Abstract: We explicitly compute the limiting transient distribution of the search-cost in the move-to-front Markov chain when the number of objects tends to infinity, for general families of deterministic or random request rates. Our techniques are based on a “law of large numbers for random partitions,” a scaling limit that allows us to exactly compute limiting expectation of empirical functionals of the request probabilities of objects. In particular, we show that the limiting search-cost can be split at an explicit deterministic threshold into one random variable in equilibrium, and a second one related to the initial ordering of the list. Our results ensure the stability of the limiting search-cost under general perturbations of the request probabilities. We provide the description of the limiting transient behavior in several examples where only the stationary regime is known, and discuss the range of validity of our scaling limit.

Abstract: The Black-Scholes equation can be interpreted from the point of view of quantum mechanics, as the imaginary time Schrodinger equation of a free particle. When deviations of this state of equilibrium are considered, as a product of some market imperfection, such as: Transaction cost, asymmetric information issues, short-term volatility, extreme discontinuities, or serial correlations; the classical non-arbitrage assumption of the Black-Scholes model is violated, implying a non-risk-free portfolio. From Haven (2002) [1] we know that an arbitrage environment is a necessary condition to embedding the Black-Scholes option pricing model in a more general quantum physics setting. The aim of this paper is to propose a new Black-Scholes-Schrodinger model based on the endogenous arbitrage option pricing formulation introduced by Contreras et al. (2010) [2]. Hence, we derive a more general quantum model of option pricing, that incorporates arbitrage as an external time dependent force, which has an associated potential related to the random dynamic of the underlying asset price. This new resultant model can be interpreted as a Schrodinger equation in imaginary time for a particle of mass 1/sigma(2) with a wave function in an external field force generated by the arbitrage potential. As pointed out above, this new model can be seen as a more general formulation, where the perfect market equilibrium state postulated by the Black-Scholes model represent a particular case. Finally, since the Schrodinger equation is in place, we can apply semiclassical methods, of common use in theoretical physics, to find an approximate analytical solution of the Black-Scholes equation in the presence of market imperfections, as it is the case of an arbitrage bubble. Here, as a numerical illustration of the potential of this Schrodinger equation analogy, the semiclassical approximation is performed for different arbitrage bubble forms (step, linear and parabolic) and compare with the exact solution of our general quantum model of option pricing. (C) 2010 Elsevier B.V. All rights reserved.

Abstract: One fundamental concept in the context of biological systems on which researches have flourished in the past decade is that of the apparent robustness of these systems, i.e., their ability to resist to perturbations or constraints induced by external or boundary elements such as electromagnetic fields acting on neural networks, micro-RNAs acting on genetic networks and even hormone flows acting both on neural and genetic networks. Recent studies have shown the importance of addressing the question of the environmental robustness of biological networks such as neural and genetic networks. In some cases, external regulatory elements can be given a relevant formal representation by assimilating them to or modeling them by boundary conditions. This article presents a generic mathematical approach to understand the influence of boundary elements on the dynamics of regulation networks, considering their attraction basins as gauges of their robustness. The application of this method on a real genetic regulation network will point out a mathematical explanation of a biological phenomenon which has only been observed experimentally until now, namely the necessity of the presence of gibberellin for the flower of the plant Arabidopsis thaliana to develop normally.

Abstract: P>Phenoxyalkanoic herbicides such as 2,4-dichlorophenoxyacetate (2,4-D), 2,4-dichlorophenoxybutyrate (2,4-DB) or mecoprop are widely used to control broad-leaf weeds. Several bacteria have been reported to degrade these herbicides using the alpha-ketoglutarate-dependent, 2,4-dichlorophenoxyacetate dioxygenase encoded by the tfdA gene, as the enzyme catalysing the first step in the catabolic pathway. The effects of exposure to different phenoxyalkanoic herbicides in the soil bacterial community and in the tfdA genes diversity were assessed using an agricultural soil exposed to these anthropogenic compounds. Total community bacterial DNA was analysed by terminal restriction fragment length polymorphism of the 16S rRNA and the tfdA gene markers, and detection and cloning of tfdA gene related sequences, using PCR primer pairs. After up to 4 months of herbicide exposure, significant changes in the bacterial community structure were detected in soil microcosms treated with mecoprop, 2,4-DB and a mixture of both plus 2,4-D. An impressive variety of novel tfdA gene related sequences were found in these soil microcosms, which cluster in new tfdA gene related sequence groups, unequally abundant depending on the specific herbicide used in soil treatment. Structural analysis of the putative protein products showed small but significant amino acid differences. These tfdA gene sequence variants are, probably, required for degradation of natural substrate(s) structurally related to these herbicides and their presence explains self-remediation of soils exposed to phenoxyalkanoic herbicides.

