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Author (up) Allende, H.; Bravo, D.; Canessa, E. pdf  doi
openurl 
  Title Robust design in multivariate systems using genetic algorithms Type
  Year 2010 Publication Quality & Quantity Abbreviated Journal Qual. Quant.  
  Volume 44 Issue 2 Pages 315-332  
  Keywords Robust design; Taguchi methods; Genetic algorithms; Desirability functions  
  Abstract This paper presents a methodology based oil genetic algorithms, which finds feasible and reasonably adequate Solutions to problems of robust design in multivariate systems. We use a genetic algorithm to determine the appropriate control factor levels for simultaneously optimizing all of the responses of the system, considering the noise factors which affect it. The algorithm is guided by a desirability function which works with only one fitness function although the system May have many responses. We validated the methodology using data obtained from a real system and also from a process simulator, considering univariate and multivariate systems. In all cases, the methodology delivered feasible solutions, which accomplished the goals of robust design: obtain responses very close to the target values of each of them, and with minimum variability. Regarding the adjustment of the mean of each response to the target value, the algorithm performed very well. However, only in some of the multivariate cases, the algorithm was able to significantly reduce the variability of the responses.  
  Address [Allende, Hector; Bravo, Daniela; Canessa, Enrique] Univ Adolfo Ibanez, Fac Ciencia & Tecnol, Balmaceda 1620, Vina Del Mar, Chile, Email: hallende@uai.cl  
  Corporate Author Thesis  
  Publisher Springer Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0033-5177 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000275327300008 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 82  
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Author (up) Barrera, J.; Fontbona, J. pdf  doi
openurl 
  Title The Limiting Move-To-Front Search-Cost In Law Of Large Numbers Asymptotic Regimes Type
  Year 2010 Publication Annals Of Applied Probability Abbreviated Journal Ann. Appl. Probab.  
  Volume 20 Issue 2 Pages 722-752  
  Keywords Move-to-front rule; search-cost; law of large numbers; propagation of chaos  
  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.  
  Address [Barrera, Javiera] Univ Adolfo Ibanez, Escuela Ingn & Ciencias, Penalolen, Chile, Email: javiera.barrera@uai.cl  
  Corporate Author Thesis  
  Publisher Inst Mathematical Statistics Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1050-5164 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000283529500012 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 101  
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Author (up) Contreras, M.; Montalva, R.; Pellicer, R.; Villena, M. pdf  doi
openurl 
  Title Dynamic option pricing with endogenous stochastic arbitrage Type
  Year 2010 Publication Physica A-Statistical Mechanics And Its Applications Abbreviated Journal Physica A  
  Volume 389 Issue 17 Pages 3552-3564  
  Keywords Black-Scholes model; Arbitrage; Option pricing  
  Abstract Only few efforts have been made in order to relax one of the key assumptions of the Black-Scholes model: the no-arbitrage assumption. This is despite the fact that arbitrage processes usually exist in the real world, even though they tend to be short-lived. The purpose of this paper is to develop an option pricing model with endogenous stochastic arbitrage, capable of modelling in a general fashion any future and underlying asset that deviate itself from its market equilibrium. Thus, this investigation calibrates empirically the arbitrage on the futures on the S&P 500 index using transaction data from September 1997 to June 2009, from here a specific type of arbitrage called “arbitrage bubble”, based on a t-step function, is identified and hence used in our model. The theoretical results obtained for Binary and European call options, for this kind of arbitrage, show that an investment strategy that takes advantage of the identified arbitrage possibility can be defined, whenever it is possible to anticipate in relative terms the amplitude and timespan of the process. Finally, the new trajectory of the stock price is analytically estimated for a specific case of arbitrage and some numerical illustrations are developed. We find that the consequences of a finite and small endogenous arbitrage not only change the trajectory of the asset price during the period when it started, but also after the arbitrage bubble has already gone. In this context, our model will allow us to calibrate the B-S model to that new trajectory even when the arbitrage already started. (C) 2010 Elsevier B.V. All rights reserved.  
