Examinando por Autor "Cárdenas, Juan Pablo"
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Ítem Análisis de ciclo de vida simplificado aplicado a viviendas de paneles SIP (structural insulated panels)(Pontificia Universidad Católica de Chile. Departamento de Ingeniería y Gestión de la Construcción, 2015-04) Cárdenas, Juan Pablo; Muñoz, Edmundo; Riquelme, Cristian; Hidalgo, FranciscoA medida que los asuntos ambientales se vuelven más importantes, las construcciones se han enfocado en su eficiencia energética y la energía necesaria para construir y producir los materiales. Esta investigación muestra un estudio de Análisis de Ciclo de Vida simplificado de energía operacional y energía contenida de cuatro viviendas nuevas ubicadas en Temuco, Chile, estructuradas con paneles SIP (Structural insulated panel) para cuantificar la energía en cada etapa de este sistema de construcción. Para obtener la energía contenida, fueron utilizadas dos bases de datos internacionales para cuantificar la energía de cada material y se determinó la energía contenida en el proceso relacionado a la estructura de paneles SIP a través de mediciones en una compañía especializada en construcción de paneles SIP. Para la energía operacional, se llevaron a cabo modelos computacionales con el software Design Builder y se proyectó esta energía con una vida útil de 50 años. El análisis de la información obtenida muestra que la energía contenida por procesos de construcción representa cerca del 1.7% de la energía contenida y mientras que el total de energía contenida representa el 11% de la energía del ciclo de vida total de las viviendas, el remanente 89% representa la energía de operación. Por otro lado, observamos que las viviendas con paneles SIP generan cifras cercanas al 60% en ahorro en demanda energética, comparadas a las viviendas de mampostería estructural normalmente construidas en esta ciudad.Ítem Architecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus(Public Library of Science, 2013-11-08) Acuña, Lillian G.; Cárdenas, Juan Pablo; Covarrubias, Paulo C.; Haristoy, Juan José; Flores, Rodrigo; Nuñez, Harold; Riadi, Gonzalo; Shmaryahu, Amir; Valdés, Jorge; Dopson, Mark; Rawlings, Douglas E.; Banfield, Jillian F.Background: Acidithiobacillus caldus is a sulfur oxidizing extreme acidophile and the only known mesothermophile within the Acidithiobacillales. As such, it is one of the preferred microbes for mineral bioprocessing at moderately high temperatures. In this study, we explore the genomic diversity of A. caldus strains using a combination of bioinformatic and experimental techniques, thus contributing first insights into the elucidation of the species pangenome. Principal Findings: Comparative sequence analysis of A. caldus ATCC 51756 and SM-1 indicate that, despite sharing a conserved and highly syntenic genomic core, both strains have unique gene complements encompassing nearly 20% of their respective genomes. The differential gene complement of each strain is distributed between the chromosomal compartment, one megaplasmid and a variable number of smaller plasmids, and is directly associated to a diverse pool of mobile genetic elements (MGE). These include integrative conjugative and mobilizable elements, genomic islands and insertion sequences. Some of the accessory functions associated to these MGEs have been linked previously to the flexible gene pool in microorganisms inhabiting completely different econiches. Yet, others had not been unambiguously mapped to the flexible gene pool prior to this report and clearly reflect strain-specific adaption to local environmental conditions. Significance: For many years, and because of DNA instability at low pH and recurrent failure to genetically transform acidophilic bacteria, gene transfer in acidic environments was considered negligible. Findings presented herein imply that a more or less conserved pool of actively excising MGEs occurs in the A. caldus population and point to a greater frequency of gene exchange in this econiche than previously recognized. Also, the data suggest that these elements endow the species with capacities to withstand the diverse abiotic and biotic stresses of natural environments, in particular those associated with its extreme econiche. © 2013 Acuña et al.Ítem Draft genome sequence of the nominated type strain of "Ferrovum myxofaciens," an acidophilic, iron-oxidizing betaproteobacterium(American Society for Microbiology, 2014) Moya-Beltrán, Ana; Cárdenas, Juan Pablo; Covarrubias, Paulo C.; Issotta, Francisco; Ossandon, Francisco J.; Grail, Barry M.; Holmes, David S.; Quatrini, Raquel; Johnson, D. BarrieFerrovum myxofaciens” is an iron-oxidizing betaproteobacterium with widespread distribution in acidic low-temperature en vironments, such as acid mine drainage streams. Here, we describe the genomic features of this novel acidophile and investigate the relevant metabolic pathways that enable its survival in these environments.