104 results on '"Gutiérrez-Preciado A"'
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2. Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments
- Author
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Baker, Brittany A., Gutiérrez-Preciado, Ana, Rodríguez del Río, Álvaro, McCarthy, Charley G. P., López-García, Purificación, Huerta-Cepas, Jaime, Susko, Edward, Roger, Andrew J., Eme, Laura, and Moreira, David
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- 2024
- Full Text
- View/download PDF
3. Semantic Maps for Knowledge Graphs: A Semantic-Based Summarization Approach.
- Author
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Pablo Camarillo-Ramírez, Francisco Cervantes-Alvarez, and Luis Fernando Gutiérrez-Preciado
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- 2024
- Full Text
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4. Metagenome-derived virus-microbe ratios across ecosystems
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López-García, Purificación, Gutiérrez-Preciado, Ana, Krupovic, Mart, Ciobanu, Maria, Deschamps, Philippe, Jardillier, Ludwig, López-Pérez, Mario, Rodríguez-Valera, Francisco, and Moreira, David
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- 2023
- Full Text
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5. Assessing the Effect of Fiscal Policies on the Gender Income Gap in Central America, Panama and the Dominican Republic
- Author
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Deza, María Cecilia, primary, Gélvez Rubio, Tatiana Andrea, additional, Gutiérrez Preciado, Diana, additional, Jara, H. Xavier, additional, and Rodríguez Guerrero, David Arturo, additional
- Published
- 2024
- Full Text
- View/download PDF
6. Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments
- Author
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European Commission, Fundación la Caixa, Simons Foundation, Gutiérrez Preciado, Ana [0000-0002-6032-466X], Rodríguez, Alvaro [0000-0003-3907-3904], 0000-0002-3880-9978, 0000-0002-0927-0651, 0000-0003-4195-5025, #NODATA#, 0000-0003-1370-9820, 0000-0002-0510-8868, 0000-0002-2064-5354, Baker, Brittany A., Gutiérrez Preciado, Ana, Rodríguez, Alvaro, McCarthy, Charley G P, López-García, Purificación, Huerta-Cepas, Jaime, Susko, Edward, Roger, Andrew J, Eme, Laura, Moreira, David, European Commission, Fundación la Caixa, Simons Foundation, Gutiérrez Preciado, Ana [0000-0002-6032-466X], Rodríguez, Alvaro [0000-0003-3907-3904], 0000-0002-3880-9978, 0000-0002-0927-0651, 0000-0003-4195-5025, #NODATA#, 0000-0003-1370-9820, 0000-0002-0510-8868, 0000-0002-2064-5354, Baker, Brittany A., Gutiérrez Preciado, Ana, Rodríguez, Alvaro, McCarthy, Charley G P, López-García, Purificación, Huerta-Cepas, Jaime, Susko, Edward, Roger, Andrew J, Eme, Laura, and Moreira, David
- Abstract
Extremely halophilic archaea (Haloarchaea, Nanohaloarchaeota, Methanonatronarchaeia and Halarchaeoplasmatales) thrive in saturating salt concentrations where they must maintain osmotic equilibrium with their environment. The evolutionary history of adaptations enabling salt tolerance remains poorly understood, in particular because the phylogeny of several lineages is conflicting. Here we present a resolved phylogeny of extremely halophilic archaea obtained using improved taxon sampling and state-of-the-art phylogenetic approaches designed to cope with the strong compositional biases of their proteomes. We describe two uncultured lineages, Afararchaeaceae and Asbonarchaeaceae, which break the long branches at the base of Haloarchaea and Nanohaloarchaeota, respectively. We obtained 13 metagenome-assembled genomes (MAGs) of these archaea from metagenomes of hypersaline aquatic systems of the Danakil Depression (Ethiopia). Our phylogenomic analyses including these taxa show that at least four independent adaptations to extreme halophily occurred during archaeal evolution. Gene-tree/species-tree reconciliation suggests that gene duplication and horizontal gene transfer played an important role in this process, for example, by spreading key genes (such as those encoding potassium transporters) across extremely halophilic lineages.
- Published
- 2024
7. A Methodology for Knowledge Discovery in Labeled and Heterogeneous Graphs
- Author
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Víctor H. Ortega-Guzmán, Luis Gutiérrez-Preciado, Francisco Cervantes, and Mildreth Alcaraz-Mejia
- Subjects
graph mining ,knowledge discovery ,labeled graphs ,heterogeneous graphs ,Technology ,Engineering (General). Civil engineering (General) ,TA1-2040 ,Biology (General) ,QH301-705.5 ,Physics ,QC1-999 ,Chemistry ,QD1-999 - Abstract
Graph mining has emerged as a significant field of research with applications spanning multiple domains, including marketing, corruption analysis, business, and politics. The exploration of knowledge within graphs has garnered considerable attention due to the exponential growth of graph-modeled data and its potential in applications where data relationships are a crucial component, and potentially being even more important than the data themselves. However, the increasing use of graphs for data storing and modeling presents unique challenges that have prompted advancements in graph mining algorithms, data modeling and storage, query languages for graph databases, and data visualization techniques. Despite there being various methodologies for data analysis, they predominantly focus on structured data and may not be optimally suited for highly connected data. Accordingly, this work introduces a novel methodology specifically tailored for knowledge discovery in labeled and heterogeneous graphs (KDG), and it presents three case studies demonstrating its successful application in addressing various challenges across different application domains.