  Address [Contreras, Mauricio; Montalva, Rodrigo; Pellicer, Rely; Villena, Marcelo] Univ Adolfo Ibanez, Fac Sci & Engn, Vina Del Mar, Chile, Email: mauricio.contreras@uai.cl  
  Corporate Author Thesis  
  Publisher Elsevier Science Bv Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0378-4371 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000280118100023 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 91  
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Author (up) Contreras, M.; Pellicer, R.; Villena, M.; Ruiz, A. pdf  doi
openurl 
  Title A quantum model of option pricing: When Black-Scholes meets Schrodinger and its semi-classical limit Type
  Year 2010 Publication Physica A-Statistical Mechanics And Its Applications Abbreviated Journal Physica A  
  Volume 389 Issue 23 Pages 5447-5459  
  Keywords Black-Scholes model; Arbitrage; Option pricing; Quantum mechanics; Semi-classical methods  
  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.  
  Address [Contreras, Mauricio; Pellicer, Rely; Villena, Marcelo; Ruiz, Aaron] Adolfo Ibanez Univ, Fac Sci & Engn, Santiago, Chile, Email: mauricio.contreras@uai.cl  
  Corporate Author Thesis  
  Publisher Elsevier Science Bv Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0378-4371 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000283904000012 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 116  
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Author (up) De la Iglesia, R.; Valenzuela-Heredia, D.; Pavissich, J.P.; Freyhoffer, S.; Andrade, S.; Correa, J.A.; Gonzalez, B. pdf  doi
openurl 
  Title Novel polymerase chain reaction primers for the specific detection of bacterial copper P-type ATPases gene sequences in environmental isolates and metagenomic DNA Type
  Year 2010 Publication Letters In Applied Microbiology Abbreviated Journal Lett. Appl. Microbiol.  
  Volume 50 Issue 6 Pages 552-562  
  Keywords ATPases; bacterial communities; copper resistance; metagenomic DNA; PCR primer pair  
  Abstract Aims: In the last decades, the worldwide increase in copper wastes release by industrial activities like mining has driven environmental metal contents to toxic levels. For this reason, the study of the biological copper-resistance mechanisms in natural environments is important. Therefore, an appropriate molecular tool for the detection and tracking of copper-resistance genes was developed. Methods and Results: In this work, we designed a PCR primer pair to specifically detect copper P-type ATPases gene sequences. These PCR primers were tested in bacterial isolates and metagenomic DNA from intertidal marine environments impacted by copper pollution. As well, T-RFLP fingerprinting of these gene sequences was used to compare the genetic composition of such genes in microbial communities, in normal and copper-polluted coastal environments. New copper P-type ATPases gene sequences were found, and a high degree of change in the genetic composition because of copper exposure was also determined. Conclusions: This PCR based method is useful to track bacterial copper-resistance gene sequences in the environment. Significance and Impact of the Study: This study is the first to report the design and use of a PCR primer pair as a molecular marker to track bacterial copper-resistance determinants, providing an excellent tool for long-term analysis of environmental communities exposed to metal pollution.  
  Address [Gonzalez, B.] Univ Adolfo Ibanez, Fac Ingn & Ciencia, Santiago 7941169, Chile, Email: bernardo.gonzalez@uai.cl  
  Corporate Author Thesis  
  Publisher Wiley-Blackwell Publishing, Inc Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0266-8254 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000277417000002 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 88  
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Author (up) Demongeot, J.; Goles, E.; Morvan, M.; Noual, M.; Sene, S. pdf  doi
openurl 
  Title Attraction Basins as Gauges of Robustness against Boundary Conditions in Biological Complex Systems Type
  Year 2010 Publication Plos One Abbreviated Journal PLoS One  
  Volume 5 Issue 8 Pages 18 pp  
  Keywords  
  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.  
