namely Rosas and Barcelona) have had good shows and the geocheniical analysis have also demonstrated the existence of good source rocks. Frorn the middle Miocene on, the sedimentation changed dramatically to a prograding continental shelf of passive margin type. Two megasequences are distinguished: the first one during the rniddle-late Miocene and the second one during Plio-Quatemary times, separated by the Messinian unconformity that locally produced important erosional canyons in the underlying sediments

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

Changes in Salivary Analytes of Horses Due to Circadian Rhythm and Season: A Pilot Study.

This study aims to evaluate the circadian and circannual variations in a panel of analytes in horse saliva that have been previously described as biomarkers related to stress and disease, in order to interpret them correctly when they are measured in this species. This panel of analytes integrated cortisol, salivary alpha-amylase (sAA), lipase (Lip), total esterase (TEA), butyrylcholinesterase (BChE), adenosine deaminase (ADA), γ-glutamyl transferase (gGT), creatine kinase (CK), urea, total bilirubin, total protein (TP), and phosphorus. These analytes were measured in saliva obtained from a population of five clinically healthy mares from 06:30 to 20:30, every 2 h over two consecutive days in two different photoperiod seasons, winter and spring. The temperature and relative humidity did not change between the two consecutive days sampled in each sampled season, and no thermal discomfort was observed. Changes throughout the course of the day were observed for cortisol, sAA, TEA, BChE, ADA, and CK. However, a circadian pattern was only observed for cortisol, TEA, BChE, ADA, and CK. Moreover, the values obtained for sAA, Lip, and BChE were significantly different between seasons, with different daily rhythms for cortisol, TEA, BChE, and ADA depending on the season. In conclusion, this pilot study indicates that the time of the day and the season influence salivary analytes in horses, showing a rhythmic pattern for cortisol, TEA, BChE, ADA, and CK. These factors should thus be taken into consideration for the interpretation of analytes in horse saliv

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