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- 2024
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8. A Methodology for Knowledge Discovery in Labeled and Heterogeneous Graphs
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Ortega-Guzmán, Víctor H., primary, Gutiérrez-Preciado, Luis, additional, Cervantes, Francisco, additional, and Alcaraz-Mejia, Mildreth, additional
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- 2024
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9. Semantic Maps for Knowledge Graphs: A Semantic-based Summarization Approach
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Camarillo-Ramirez, P., primary, Cervantes-Alvarez, F., additional, and Gutiérrez-Preciado, L. F., additional
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- 2024
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10. Optimización del Espacio de Trabajo de un Robot Deltoide
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Alfredo Gutiérrez-Preciado, Max Antonio González-Palacios, Luz Antonio Aguilera-Cortés, and Francisco Javier Mendoza-Patiño
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Robot Deltoide ,Diseño ,Optimización ,Simulación por computadora ,Espacio de trabajo ,ADEFID ,Control engineering systems. Automatic machinery (General) ,TJ212-225 - Abstract
Los estudios realizados en el robot Delta han reportado inconveniencias con respecto a su limitado espacio de trabajo. Este artículo propone una modificación en la colocación de sus actuadores, convirtiéndose así en lo que se denomina robot Deltoide. Con este cambio, el espacio de trabajo puede aumentar o disminuir considerablemente. De esta manera, se propone una optimización usando algoritmos genéticos para encontrar el mayor espacio de trabajo que el robot puede tener dependiendo de las variables de diseño. Además, se explica e implementa el análisis general de la cinemática directa e inversa del robot Deltoide, en un software creado especialmente para esta aplicación.
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- 2019
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11. A task-based evaluation methodology for visual representation of dynamic networks.
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Pablo Camarillo-Ramírez, Francisco Cervantes-Alvarez, and Luis Fernando Gutiérrez-Preciado
- Published
- 2020
12. Functional shifts in microbial mats recapitulate early Earth metabolic transitions
- Author
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Gutiérrez-Preciado, Ana, Saghaï, Aurélien, Moreira, David, Zivanovic, Yvan, Deschamps, Philippe, and López-García, Purificación
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- 2018
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13. Description of Gloeomargarita ahousahtiae sp. nov. (Gloeomargaritales), a thermophilic cyanobacterium with intracellular carbonate inclusions
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Bacchetta, Thomas, primary, López-García, Purificación, additional, Gutiérrez-Preciado, Ana, additional, Mehta, Neha, additional, Skouri-Panet, Feriel, additional, Benzerara, Karim, additional, Ciobanu, Maria, additional, Yubuki, Naoji, additional, Tavera, Rosaluz, additional, and Moreira, David, additional
- Published
- 2023
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14. Effect of changes in fertility and household structure on the educational level and labor market participation of women: analysis for Latin America
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Gutiérrez Preciado, Diana Marcela and Bula Escobar, Jorge Iván
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Employment ,Hogares ,Crecimiento demográfico ,Escolaridad ,Population increase ,Mujeres ,Fecundidad ,Trabajadora ,Womens education ,Households ,Women workers ,Fertility ,Educación de la mujer ,331 - Economía laboral [330 - Economía] ,Women ,Empleo ,Schooling - Abstract
ilustraciones En el marco de un avance significativo para las mujeres en las últimas décadas en referencia a sus oportunidades y su papel en la sociedad, pero teniendo en cuenta que no ha sido suficiente para alcanzar la igualdad de género en los diferentes escenarios. Este trabajo analiza el efecto de los cambios en la fecundidad y la estructura de los hogares con el nivel educativo y la participación en el mercado laboral en las mujeres con el fin de establecer si es pertinente generar políticas que apoyen el cambio en las condiciones de las mujeres a través de estas dos aristas. Se realizan dos estimaciones con datos panel para 13 países de América Latina teniendo como fuente datos de la Comisión Económica para América Latina y el Caribe (CEPAL) para el periodo 2000-2020. Se encuentra una relación inversa de causa y no de consecuencia entre estas variables como comúnmente se ha visto en la literatura. Se presentan algunas recomendaciones de política sobre el control de la fecundidad y en el apoyo a los cambios en las estructuras de los hogares para el mejoramiento del nivel educativo y la participación laboral de las mujeres. (Texto tomado de la fuente). Within the framework of a significant advance for women in recent decades in reference to their opportunities and their role in society, but taking into account that it has not been enough to achieve gender equality in the different scenarios. This paper analyzes the effect of changes in fertility and the structure of households with educational attainment and women's labour market participation in order to establish whether it is pertinent to generate policies that support the change in the conditions of women through these two edges. Two estimates are made with panel data for 13 Latin American countries based on data from the Economic Commission for Latin America and the Caribbean (ECLAC) for the period 2000-2020. An inverse relationship of cause and not of consequence is found between these variables as has been commonly seen in the literature. Some policy recommendations on fertility control and support for changes in household structures are presented for the improvement of the educational level and labor participation of women. Incluye anexos Maestría Magíster en Ciencias Económicas Economía del desarrollo
- Published
- 2023
15. Workspace Analysis of a Delta-Like Robot Using an Alternative Approach
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Gutiérrez-Preciado, A., González-Palacios, M. A., Aguilera-Cortés, L. A., Ceccarelli, Marco, Series editor, and Hernández Martinez, Eusebio Eduardo, editor
- Published
- 2015
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16. Genome Sequence Databases: Types of Data and Bioinformatic Tools
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Gutiérrez-Preciado, Ana, primary, Deschamps, Philippe, additional, Delmont, Tom O., additional, Chica, Claudia, additional, Chrismas, Nathan A.M., additional, and Rodríguez de la Vega, Ricardo C., additional
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- 2019
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17. Description of Gloeomargarita ahousahtiae sp. nov. (Gloeomargaritales), a thermophilic cyanobacterium with intracellular carbonate inclusions.