  Address [Demongeot, Jacques] Univ Grenoble 1, TIMC IMAG, CNRS, UMR 5525, La Tronche, France, Email: Sylvain.Sene@ibisc.univ-evry.fr  
  Corporate Author Thesis  
  Publisher Public Library Science Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1932-6203 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000280605400002 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 92  
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Author (up) Fomin, F.V.; Golovach, P.A.; Kratochvil, J.; Nisse, N.; Suchan, K. pdf  doi
openurl 
  Title Pursuing a fast robber on a graph Type
  Year 2010 Publication Theoretical Computer Science Abbreviated Journal Theor. Comput. Sci.  
  Volume 411 Issue 7-9 Pages 1167-1181  
  Keywords Pursuit-evasion game on graphs; Cops and Robbers; Complexity; Parameterized complexity; Cliquewidth; Planar graph  
  Abstract The Cops and Robbers game as originally defined independently by Quilliot and by Nowakowski and Winkler in the 1980s has been Much Studied, but very few results pertain to the algorithmic and complexity aspects of it. In this paper we prove that computing the minimum number of cops that are guaranteed to catch a robber on a given graph is NP-hard and that the parameterized version of the problem is W[2]-hard; the proof extends to the case where the robber moves s time faster than the cops. We show that on split graphs, the problem is polynomially solvable if s = 1 but is NP-hard if s = 2. We further prove that on graphs of bounded cliquewidth the problem is polynomially solvable for s <= 2. Finally, we show that for planar graphs the minimum number of cops is unbounded if the robber is faster than the cops. (C) 2009 Elsevier B.V. All rights reserved.  
  Address [Fomin, Fedor V.; Golovach, Petr A.] Univ Bergen, Dept Informat, N-5020 Bergen, Norway, Email: petr.golovach@durham.ac.uk  
  Corporate Author Thesis  
  Publisher Elsevier Science Bv Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0304-3975 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000274886700020 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 83  
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Author (up) Gazitua, M.C.; Slater, A.W.; Melo, F.; Gonzalez, B. pdf  doi
openurl 
  Title Novel alpha-ketoglutarate dioxygenase tfdA-related genes are found in soil DNA after exposure to phenoxyalkanoic herbicides Type
  Year 2010 Publication Environmental Microbiology Abbreviated Journal Environ. Microbiol.  
  Volume 12 Issue 9 Pages 2411-2425  
  Keywords  
  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.  
  Address [Gazitua, M. C.; Slater, A. W.; Melo, F.; Gonzalez, B.] Pontificia Univ Catolica Chile, Fac Ciencias Biol, Dept Mol Genet & Microbiol, Ctr Adv Studies Ecol & Biodivers, Santiago, Chile, Email: bernardo.gonzalez@uai.cl  
  Corporate Author Thesis  
  Publisher Wiley-Blackwell Publishing, Inc Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1462-2912 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000281556900003 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 97  
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Author (up) Goles, E.; Salinas, L. pdf  doi
openurl 
  Title Sequential operator for filtering cycles in Boolean networks Type
  Year 2010 Publication Advances In Applied Mathematics Abbreviated Journal Adv. Appl. Math.  
  Volume 45 Issue 3 Pages 346-358  
  Keywords  
  Abstract Given a Boolean network without negative circuits, we propose a polynomial algorithm to build another network such that, when updated in parallel, it has the same fixed points than the original one, but it does not have any dynamical cycle. To achieve that, we apply a network transformation related to the sequential update. As a corollary, we can find a fixed point in polynomial time for this kind of networks. (C) 2010 Elsevier Inc. All rights reserved.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0196-8858 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000281294000004 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 94  
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Author (up) Hengst, M.B.; Andrade, S.; Gonzalez, B.; Correa, J.A. pdf  doi
openurl 
  Title Changes in Epiphytic Bacterial Communities of Intertidal Seaweeds Modulated by Host, Temporality, and Copper Enrichment Type
  Year 2010 Publication Microbial Ecology Abbreviated Journal Microb. Ecol.  