Abstract: This study reports on the factors involved in regulating the composition and structure of bacterial communities epiphytic on intertidal macroalgae, exploring their temporal variability and the role of copper pollution. Culture-independent, molecular approaches were chosen for this purpose and three host species were used as models: the ephemeral Ulva spp. (Chlorophyceae) and Scytosiphon lomentaria (Phaeophyceae) and the long-living Lessonia nigrescens (Phaeophyceae). The algae were collected from two coastal areas in Northern Chile, where the main contrast was the concentration of copper in the seawater column resulting from copper-mine waste disposals. We found a clear and strong effect in the structure of the bacterial communities associated with the algal species serving as host. The structure of the bacterial communities also varied through time. The effect of copper on the structure of the epiphytic bacterial communities was significant in Ulva spp., but not on L. nigrescens. The use of 16S rRNA gene library analysis to compare bacterial communities in Ulva revealed that they were composed of five phyla and six classes, with approximately 35 bacterial species, dominated by members of Bacteroidetes (Cytophaga-Flavobacteria-Bacteroides) and alpha-Proteobacteria, in both non-polluted and polluted sites. Less common groups, such as the Verrucomicrobiae, were exclusively found in polluted sites. This work shows that the structure of bacterial communities epiphytic on macroalgae is hierarchically determined by algal species > temporal changes > copper levels.

Abstract: P>The eastern tropical Pacific Ocean holds two of the main oceanic oxygen minimum zones of the global ocean. The presence of an oxygen-depleted layer at intermediate depths, which also impinges on the seafloor and in some cases the euphotic zone, plays a significant role in structuring both pelagic and benthic communities, and also in the vertical partitioning of microbial assemblages. Here, we assessed the genetic diversity and distribution of natural populations of the cyanobacteria Prochlorococcus and Synechococcus within oxic and suboxic waters of the eastern tropical Pacific using cloning and sequencing, and terminal restriction fragment length polymorphism (T-RFLP) analyses applied to the 16S-23S rRNA internal transcribed spacer region. With the T-RFLP approach we could discriminate 19 cyanobacterial clades, of which 18 were present in the study region. Synechococcus was more abundant in the surface oxic waters of the eastern South Pacific, while Prochlorococcus dominated the subsurface low-oxygen waters. Two of the dominant clades in the oxygen-deficient waters belong to novel and yet uncultivated lineages of low-light adapted Prochlorococcus.

Abstract: Catechols are central intermediates in the metabolism of aromatic compounds. Degradation of 4-methyl-catechol via intradiol cleavage usually leads to the formation of 4-methylmuconolactone (4-ML) as a dead-end metabolite. Only a few microorganisms are known to mineralize 4-ML. The mml gene cluster of Pseudomonas reinekei MT1, which encodes enzymes involved in the metabolism of 4-ML, is shown here to encode 10 genes found in a 9.4-kb chromosomal region. Reverse transcription assays revealed that these genes form a single operon, where their expression is controlled by two promoters. Promoter fusion assays identified 4-methyl-3-oxoadipate as an inducer. Mineralization of 4-ML is initiated by the 4-methylmuconolactone methylisomerase encoded by mmlI. This reaction produces 3-ML and is followed by a rearrangement of the double bond catalyzed by the methylmuconolactone isomerase encoded by mmlJ. Deletion of mmlL, encoding a protein of the metallo-beta-lactamase superfamily, resulted in a loss of the capability of the strain MT1 to open the lactone ring, suggesting its function as a 4-methyl-3-oxoadipate enol-lactone hydrolase. Further metabolism can be assumed to occur by analogy with reactions known from the 3-oxoadipate pathway. mmlF and mmlG probably encode a 4-methyl-3-oxoadipyl-coenzyme A (CoA) transferase, and the mmlC gene product functions as a thiolase, transforming 4-methyl-3-oxoadipyl-CoA into methylsuccinyl-CoA and acetyl-CoA, as indicated by the accumulation of 4-methyl-3-oxoadipate in the respective deletion mutant. Accumulation of methylsuccinate by an mmlK deletion mutant indicates that the encoded acetyl-CoA hydrolase/transferase is crucial for channeling methylsuccinate into the central metabolism.