- Author
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Bacchetta, Thomas, López-García, Purificación, Gutiérrez-Preciado, Ana, Mehta, Neha, Skouri-Panet, Feriel, Benzerara, Karim, Ciobanu, Maria, Yubuki, Naoji, Tavera, Rosaluz, and Moreira, David
- Subjects
ENERGY dispersive X-ray spectroscopy ,MICROBIAL mats ,TRANSMISSION electron microscopy ,ALGAE culture ,SCANNING electron microscopy ,CHLOROPHYLL - Abstract
A unicellular cyanobacterium, strain VI4D9, was isolated from thermophilic microbial mats thriving in a hot spring of the Ahousaht territory of Vancouver Island, Canada, and characterized using optical and electron microscopy, genome sequencing and cultivation approaches. The cells were elongated rods (5.1 µm in length and 1.2 µm in width, on average). Their UV visible absorption spectra revealed that they contain chlorophyll a, phycocyanin and carotenoids. Transmission electron microscopy showed the presence of thylakoids concentrated on one side of the cells. The strain grew within a temperature range of 37–50°C, with an optimum growth at 45°C. Its genome had a size of 3 049 282 bp and a DNA G + C content of 51.8 mol%. The cells contained numerous intracellular spherical granules easily visible under scanning electron microscopy. Energy dispersive X-ray spectroscopy revealed that these granules were made of Ca-, Ba- and Sr-containing carbonates. A phylogenetic 16S rRNA gene tree robustly placed this strain as sister to several environmental sequences and the described species Gloeomargarita lithophora, also characterized by the possession of intracellular carbonate inclusions. We consider strain VI4D9 to represent a new Gloeomargarita species based on its marked phenotypic differences with G. lithophora, notably, its thermophilic nature and different thylakoid organization, therefore we propose the name Gloeomargarita ahousahtiae sp. nov. The type strain is VI4D9 (Culture Collection of Algae and Protozoa strain 1472/1; Laboratorio de Algas Continentales Mexico strain LAC 140). Gloeomargarita ahousahtiae is the second species described within the recently discovered order Gloeomargaritales. Gloeomargarita ahousahtiae is a new thermophilic cyanobacterium. Growth temperature and thylakoid morphology differentiate G. ahousahtiae and G. lithophora. All described Gloeomargaritales synthesize intracellular carbonate inclusions. [ABSTRACT FROM AUTHOR]
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- 2024
- Full Text
- View/download PDF
18. The Skin Microbiome of the Neotropical Frog Craugastor fitzingeri: Inferring Potential Bacterial-Host-Pathogen Interactions From Metagenomic Data
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Eria A. Rebollar, Ana Gutiérrez-Preciado, Cecilia Noecker, Alexander Eng, Myra C. Hughey, Daniel Medina, Jenifer B. Walke, Elhanan Borenstein, Roderick V. Jensen, Lisa K. Belden, and Reid N. Harris
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skin microbiome ,shotgun metagenomics ,host-bacteria interactions ,amphibians ,Batrachochytrium dendrobatidis ,Microbiology ,QR1-502 - Abstract
Skin symbiotic bacteria on amphibians can play a role in protecting their host against pathogens. Chytridiomycosis, the disease caused by Batrachochytrium dendrobatidis, Bd, has caused dramatic population declines and extinctions of amphibians worldwide. Anti-Bd bacteria from amphibian skin have been cultured, and skin bacterial communities have been described through 16S rRNA gene amplicon sequencing. Here, we present a shotgun metagenomic analysis of skin bacterial communities from a Neotropical frog, Craugastor fitzingeri. We sequenced the metagenome of six frogs from two different sites in Panamá: three frogs from Soberanía (Sob), a Bd-endemic site, and three frogs from Serranía del Sapo (Sapo), a Bd-naïve site. We described the taxonomic composition of skin microbiomes and found that Pseudomonas was a major component of these communities. We also identified that Sob communities were enriched in Actinobacteria while Sapo communities were enriched in Gammaproteobacteria. We described gene abundances within the main functional classes and found genes enriched either in Sapo or Sob. We then focused our study on five functional classes of genes: biosynthesis of secondary metabolites, metabolism of terpenoids and polyketides, membrane transport, cellular communication and antimicrobial drug resistance. These gene classes are potentially involved in bacterial communication, bacterial-host and bacterial-pathogen interactions among other functions. We found that C. fitzingeri metagenomes have a wide array of genes that code for secondary metabolites, including antibiotics and bacterial toxins, which may be involved in bacterial communication, but could also have a defensive role against pathogens. Several genes involved in bacterial communication and bacterial-host interactions, such as biofilm formation and bacterial secretion systems were found. We identified specific genes and pathways enriched at the different sites and determined that gene co-occurrence networks differed between sites. Our results suggest that skin microbiomes are composed of distinct bacterial taxa with a wide range of metabolic capabilities involved in bacterial defense and communication. Differences in taxonomic composition and pathway enrichments suggest that skin microbiomes from different sites have unique functional properties. This study strongly supports the need for shotgun metagenomic analyses to describe the functional capacities of skin microbiomes and to tease apart their role in host defense against pathogens.