  Volume 60 Issue 2 Pages 282-290  
  Keywords  
  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.  
  Address [Hengst, Martha B.] Univ Antofagasta, Antofagasta Inst Renewable Resources, Antofagasta, Chile, Email: bernardo.gonzalez@uai.cl  
  Corporate Author Thesis  
  Publisher Springer Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0095-3628 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000281981300003 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 98  
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Author (up) Lardies, M.A.; Arias, M.B.; Bacigalupe, L.D. pdf  doi
openurl 
  Title Phenotypic covariance matrix in life-history traits along a latitudinal gradient: a study case in a geographically widespread crab on the coast of Chile Type
  Year 2010 Publication Marine Ecology-Progress Series Abbreviated Journal Mar. Ecol.-Prog. Ser.  
  Volume 412 Issue Pages 179-187  
  Keywords Intertidal; Reproduction; Crustacea; Plasticity; Clinical variation  
  Abstract Geographically widely spread species can cope with environmental differences among habitats by genetic differentiation and/or phenotypic flexibility. In marine crustaceans, intraspecific variations in life-history traits are pervasive along latitudinal clines. Replicated latitudinal clines are of evolutionary interest because they provide evidence of the occurrence of natural selection. If the means of traits along the latitudinal gradient are expected to be the result of natural selection, there is no reason why variances and covariances will not also be subject to selection, since selection is essentially a multivariate phenomenon. We studied life-history changes in means, variances, and covariances (i.e. P matrix) in 6 populations of the endemic crab Cyclograpsus cinereus (Decapoda: Grapsidae) along a latitudinal gradient over 19 degrees on the Chilean coast. Trait means differed among localities for all traits analyzed (i.e. female size, number and size of eggs, and reproductive output), and the variation displayed a clinal pattern. In general, the main result that emerged from planned comparisons of P matrices is that, when detected, differences between localities mainly reflect differences in the magnitude of phenotypic variation (i.e. eigenvalues), rather than in the relationships between traits (i.e. eigenvectors). Sea-surface temperature was only correlated with the covariance between egg numbers and reproductive output. Matrices comparisons for Flury and jackknife methods were highly linked, with limits of biogeographic provinces described for the coast of Chile. Our study strongly highlights the importance of estimating the P matrix, not only mean values, in order to understand the evolution of life-history traits along a latitudinal gradient. Furthermore, the study of the variation in the P matrix might provide important insights into those evolutionary forces acting on it.  
  Address [Lardies, Marco A.; Belen Arias, Maria] Univ Adolfo Ibanez, Dept Ciencias, Fac Artes Liberaies, Santiago, Chile, Email: marco.lardies@uai.cl  
  Corporate Author Thesis  
  Publisher Inter-Research Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0171-8630 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000281565900015 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 96  
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Author (up) Lavin, P.; Gonzalez, B.; Santibanez, J.F.; Scanlan, D.J.; Ulloa, O. pdf  doi
openurl 
  Title Novel lineages of Prochlorococcus thrive within the oxygen minimum zone of the eastern tropical South Pacific Type
  Year 2010 Publication Environmental Microbiology Reports Abbreviated Journal Environ. Microbiol. Rep.  
  Volume 2 Issue 6 Pages 728-738  
  Keywords  
  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.  