Abstract: Bioremediation is an important technology for the removal of persistent organic pollutants from the environment. Bioaugmentation with the encapsulated Pseudomonas sp. strain MHP41 of agricultural soils contaminated with the herbicide simazine was studied. The experiments were performed in microcosm trials using two soils: soil that had never been previously exposed to s-triazines (NS) and soil that had > 20 years of s-triazine application (AS). The efficiency of the bioremediation process was assessed by monitoring simazine removal by HPLC. The simazine-degrading microbiota was estimated using an indicator for respiration combined with most-probable-number enumeration. The soil bacterial community structures and the effect of bioaugmentation on these communities were determined using 16S RNA gene clone libraries and FISH analysis. Bioaugmentation with MHP41 cells enhanced simazine degradation and increased the number of simazine-degrading microorganisms in the two soils. In highly contaminated NS soil, bioaugmentation with strain MHP41 was essential for simazine removal. Comparative analysis of 16S rRNA gene clone libraries from NS and AS soils revealed high bacterial diversity. Bioaugmentation with strain MHP41 promoted soil bacterial community shifts. FISH analysis revealed that bioaugmentation increased the relative abundances of two phylogenetic groups (Acidobacteria and Planctomycetes) in both soils. Although members of the Archaea were metabolically active in these soils, their relative abundance was not altered by bioaugmentation.

Abstract: Aims: This study used culture-dependent and culture-independent approaches to characterize bacterial communities in copper plumbing corrosion and to assess biofilm formation and copper resistance of heterotrophic bacteria isolated from copper pipes. Methods and Results: Water and copper pipes were collected from a cold-water household distribution system affected by 'blue water' corrosion and presenting biofilm formation. Corrosion-promoting ageing experiments were performed with conditioned unused copper pipes filled with unfiltered and filtered sampled water as nonsterile and sterile treatments, respectively. During 8 weeks, stagnant water within the pipes was replaced with aerated fresh water every 2 or 3 days. Total copper and pH were determined in sampled water, and copper pipe coupons were cut for microscopic analyses. Biofilms were extracted from field and laboratory pipes, and total DNA was isolated. Bacterial communities' composition was analysed by terminal restriction fragment length polymorphism (T-RFLP) and clonal libraries of 16S rRNA genes. Heterotrophic bacterial isolates were obtained from water and biofilm extracts and characterized in terms of biofilm formation capacity and copper minimum inhibitory concentration. The results indicated that copper concentration in stagnant water from nonsterile treatments was much higher than in sterile treatments and corrosion by-products structure in coupon surfaces was different. Multivariate analysis of T-RFLP profiles and clone sequencing showed significant dissimilarity between field and laboratory biofilm communities, and a low richness and the dominant presence of Gamma- and Betaproteobacteria in both cases. Several bacterial isolates formed biofilm and tolerated high copper concentrations. Conclusions: The study demonstrates microbially influenced corrosion (MIC) in copper plumbing. Gamma- and Betaproteobacteria dominated the corroded copper piping bacterial community, whose ability to form biofilms may be important for bacterial corrosion promotion and survival in MIC events. Significance and Impact of the Study: The characterization of micro-organisms that influence copper plumbing corrosion has significant implications for distribution system management and copper corrosion control.

Abstract: Cell walls polysaccharides from murta fruit (Ugni molinae Turcz), an endemic Chilean species with relevant food uses, were fractionated by water, ammonium oxalate, hot diluted HCl and cold diluted NaOH extractions. The polysaccharide fractions were analysed for monosaccharide composition and physicochemical properties. Pectic substances were found in all extracts, but mainly in the oxalate and acid soluble fractions, in which they appear as homogalacturonan polymers. Murta pectin was further extracted by hot diluted acid treatment using industrial conditions, yielding 30% by weight of dry fruit. The polymer showed similar composition and physicochemical properties to those of commercial citrus pectin, presenting a galacturonic acid content of 70.9% (w/w), a molecular weight of 597 kDa, and a methoxylation degree of 57%. The FT-IR spectrum of murta pectin suggests the presence of ferulic acid residues on its structure and the NMR analysis confirmed the structure of this polysaccharide. It is concluded that murta fruit can be considered as a valuable source of high quality pectin. (C) 2010 Elsevier Ltd. All rights reserved.