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- 2018
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19. Description of Gloeomargarita ahousahtiae sp. nov. (Gloeomargaritales), a thermophilic cyanobacterium with intracellular carbonate inclusions
- Author
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Bacchetta, Thomas, López-García, Purificación, Gutiérrez-Preciado, Ana, Mehta, Neha, Skouri-Panet, Feriel, Benzerara, Karim, Ciobanu, Maria, Yubuki, Naoji, Tavera, Rosaluz, and Moreira, David
- Abstract
A unicellular cyanobacterium, strain VI4D9, was isolated from thermophilic microbial mats thriving in a hot spring of the Ahousaht territory of Vancouver Island, Canada, and characterized using optical and electron microscopy, genome sequencing and cultivation approaches. The cells were elongated rods (5.1 µm in length and 1.2 µm in width, on average). Their UV visible absorption spectra revealed that they contain chlorophyll a, phycocyanin and carotenoids. Transmission electron microscopy showed the presence of thylakoids concentrated on one side of the cells. The strain grew within a temperature range of 37–50°C, with an optimum growth at 45°C. Its genome had a size of 3 049 282 bp and a DNA G + C content of 51.8 mol%. The cells contained numerous intracellular spherical granules easily visible under scanning electron microscopy. Energy dispersive X-ray spectroscopy revealed that these granules were made of Ca-, Ba- and Sr-containing carbonates. A phylogenetic 16S rRNA gene tree robustly placed this strain as sister to several environmental sequences and the described species Gloeomargarita lithophora, also characterized by the possession of intracellular carbonate inclusions. We consider strain VI4D9 to represent a new Gloeomargarita species based on its marked phenotypic differences with G. lithophora, notably, its thermophilic nature and different thylakoid organization, therefore we propose the name Gloeomargarita ahousahtiae sp. nov. The type strain is VI4D9 (Culture Collection of Algae and Protozoa strain 1472/1; Laboratorio de Algas Continentales Mexico strain LAC 140). Gloeomargarita ahousahtiae is the second species described within the recently discovered order Gloeomargaritales. Gloeomargarita ahousahtiae is a new thermophilic cyanobacterium.Growth temperature and thylakoid morphology differentiate G. ahousahtiae and G. lithophora.All described Gloeomargaritales synthesize intracellular carbonate inclusions. Gloeomargarita ahousahtiae is a new thermophilic cyanobacterium. Growth temperature and thylakoid morphology differentiate G. ahousahtiae and G. lithophora. All described Gloeomargaritales synthesize intracellular carbonate inclusions.
- Published
- 2023
- Full Text
- View/download PDF
20. The genomic sequence of Exiguobacterium chiriqhucha str. N139 reveals a species that thrives in cold waters and extreme environmental conditions
- Author
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Ana Gutiérrez-Preciado, Carlos Vargas-Chávez, Mariana Reyes-Prieto, Omar F. Ordoñez, Diego Santos-García, Tania Rosas-Pérez, Jorge Valdivia-Anistro, Eria A. Rebollar, Andrés Saralegui, Andrés Moya, Enrique Merino, María Eugenia Farías, Amparo Latorre, and Valeria Souza
- Subjects
High altitude Andean lakes ,Exiguobacterium ,Extremophiles ,Arsenic resistance ,Tryptophan biosynthesis ,Bacterial metabolism ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
We report the genome sequence of Exiguobacterium chiriqhucha str. N139, isolated from a high-altitude Andean lake. Comparative genomic analyses of the Exiguobacterium genomes available suggest that our strain belongs to the same species as the previously reported E. pavilionensis str. RW-2 and Exiguobacterium str. GIC 31. We describe this species and propose the chiriqhucha name to group them. ‘Chiri qhucha’ in Quechua means ‘cold lake’, which is a common origin of these three cosmopolitan Exiguobacteria. The 2,952,588-bp E. chiriqhucha str. N139 genome contains one chromosome and three megaplasmids. The genome analysis of the Andean strain suggests the presence of enzymes that confer E. chiriqhucha str. N139 the ability to grow under multiple environmental extreme conditions, including high concentrations of different metals, high ultraviolet B radiation, scavenging for phosphorous and coping with high salinity. Moreover, the regulation of its tryptophan biosynthesis suggests that novel pathways remain to be discovered, and that these pathways might be fundamental in the amino acid metabolism of the microbial community from Laguna Negra, Argentina.
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- 2017
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21. Description ofGloeomargarita ahousahtiaesp. nov., a thermophilic member of the order Gloeomargaritales with intracellular carbonate inclusions
- Author
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Thomas Bacchetta, Purificación López-García, Ana Gutiérrez-Preciado, Neha Mehta, Feriel Skouri-Panet, Karim Benzerara, Maria Ciobanu, Naoji Yubuki, Rosaluz Tavera, and David Moreira
- Abstract
A unicellular cyanobacterium, strain VI4D9, was isolated from thermophilic microbial mats thriving in a hot spring of the Ahousaht territory of Vancouver Island, Canada. The cells were elongated rods (5.1 μm in length and 1.2 μm in width on average). Their UV-visible absorption spectra revealed that they contain chlorophylla, phycocyanin, and carotenoids. Transmission electron microscopy showed the presence of thylakoids concentrated on one side of the cells. The strain grew within a temperature range of 37–50°C, with an optimum at 45°C. Its genome had a size of 3,049,282 bp and a DNA G+C content of 51.8 mol%. The cells contained numerous intracellular spherical granules easily visible under scanning electron microscopy. Energy-dispersive x-ray spectroscopy revealed that these granules were made of Ca-, Ba- and Sr-containing carbonates. A phylogenetic 16S rRNA gene tree robustly placed this strain as sister to several environmental sequences and the described speciesGloeomargarita lithophora, also characterized by the possession of intracellular carbonate inclusions. We consider strain VI4D9 to represent a newGloeomargaritaspecies based on its marked phenotypic differences withG. lithophora, notably, its thermophilic nature and different thylakoid organization. We propose the nameGloeomargarita ahousahtiaesp. nov. for this newly isolated thermophilic cyanobacterium. The type strain is VI4D9 (Culture Collection of Algae and Protozoa strain 1472/1; Laboratorio de Algas Continentales Mexico strain LAC 140).G. ahousahtiaeis the second species described within the recently discovered order Gloeomargaritales.