  Address [Lavin, Paris; Francisco Santibanez, J.; Ulloa, Osvaldo] Univ Concepcion, Dept Oceanog, Concepcion, Chile, Email: oulloa@udec.cl  
  Corporate Author Thesis  
  Publisher Wiley-Blackwell Publishing, Inc Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1758-2229 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000284484700004 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 107  
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Author (up) Lykidis, A.; Perez-Pantoja, D.; Ledger, T.; Mavromatis, K.; Anderson, I.J.; Ivanova, N.N.; Hooper, S.D.; Lapidus, A.; Lucas, S.; Gonzalez, B.; Kyrpides, N.C. pdf  doi
openurl 
  Title The Complete Multipartite Genome Sequence of Cupriavidus necator JMP134, a Versatile Pollutant Degrader Type
  Year 2010 Publication Plos One Abbreviated Journal PLoS One  
  Volume 5 Issue 3 Pages 13 pp  
  Keywords  
  Abstract Background: Cupriavidus necator JMP134 is a Gram-negative beta-proteobacterium able to grow on a variety of aromatic and chloroaromatic compounds as its sole carbon and energy source. Methodology/ Principal Findings: Its genome consists of four replicons (two chromosomes and two plasmids) containing a total of 6631 protein coding genes. Comparative analysis identified 1910 core genes common to the four genomes compared (C. necator JMP134, C. necator H16, C. metallidurans CH34, R. solanacearum GMI1000). Although secondary chromosomes found in the Cupriavidus, Ralstonia, and Burkholderia lineages are all derived from plasmids, analyses of the plasmid partition proteins located on those chromosomes indicate that different plasmids gave rise to the secondary chromosomes in each lineage. The C. necator JMP134 genome contains 300 genes putatively involved in the catabolism of aromatic compounds and encodes most of the central ring-cleavage pathways. This strain also shows additional metabolic capabilities towards alicyclic compounds and the potential for catabolism of almost all proteinogenic amino acids. This remarkable catabolic potential seems to be sustained by a high degree of genetic redundancy, most probably enabling this catabolically versatile bacterium with different levels of metabolic responses and alternative regulation necessary to cope with a challenging environment. From the comparison of Cupriavidus genomes, it is possible to state that a broad metabolic capability is a general trait for Cupriavidus genus, however certain specialization towards a nutritional niche (xenobiotics degradation, chemolithoautotrophy or symbiotic nitrogen fixation) seems to be shaped mostly by the acquisition of “specialized” plasmids. Conclusions/Significance: The availability of the complete genome sequence for C. necator JMP134 provides the groundwork for further elucidation of the mechanisms and regulation of chloroaromatic compound biodegradation.  
  Address [Lykidis, Athanasios; Mavromatis, Kostantinos; Anderson, Iain J.; Ivanova, Natalia N.; Hooper, Sean D.; Lapidus, Alla; Lucas, Susan; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA, Email: alykidis@lbl.gov  
  Corporate Author Thesis  
  Publisher Public Library Science Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1932-6203 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000275894300005 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 86  
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Author (up) Marin, M.; Perez-Pantoja, D.; Donoso, R.; Wray, V.; Gonzalez, B.; Pieper, D.H. pdf  doi
openurl 
  Title Modified 3-Oxoadipate Pathway for the Biodegradation of Methylaromatics in Pseudomonas reinekei MT1 Type
  Year 2010 Publication Journal Of Bacteriology Abbreviated Journal J. Bacteriol.  
  Volume 192 Issue 6 Pages 1543-1552  
  Keywords  
  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.  
  Address [Marin, Macarena; Pieper, Dietmar H.] Helmholtz Zentrum Infekt Forsch, Dept Microbial Pathogenesis, D-38124 Braunschweig, Germany, Email: dpi@helmholtz-hzi.de  
  Corporate Author Thesis  
  Publisher Amer Soc Microbiology Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0021-9193 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000274891300009 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 84  
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Author (up) Martinez, J.; Simon, V.; Gonzalez, B.; Conget, P. pdf  doi
openurl 
  Title A real-time PCR-based strategy for the detection of Paenibacillus larvae vegetative cells and spores to improve the diagnosis and the screening of American foulbrood Type
  Year 2010 Publication Letters In Applied Microbiology Abbreviated Journal Lett. Appl. Microbiol.  