Ítem Genomic and metagenomic challenges and opportunities for bioleaching: a mini-review(Elsevier Masson SAS, 2016-09) Cárdenas, Juan Pablo; Quatrini, Raquel; Holmes, David SHigh-throughput genomic technologies are accelerating progress in understanding the diversity of microbial life in many environments. Here we highlight advances in genomics and metagenomics of microorganisms from bioleaching heaps and related acidic mining environments. Bioleaching heaps used for copper recovery provide significant opportunities to study the processes and mechanisms underlying microbial successions and the influence of community composition on ecosystem functioning. Obtaining quantitative and process-level knowledge of these dynamics is pivotal for understanding how microorganisms contribute to the solubilization of copper for industrial recovery. Advances in DNA sequencing technology provide unprecedented opportunities to obtain information about the genomes of bioleaching microorganisms, allowing predictive models of metabolic potential and ecosystem-level interactions to be constructed. These approaches are enabling predictive phe notyping of organisms many of which are recalcitrant to genetic approaches or are unculturable. This mini-review describes current bioleaching genomic and metagenomic projects and addresses the use of genome information to: (i) build metabolic models; (ii) predict microbial in teractions; (iii) estimate genetic diversity; and (iv) study microbial evolution. Key challenges and perspectives of bioleaching genomics/met agenomics are addressed. © 2016 The Author(s). Published by Elsevier Masson SAS on behalf of Institut Pasteur. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).Ítem Molecular systematics of the Genus Acidithiobacillus: Insights into the phylogenetic structure and diversification of the taxon(Frontiers Media S.A., 2017-01) Nuñez, Harold; Moya-Beltrán; Ana; Covarrubias, Paulo C.; Issotta, Francisco; Cárdenas, Juan Pablo; González, Mónica; Atavales, Joaquín; Acuña, Lillian G.; Johnson, D. Barrie; Quatrini, RaquelThe acidithiobacilli are sulfur-oxidizing acidophilic bacteria that thrive in both natural and anthropogenic low pH environments. They contribute to processes that lead to the generation of acid rock drainage in several different geoclimatic contexts, and their properties have long been harnessed for the biotechnological processing of minerals. Presently, the genus is composed of seven validated species, described between 1922 and 2015: Acidithiobacillus thiooxidans, A. ferrooxidans, A. albertensis, A. caldus, A. ferrivorans, A. ferridurans, and A. ferriphilus. However, a large number of Acidithiobacillus strains and sequence clones have been obtained from a variety of ecological niches over the years, and many isolates are thought to vary in phenotypic properties and cognate genetic traits. Moreover, many isolates remain unclassified and several conflicting specific assignments muddle the picture from an evolutionary standpoint. Here we revise the phylogenetic relationships within this species complex and determine the phylogenetic species boundaries using three different typing approaches with varying degrees of resolution: 16S rRNA gene-based ribotyping, oligotyping, and multi-locus sequencing analysis (MLSA). To this end, the 580 16S rRNA gene sequences affiliated to the Acidithiobacillus spp. were collected from public and private databases and subjected to a comprehensive phylogenetic analysis. Oligotyping was used to profile high-entropy nucleotide positions and resolve meaningful differences between closely related strains at the 16S rRNA gene level. Due to its greater discriminatory power, MLSA was used as a proxy for genome-wide divergence in a smaller but representative set of strains. Results obtained indicate that there is still considerable unexplored diversity within this genus. At least six new lineages or phylotypes, supported by the different methods used herein, are evident within the Acidithiobacillus species complex. Although the diagnostic characteristics of these subgroups of strains are as yet unresolved, correlations to specific metadata hint to the mechanisms behind econiche-driven divergence of some of the species/phylotypes identified. The emerging phylogenetic structure for the genus outlined in this study can be used to guide isolate selection for future population genomics and evolutionary studies in this important acidophile model. © 2017 Nuñez, Moya-Beltrán, Covarrubias, Issotta, Cárdenas, González, Atavales, Acuña, Johnson and Quatrini.