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- 2022
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22. Elucidating metabolic pathways and digging for genes of unknown function in microbial communities: the riboswitch approach
- Author
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Gutiérrez-Preciado, A. and Merino, E.
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- 2012
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23. Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies
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Galindo, Luis Javier, primary, Torruella, Guifré, additional, López-García, Purificación, additional, Ciobanu, Maria, additional, Gutiérrez-Preciado, Ana, additional, Karpov, Sergey A, additional, and Moreira, David, additional
- Published
- 2022
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24. Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies.
- Author
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Galindo, Luis Javier, Torruella, Guifré, López-García, Purificación, Ciobanu, Maria, Gutiérrez-Preciado, Ana, Karpov, Sergey A, and Moreira, David
- Subjects
HORIZONTAL gene transfer ,FUNGI ,ALGAL cells ,GENOMICS ,UNICELLULAR organisms - Abstract
The supergroup Holomycota, composed of Fungi and several related lineages of unicellular organisms (Nucleariida, Rozellida, Microsporidia, and Aphelida), represents one of the major branches in the phylogeny of eukaryotes. Nevertheless, except for the well-established position of Nucleariida as the first holomycotan branch to diverge, the relationships among the other lineages have so far remained unresolved largely owing to the lack of molecular data for some groups. This was notably the case aphelids, a poorly known group of endobiotic phagotrophic protists that feed on algae with cellulose walls. The first molecular phylogenies including aphelids supported their sister relationship with Rozellida and Microsporidia which, collectively, formed a new group called Opisthosporidia (the "Opisthosporidia hypothesis"). However, recent phylogenomic analyses including massive sequence data from two aphelid genera, Paraphelidium and Amoeboaphelidium , suggested that the aphelids are sister to fungi (the "Aphelida |$+$| Fungi hypothesis"). Should this position be confirmed, aphelids would be key to understanding the early evolution of Holomycota and the origin of Fungi. Here, we carry out phylogenomic analyses with an expanded taxonomic sampling for aphelids after sequencing the transcriptomes of two species of the genus Aphelidium (Aphelidium insulamus and Aphelidium tribonematis) in order to test these competing hypotheses. Our new phylogenomic analyses including species from the three known aphelid genera strongly rejected the Opisthosporidia hypothesis. Furthermore, comparative genomic analyses further supported the Aphelida |$+$| Fungi hypothesis via the identification of 19 orthologous genes exclusively shared by these two lineages. Seven of them originated from ancient horizontal gene transfer events predating the aphelid–fungal split and the remaining 12 likely evolved de novo , constituting additional molecular synapomorphies for this clade. Ancestral trait reconstruction based on our well-resolved phylogeny of Holomycota suggests that the progenitor of both fungi and rozellids, was aphelid-like, having an amoeboflagellate state and likely preying endobiotically on cellulose-containing, cell-walled organisms. Two lineages, which we propose to call Phytophagea and Opisthophagea, evolved from this ancestor. Phytophagea, grouping aphelids and classical fungi, mainly specialized in endobiotic predation of algal cells. Fungi emerged from this lineage after losing phagotrophy in favor of osmotrophy. Opisthophagea, grouping rozellids and Microsporidia, became parasites, mostly of chitin-containing hosts. This lineage entered a progressive reductive process that resulted in a unique lifestyle, especially in the highly derived Microsporidia. [Aphelida, fungi, Holomycota, horizontal gene transfer, phylogenomics, synapomorphy.] [ABSTRACT FROM AUTHOR]
- Published
- 2023
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25. Extensive Identification of Bacterial Riboflavin Transporters and Their Distribution across Bacterial Species.
- Author
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Ana Gutiérrez-Preciado, Alfredo Gabriel Torres, Enrique Merino, Hernán Ruy Bonomi, Fernando Alberto Goldbaum, and Víctor Antonio García-Angulo
- Subjects
Medicine ,Science - Abstract
Riboflavin, the precursor for the cofactors flavin mononucleotide (FMN) and flavin adenine dinucleotide, is an essential metabolite in all organisms. While the functions for de novo riboflavin biosynthesis and riboflavin import may coexist in bacteria, the extent of this co-occurrence is undetermined. The RibM, RibN, RfuABCD and the energy-coupling factor-RibU bacterial riboflavin transporters have been experimentally characterized. In addition, ImpX, RfnT and RibXY are proposed as riboflavin transporters based on positional clustering with riboflavin biosynthetic pathway (RBP) genes or conservation of the FMN riboswitch regulatory element. Here, we searched for the FMN riboswitch in bacterial genomes to identify genes encoding riboflavin transporters and assessed their distribution among bacteria. Two new putative riboflavin transporters were identified: RibZ in Clostridium and RibV in Mesoplasma florum. Trans-complementation of an Escherichia coli riboflavin auxotroph strain confirmed the riboflavin transport activity of RibZ from Clostridium difficile, RibXY from Chloroflexus aurantiacus, ImpX from Fusobacterium nucleatum and RfnT from Ochrobactrum anthropi. The analysis of the genomic distribution of all known bacterial riboflavin transporters revealed that most occur in species possessing the RBP and that some bacteria may even encode functional riboflavin transporters from two different families. Our results indicate that some species possess ancestral riboflavin transporters, while others possess transporters that appear to have evolved recently. Moreover, our data suggest that unidentified riboflavin transporters also exist. The present study doubles the number of experimentally characterized riboflavin transporters and suggests a specific, non-accessory role for these proteins in riboflavin-prototrophic bacteria.