  Volume 50 Issue 6 Pages 603-610  
  Keywords American foulbrood; flow cytometry; Paenibacillus larvae; real-time PCR; 16S rRNA specific primers  
  Abstract Aim: To develop a real-time PCR-based strategy for the detection of Paenibacillus larvae vegetative cells and spores to improve the diagnosis and the screening of American foulbrood (AFB), the most harmful pathology of honeybee brood. Methods and Results: A real-time PCR that allowed selective identification and quantification of P. larvae 16S rRNA sequence was developed. Using standard samples quantified by flow cytometry, detection limits of 37 center dot 5 vegetative cells ml-1 and 10 spores ml-1 were determined. Compared to spread plate method, this real-time PCR-based strategy allowed, in only 2 h, the detection of P. larvae in contaminated honeys. No false-positive results were obtained. Moreover, its detection limit was 100 times lower than that of the culture method (2 vs 200 spores g-1 of honey). Conclusion: A rapid, selective, with low detection limit, sensitive and specific method to detect and quantify vegetative cells and spores of P. larvae is now available. Significance and Impact of Study: In addition to honey samples, this real-time PCR-based strategy may be also applied to confirm AFB diagnosis in honeybee brood and to screen other apiary supplies and products (bees, pollen, wax), thus broadening the control of AFB spreading.  
  Address [Martinez, J.; Simon, V.; Conget, P.] Clin Alemana Univ Desarrollo, Fac Med, Inst Ciencias, Santiago 7710162, Chile, Email: pconget@udd.cl  
  Corporate Author Thesis  
  Publisher Wiley-Blackwell Publishing, Inc Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0266-8254 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000277417000009 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 89  
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Author (up) Morgante, V.; Lopez-Lopez, A.; Flores, C.; Gonzalez, M.; Gonzalez, B.; Vasquez, M.; Rossello-Mora, R.; Seeger, M. pdf  doi
openurl 
  Title Bioaugmentation with Pseudomonas sp strain MHP41 promotes simazine attenuation and bacterial community changes in agricultural soils Type
  Year 2010 Publication Fems Microbiology Ecology Abbreviated Journal FEMS Microbiol. Ecol.  
  Volume 71 Issue 1 Pages 114-126  
  Keywords  
  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.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0168-6496 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000272452100013 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 76  
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Author (up) Pavissich, J.P.; Silva, M.; Gonzalez, B. pdf  doi
openurl 
  Title Sulfate Reduction, Molecular Diversity, And Copper Amendment Effects In Bacterial Communities Enriched From Sediments Exposed To Copper Mining Residues Type
  Year 2010 Publication Environmental Toxicology And Chemistry Abbreviated Journal Environ. Toxicol. Chem.  
  Volume 29 Issue 2 Pages 256-264  
  Keywords Sulfate reduction; Coastal sediments; Sulfate-reducing bacteria; Copper; Molecular diversity  
  Abstract Sulfate-reducing bacterial communities from coastal sediments with a long-term exposure to copper (Cu)-mining residues were studied in lactate enrichments. The toxicity of excess copper may affect sulfate-reducing bacterial communities. Sulfate reduction was monitored by sulfate and organic acid measurements. Molecular diversity was analyzed by 16S rRNA, dissimilatory sulfate reduction dsrAB, and Cu translocating phospho-type adenosine triphosphatases (P-ATPases) cop-like gene sequence profiling. The influence of Cu amendment was tested in these enrichments. Results showed fast sulfate reduction mostly coupled to incomplete organic carbon oxidation and partial sulfate reduction inhibition due to copper amendment. The 16S rRNA clonal libraries analysis indicated that delta- and gamma-Proteobacteria and Cytophaga-Flexibacter-Bacteroides dominated the enrichments. The dsrAB libraries revealed the presence of Desulfobacteraceae and Desulfovibrionaceae families-related sequences. Copper produced significant shifts (i.e., a decrease in the relative abundance of sulfate-reducing microorganisms) in the enriched bacterial community structure as determined by terminal-restriction fragment length polymorphism (T-RFLP) profiling and multivariate analyses. Clonal libraries of cop-like sequences showed low richness in the enriched microbial communities, and a strong effect of copper on its relative abundance. Novel Cu-P-IB-ATPase sequences encoding Cu resistance were detected. The present study indicates that Cu does not significantly affect sulfate reduction and genetic diversity of taxonomic and dissimilatory sulfate-reduction molecular markers. However, the diversity of Cu resistance genetic determinants was strongly modified by this toxic metal. Environ. Toxicol. Chem. 2010;29:256-264. (C) 2009 SETAC  