Ítem Molecular systematics of the Genus Acidithiobacillus: Insights into the phylogenetic structure and diversification of the taxon(Frontiers Media S.A., 2017-01) Nuñez, Harold; Moya Beltrán, Ana; Covarrubias, Paulo C.; Issotta, Francisco; Cárdenas, Juan Pablo; González, Mónica; Atavales, Joaquín; Acuña, Lillian G.; Johnson, D.Barrie; Quatrini, RaquelThe acidithiobacilli are sulfur-oxidizing acidophilic bacteria that thrive in both natural and anthropogenic low pH environments. They contribute to processes that lead to the generation of acid rock drainage in several different geoclimatic contexts, and their properties have long been harnessed for the biotechnological processing of minerals. Presently, the genus is composed of seven validated species, described between 1922 and 2015: Acidithiobacillus thiooxidans, A. ferrooxidans, A. albertensis, A. caldus, A. ferrivorans, A. ferridurans, and A. ferriphilus. However, a large number of Acidithiobacillus strains and sequence clones have been obtained from a variety of ecological niches over the years, and many isolates are thought to vary in phenotypic properties and cognate genetic traits. Moreover, many isolates remain unclassified and several conflicting specific assignments muddle the picture from an evolutionary standpoint. Here we revise the phylogenetic relationships within this species complex and determine the phylogenetic species boundaries using three different typing approaches with varying degrees of resolution: 16S rRNA gene-based ribotyping, oligotyping, and multi-locus sequencing analysis (MLSA). To this end, the 580 16S rRNA gene sequences affiliated to the Acidithiobacillus spp. were collected from public and private databases and subjected to a comprehensive phylogenetic analysis. Oligotyping was used to profile high-entropy nucleotide positions and resolve meaningful differences between closely related strains at the 16S rRNA gene level. Due to its greater discriminatory power, MLSA was used as a proxy for genome-wide divergence in a smaller but representative set of strains. Results obtained indicate that there is still considerable unexplored diversity within this genus. At least six new lineages or phylotypes, supported by the different methods used herein, are evident within the Acidithiobacillus species complex. Although the diagnostic characteristics of these subgroups of strains are as yet unresolved, correlations to specific metadata hint to the mechanisms behind econiche-driven divergence of some of the species/phylotypes identified. The emerging phylogenetic structure for the genus outlined in this study can be used to guide isolate selection for future population genomics and evolutionary studies in this important acidophile model. © 2017 Nuñez, Moya-Beltrán, Covarrubias, Issotta, Cárdenas, González, Atavales, Acuña, Johnson and Quatrini.Ítem Multi Locus Sequence Typing scheme for Acidithiobacillus caldus strain evaluation and differentiation(Elsevier Masson s.r.l., 2014) Nuñez, Harold; Loyola, David; Cárdenas, Juan Pablo; Holmes, David S.; Johnson, D. Barrie; Quatrini, RaquelPhenotypic, metabolic and genetic properties of several Acidithiobacillus caldus strains indicate the existence of as yet undefined levels of variation within the species. Inspite of this, intraspecies genetic diversity has not yet been explored in detail. In this study, the design and implementation of a Multi Locus Sequence Typing (MLST) scheme for At. caldus is described. This represents the first MLST-based study applied to industrial isolates of the species. Seven informative and discriminant MLST markers were selected using a sequence-driven approach and a custom-designed bioinformatic pipeline. The allelic profiles of thirteen At. caldus strains from diverse geographical origins and industrial settings were derived using this scheme. MLST-based population structure analysis indicated only moderate amounts of genetic diversity within the set of strains, further supporting their current assignment to a single species. Also, no clear evidence for geographical isolation could be derived from this study. However, the prevalence of sequence type 1 in heap leaching industrial settings support the view that bioprocess conditions and dynamics may have a strong influence on At. caldus (microbial) microdiversity patterns. The MLST scheme presented herein is a valuable tool for the identification and classification of strains of At. caldus for either ecological or evolutionary studies and possibly also for industrial monitoring purposes. © 2014 The Authors.