- Published
- 2015
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26. Workspace Analysis of a Delta-Like Robot Using an Alternative Approach
- Author
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Gutiérrez-Preciado, A., primary, González-Palacios, M. A., additional, and Aguilera-Cortés, L. A., additional
- Published
- 2014
- Full Text
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27. Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies
- Author
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Luis Javier Galindo, Guifré Torruella, Purificación López-García, Maria Ciobanu, Ana Gutiérrez-Preciado, Sergey A Karpov, and David Moreira
- Subjects
Genetics ,Ecology, Evolution, Behavior and Systematics - Abstract
The supergroup Holomycota, composed of Fungi and several related lineages of unicellular organisms (Nucleariida, Rozellida, Microsporidia, and Aphelida), represents one of the major branches in the phylogeny of eukaryotes. Nevertheless, except for the well-established position of Nucleariida as the first holomycotan branch to diverge, the relationships among the other lineages have so far remained unresolved largely owing to the lack of molecular data for some groups. This was notably the case aphelids, a poorly known group of endobiotic phagotrophic protists that feed on algae with cellulose walls. The first molecular phylogenies including aphelids supported their sister relationship with Rozellida and Microsporidia which, collectively, formed a new group called Opisthosporidia (the “Opisthosporidia hypothesis”). However, recent phylogenomic analyses including massive sequence data from two aphelid genera, Paraphelidium and Amoeboaphelidium, suggested that the aphelids are sister to fungi (the “Aphelida $+$ Fungi hypothesis”). Should this position be confirmed, aphelids would be key to understanding the early evolution of Holomycota and the origin of Fungi. Here, we carry out phylogenomic analyses with an expanded taxonomic sampling for aphelids after sequencing the transcriptomes of two species of the genus Aphelidium (Aphelidium insulamus and Aphelidium tribonematis) in order to test these competing hypotheses. Our new phylogenomic analyses including species from the three known aphelid genera strongly rejected the Opisthosporidia hypothesis. Furthermore, comparative genomic analyses further supported the Aphelida $+$ Fungi hypothesis via the identification of 19 orthologous genes exclusively shared by these two lineages. Seven of them originated from ancient horizontal gene transfer events predating the aphelid–fungal split and the remaining 12 likely evolved de novo, constituting additional molecular synapomorphies for this clade. Ancestral trait reconstruction based on our well-resolved phylogeny of Holomycota suggests that the progenitor of both fungi and rozellids, was aphelid-like, having an amoeboflagellate state and likely preying endobiotically on cellulose-containing, cell-walled organisms. Two lineages, which we propose to call Phytophagea and Opisthophagea, evolved from this ancestor. Phytophagea, grouping aphelids and classical fungi, mainly specialized in endobiotic predation of algal cells. Fungi emerged from this lineage after losing phagotrophy in favor of osmotrophy. Opisthophagea, grouping rozellids and Microsporidia, became parasites, mostly of chitin-containing hosts. This lineage entered a progressive reductive process that resulted in a unique lifestyle, especially in the highly derived Microsporidia. [Aphelida, fungi, Holomycota, horizontal gene transfer, phylogenomics, synapomorphy.]
- Published
- 2021
28. Comparison of tryptophan biosynthetic operon regulation in different Gram-positive bacterial species
- Author
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Gutiérrez-Preciado, Ana, Yanofsky, Charles, and Merino, Enrique
- Published
- 2007
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- View/download PDF
29. Metagenome-derived virus-microbe ratios across ecosystems
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López-García, Purificación, primary, Gutiérrez-Preciado, Ana, additional, Krupovic, Mart, additional, Ciobanu, Maria, additional, Deschamps, Philippe, additional, Jardillier, Ludwig, additional, López-Pérez, Mario, additional, Rodríguez-Valera, Francisco, additional, and Moreira, David, additional
- Published
- 2021
- Full Text
- View/download PDF
30. An educational software for teaching database normalization
- Author
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Luis F. Gutiérrez-Preciado, Víctor H. Ortega-Guzmán, and Hugo I. Piza-Dávila
- Subjects
Normalization (statistics) ,General Computer Science ,Computer science ,Business rule ,business.industry ,Software tool ,05 social sciences ,General Engineering ,050301 education ,02 engineering and technology ,computer.software_genre ,Education ,Database normalization ,Software ,020204 information systems ,0202 electrical engineering, electronic engineering, information engineering ,Software engineering ,business ,0503 education ,computer ,Educational software - Abstract
Database normalization is a key process for designing databases. However, it is one of the most complex topics for students in IT undergraduate programs. This work proposes a new software tool that supports students in the process of normalization. This learning tool allows the students to see step by step how to carry out each normal form up to the 3NF. This tool is based on data analysis of the input table as it is explained in class, and not on analyzing the scheme or initial dependencies defined by business rules. Thus, novel algorithms were developed to process the input table (user-defined) as well as the tables created during the normalization process. The software was tested in two Database courses, obtaining an important increase in the performance of students who used the tool.