  Address [Pavissich, Juan P.; Silva, Macarena; Gonzalez, Bernardo] Pontificia Univ Catolica Chile, Fac Ciencias Biol, Millennium Nucleus Microbial Ecol & Environm Micr, Dept Mol Genet & Microbiol,CASEB, Santiago, Chile, Email: bernardo.gonzalez@uai.cl  
  Corporate Author Thesis  
  Publisher Setac Press Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0730-7268 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000274272500004 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 81  
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Author (up) Pavissich, J.P.; Vargas, I.T.; Gonzalez, B.; Pasten, P.A.; Pizarro, G.E. pdf  doi
openurl 
  Title Culture dependent and independent analyses of bacterial communities involved in copper plumbing corrosion Type
  Year 2010 Publication Journal Of Applied Microbiology Abbreviated Journal J. Appl. Microbiol.  
  Volume 109 Issue 3 Pages 771-782  
  Keywords bacterial community; biofilm; copper plumbing; microbially influenced corrosion; water quality  
  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.  
  Address [Pavissich, J. P.; Vargas, I. T.; Pasten, P. A.; Pizarro, G. E.] Pontificia Univ Catolica Chile, Dept Ingn Hidraul & Ambiental, Escuela Ingn, Santiago 6904411, Chile, Email: gpizarro@ing.puc.cl  
  Corporate Author Thesis  
  Publisher Wiley-Blackwell Publishing, Inc Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1364-5072 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000280979700004 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 93  
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Author (up) Sepulveda, N.; Josserand, C.; Rica, S. pdf  doi
openurl 
  Title Superfluid density in a two-dimensional model of supersolid Type
  Year 2010 Publication European Physical Journal B Abbreviated Journal Eur. Phys. J. B  
  Volume 78 Issue 4 Pages 439-447  
  Keywords  
  Abstract We study in 2-dimensions the superfluid density of periodically modulated states in the framework of the mean-field Gross-Pitaevskii model of a quantum solid. We obtain a full agreement for the superfluid fraction between a semi-theoretical approach and direct numerical simulations. As in 1-dimension, the superfluid density decreases exponentially with the amplitude of the particle interaction. We discuss the case when defects are present in this modulated structure. In the case of isolated defects (e.g. dislocations) the superfluid density only shows small changes. Finally, we report an increase of the superfluid fraction up to 50% in the case of extended macroscopical defects. We show also that this excess of superfluid fraction depends on the length of the complex network of grain boundaries in the system.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1434-6028 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000286669400004 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 121  
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Author (up) Taboada, E.; Fisher, P.; Jara, R.; Zuniga, E.; Gidekel, M.; Cabrera, J.C.; Pereira, E.; Gutierrez-Moraga, A.; Villalonga, R.; Cabrera, G. pdf  doi
openurl 
  Title Isolation and characterisation of pectic substances from murta (Ugni molinae Turcz) fruits Type
  Year 2010 Publication Food Chemistry Abbreviated Journal Food Chem.  
  Volume 123 Issue 3 Pages 669-678  
  Keywords Pectin; Murta; Ugni molinae; Polysaccharide extraction; Pectin characterisation  
  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.  
  Address [Gidekel, Manuel; Cabrera, Gustavo] Univ Adolfo Ibanez, VentureLab, Escuela Negocios, Santiago, Chile, Email: gustavo.cabrera@uai.cl  
  Corporate Author Thesis  
  Publisher Elsevier Sci Ltd Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0308-8146 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000280917800016 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 80  
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