Ítem Reclassification of ‘Thiobacillus prosperus’ Huber and Stetter 1989 as Acidihalobacter prosperus gen. nov., sp. nov., a member of the family Ectothiorhodospiraceae(Microbiology Society, 2015-10) Cárdenas, Juan Pablo; Ortiz, Rodrigo; Norris, Paul R.; Watkin, Elizabeth; Holmes, David S.Analysis of phylogenomic metrics of a recently released draft genome sequence of the halotolerant, acidophile ‘Thiobacillus prosperus’ DSM 5130 indicates that it is not a member of the genus Thiobacillus within the class Betaproteobacteria as originally proposed. Based on data from 16S rRNA gene phylogeny, and analyses of multiprotein phylogeny and average nucleotide identity (ANI), we show that it belongs to a new genus within the family Ectothiorhodospiraceae, for which we propose the name Acidihalobacter gen. nov. In accordance, it is proposed that ‘Thiobacillus prosperus’ DSM 5130 be named Acidihalobacter prosperus gen. nov., sp. nov. DSM 5130T (5JCM 30709T) and that it becomes the type strain of the type species of this genus. © 2015 IUMS.Ítem Spatial distribution of particulate matter on winter nights in Temuco, Chile: Studying the impact of residential wood-burning using mobile monitoring(Elsevier Ltd, 2022-10-01) Blanco, Estela; Rubilar, Francisco; Quinteros, Maria Elisa; Cayupi, Karen; Ayala, Salvador; Lu, Siyao; Jimenez, Raquel B.; Cárdenas, Juan Pablo; Blazquez, Carola A.; Delgado Saborit, Juana Maria; Harrison, Roy M.; Ruiz Rudolph, PabloTemuco, a medium-sized city in the south of Chile, is heavily impacted by residential wood-burning particularly in winter, which causes strong episodes of air pollution. We spatially characterized the distribution of particulate matter (PM) during winter nights in Temuco using mobile measurements. In winter 2016 (June 8-July 15th), continuous monitors for PM ≤ 2.5 μm (PM2.5) and ultrafine particles <0.1 μm (UFP) were deployed in a vehicle along with a positioning system during 20 nights (20:00 to 2:00) in assigned routes that crossed the city and additional sampling was conducted at a central site. Measurements were expressed as concentrations and ratios to central site concentrations and collapsed by spatial grids of 50, 100, 200, and 400 m. Average PM2.5 concentrations were ∼100 μg m−3, while UFP ∼30,000 counts cm−3. Some neighborhoods had concentrations of PM2.5 nearly double those measured at a centrally located site, while other neighborhoods had less than half the measured level. We identified hotspots and cold spots of PM2.5 and UFP throughout the urban area—and observed some neighborhoods in which over 20% of the area was categorized as a hotspot for one of the pollutants (14 for PM2.5 and 11 for UFP out of 34). Using mobile monitoring—a relatively simple and inexpensive methodology— we characterized the spatial distribution of pollutants and likely clusters for the time period, which may guide future spatial campaigns and help targeting local interventions aimed at air pollution mitigation. © 2022 Elsevier LtdÍtem The Structure of Online Information Behind Social Crises(Frontiers Media S.A., 2021-12) Cárdenas, Juan Pablo; Olivares, Gastón; Vidal, Gerardo; Urbina, Carolina; Fuentes, MiguelThe adaptive nature of the social system allows it to overcome the challenges imposed by its environment as well as to overcome those internal pressures. This adaptive process is associated with an increase in complexity manifested in a greater diversity of its components, new forms of organization, among other transformations. However, these adaptations have a cost and need to be administered, otherwise, they can trigger social unrest and crisis processes. Currently, the adaptive process of social systems has been accelerated and magnified by the emergence of information technologies. In this work, we explore the close relationship between adaptation, complexity, and crisis, showing it expression in a digital social environment, although with some particularities. Specifically, we have observed expected behaviors, such as the polarization of society and negative sentiment of messages during times of crisis, however, our results show something interesting. Despite the loss of order in the social organization questioned by the crisis, we observe the emergence of new complex ephemeral structures of information which seem to be early-warnings signals of profound social transformations. © Copyright © 2021 Cárdenas, Olivares, Vidal, Urbina and Fuentes.