- Published
- 2017
- Full Text
- View/download PDF
31. Unveiling microbial interactions in stratified mat communities from a warm saline shallow pond
- Author
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Aurélien Saghaï, David Moreira, Purificación López-García, Ana Gutiérrez-Preciado, Philippe Deschamps, Paola Bertolino, and Marie Ragon
- Subjects
0301 basic medicine ,Phototroph ,biology ,Ecology ,Biodiversity ,Protist ,Biogeochemistry ,medicine.disease_cause ,biology.organism_classification ,Microbiology ,03 medical and health sciences ,030104 developmental biology ,Botany ,medicine ,Lokiarchaeota ,Ecosystem ,Microbial mat ,Ecology, Evolution, Behavior and Systematics ,Archaea - Abstract
Modern phototrophic microbial mats are complex communities often used as analogs of major Precambrian ecosystems. Characterizing biotic, notably metabolic, interactions among different microbial mat members is essential to gain insights into the ecology and biogeochemistry of these systems. We applied 16S/18S rRNA metabarcoding approaches to characterize the structure of archaea, bacteria and protist communities from microbial mats collected along strong physicochemical (oxygen, salinity, temperature, depth) gradients in a shallow pond at the salar de Llamara (Chile). All mats were highly diverse, including members of virtually all known high-rank eukaryotic and prokaryotic taxa but also many novel lineages. Bacterial candidate divisions accounted for almost 50% of sequences in deeper mats, while Archaea represented up to 40% of sequences in some mat layers. Molecular phylogenetic analyses revealed six novel deeply divergent archaeal groups, along abundant and diverse Pacearchaeota and Woesearchaeota. Multivariate statistical analyses showed that local environmental conditions strongly influenced community composition. Co-occurrence network structure was markedly different between surface mats located in the oxygenated zone and mats located in transition and anoxic water layers. We identified potential biotic interactions between various high- and low-rank taxa. Notably, a strong positive correlation was observed between Lokiarchaeota and the poorly known candidate bacterial division TA06.
- Published
- 2017
- Full Text
- View/download PDF
32. New insights into regulation of the tryptophan biosynthetic operon in Gram-positive bacteria
- Author
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Gutierrez-Preciado, A., Jensen, R.A., Yanofsky, C., and Merino, E.
- Published
- 2005
- Full Text
- View/download PDF
33. Optimización del Espacio de Trabajo de un Robot Deltoide
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Gutiérrez-Preciado, Alfredo, González-Palacios, Max Antonio, Aguilera-Cortés, Luz Antonio, and Mendoza-Patiño, Francisco Javier
- Subjects
Robot Deltoide ,Diseño ,Optimization ,Workspace ,Simulación por computadora ,Espacio de trabajo ,Design ,ADEFID ,Computer simulation ,Deltoid Robot ,Optimización - Abstract
[EN] Studies conducted on the Delta robot have reported drawbacks regarding its limited workspace. In this paper, it is proposed a modification in the placement of its actuators, thus becoming what is called the Deltoide robot. With this change, the workspace can greatly increase or decrease. This way, an optimization using genetic algorithms is proposed to find the largest workspace that the robot can have depending on the design variables. Additionally, the general analysis of the forward and inverse kinematics of the Deltoide robot, is explained and implemented in a software specially created for this application. [ES] Los estudios realizados en el robot Delta han reportado inconveniencias con respecto a su limitado espacio de trabajo. Este artículo propone una modificación en la colocación de sus actuadores, convirtiéndose así en lo que se denomina robot Deltoide. Con este cambio, el espacio de trabajo puede aumentar o disminuir considerablemente. De esta manera, se propone una optimización usando algoritmos genéticos para encontrar el mayor espacio de trabajo que el robot puede tener dependiendo de las variables de diseño. Además, se explica e implementa el análisis general de la cinemática directa e inversa del robot Deltoide, en un software creado especialmente para esta aplicación.
- Published
- 2019
34. Functional shifts in microbial mats recapitulate early Earth metabolic transitions
- Author
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Ana Gutiérrez-Preciado, Aurélien Saghaï, Philippe Deschamps, David Moreira, Yvan Zivanovic, Purificación López-García, Ecologie Systématique et Evolution (ESE), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11), Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Radiorésistance des bactéries et des archées (RBA), Département Biologie des Génomes (DBG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
- Subjects
0301 basic medicine ,[SDV.BID]Life Sciences [q-bio]/Biodiversity ,Photosynthesis ,Cyanobacteria ,[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy ,Article ,03 medical and health sciences ,Ecosystem ,Microbial mat ,Ecology, Evolution, Behavior and Systematics ,Ecology ,Phototroph ,Chemistry ,Great Oxygenation Event ,[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,15. Life on land ,Early Earth ,Anoxygenic photosynthesis ,Biological Evolution ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,Oxygen ,030104 developmental biology ,13. Climate action ,Autotrophic Processes ,Biofilms ,Metagenome - Abstract
Phototrophic microbial mats dominated terrestrial ecosystems for billions of years, largely causing, through cyanobacterial oxygenic photosynthesis, but also undergoing, the Great Oxidation Event approximately 2.5 billion years ago. Taking a space-for-time approach based on the universality of core metabolic pathways expressed at ecosystem level, we studied gene content and co-occurrence networks in high-diversity metagenomes from spatially close microbial mats along a steep redox gradient. The observed functional shifts suggest that anoxygenic photosynthesis was present but not predominant under early Precambrian conditions, being accompanied by other autotrophic processes. Our data also suggest that, in contrast to general assumptions, anoxygenic photosynthesis largely expanded in parallel with the subsequent evolution of oxygenic photosynthesis and aerobic respiration. Finally, our observations might represent space-for-time evidence that the Wood–Ljungdahl carbon fixation pathway dominated phototrophic mats in early ecosystems, whereas the Calvin cycle probably evolved from pre-existing variants before becoming the dominant contemporary form of carbon fixation. Microbial mats in extreme environments are analogues of Precambrian ecosystems. Here, the authors analyse metagenomes of microbial mats from a pond along a steep redox gradient and apply a space-for-time approach to infer early Earth metabolic transitions.
- Published
- 2018
- Full Text
- View/download PDF
35. Frontiers in Microbiology
- Author
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Eria A. Rebollar, Ana Gutiérrez-Preciado, Cecilia Noecker, Alexander Eng, Myra C. Hughey, Daniel Medina, Jenifer B. Walke, Elhanan Borenstein, Roderick V. Jensen, Lisa K. Belden, Reid N. Harris, and Biological Sciences
- Subjects
0301 basic medicine ,Microbiology (medical) ,Amphibian ,Population ,lcsh:QR1-502 ,host-bacteria interactions ,Microbiology ,lcsh:Microbiology ,03 medical and health sciences ,biology.animal ,Gammaproteobacteria ,Chytridiomycosis ,Microbiome ,education ,Batrachochytrium dendrobatidis ,Genetics ,education.field_of_study ,amphibians ,biology ,Craugastor fitzingeri ,15. Life on land ,biology.organism_classification ,030104 developmental biology ,Metagenomics ,skin microbiome ,shotgun metagenomics ,Symbiotic bacteria - Abstract
Skin symbiotic bacteria on amphibians can play a role in protecting their host against pathogens. Chytridiomycosis, the disease caused by Batrachochytrium dendrobatidis, Bd, has caused dramatic population declines and extinctions of amphibians worldwide. Anti-Bd bacteria from amphibian skin have been cultured, and skin bacterial communities have been described through 16S rRNA gene amplicon sequencing. Here, we present a shotgun metagenomic analysis of skin bacterial communities from a Neotropical frog, Craugastor fitzingeri. We sequenced the metagenome of six frogs from two different sites in Panamá: three frogs from Soberanía (Sob), a Bd-endemic site, and three frogs from Serranía del Sapo (Sapo), a Bd-naïve site. We described the taxonomic composition of skin microbiomes and found that Pseudomonas was a major component of these communities. We also identified that Sob communities were enriched in Actinobacteria while Sapo communities were enriched in Gammaproteobacteria. We described gene abundances within the main functional classes and found genes enriched either in Sapo or Sob. We then focused our study on five functional classes of genes: biosynthesis of secondary metabolites, metabolism of terpenoids and polyketides, membrane transport, cellular communication and antimicrobial drug resistance. These gene classes are potentially involved in bacterial communication, bacterial-host and bacterial-pathogen interactions among other functions. We found that C. fitzingeri metagenomes have a wide array of genes that code for secondary metabolites, including antibiotics and bacterial toxins, which may be involved in bacterial communication, but could also have a defensive role against pathogens. Several genes involved in bacterial communication and bacterial-host interactions, such as biofilm formation and bacterial secretion systems were found. We identified specific genes and pathways enriched at the different sites and determined that gene co-occurrence networks differed between sites. Our results suggest that skin microbiomes are composed of distinct bacterial taxa with a wide range of metabolic capabilities involved in bacterial defense and communication. Differences in taxonomic composition and pathway enrichments suggest that skin microbiomes from different sites have unique functional properties. This study strongly supports the need for shotgun metagenomic analyses to describe the functional capacities of skin microbiomes and to tease apart their role in host defense against pathogens.
- Published
- 2018
36. Optimización del Espacio de Trabajo de un Robot Deltoide
- Author
-
Gutiérrez-Preciado, Alfredo, primary, González-Palacios, Max Antonio, additional, Aguilera-Cortés, Luz Antonio, additional, and Mendoza-Patiño, Francisco Javier, additional
- Published
- 2019
- Full Text
- View/download PDF
37. The Skin Microbiome of the Neotropical Frog
- Author
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Eria A, Rebollar, Ana, Gutiérrez-Preciado, Cecilia, Noecker, Alexander, Eng, Myra C, Hughey, Daniel, Medina, Jenifer B, Walke, Elhanan, Borenstein, Roderick V, Jensen, Lisa K, Belden, and Reid N, Harris
- Subjects
amphibians ,skin microbiome ,host-bacteria interactions ,Microbiology ,Batrachochytrium dendrobatidis ,Original Research ,shotgun metagenomics - Abstract
Skin symbiotic bacteria on amphibians can play a role in protecting their host against pathogens. Chytridiomycosis, the disease caused by Batrachochytrium dendrobatidis, Bd, has caused dramatic population declines and extinctions of amphibians worldwide. Anti-Bd bacteria from amphibian skin have been cultured, and skin bacterial communities have been described through 16S rRNA gene amplicon sequencing. Here, we present a shotgun metagenomic analysis of skin bacterial communities from a Neotropical frog, Craugastor fitzingeri. We sequenced the metagenome of six frogs from two different sites in Panamá: three frogs from Soberanía (Sob), a Bd-endemic site, and three frogs from Serranía del Sapo (Sapo), a Bd-naïve site. We described the taxonomic composition of skin microbiomes and found that Pseudomonas was a major component of these communities. We also identified that Sob communities were enriched in Actinobacteria while Sapo communities were enriched in Gammaproteobacteria. We described gene abundances within the main functional classes and found genes enriched either in Sapo or Sob. We then focused our study on five functional classes of genes: biosynthesis of secondary metabolites, metabolism of terpenoids and polyketides, membrane transport, cellular communication and antimicrobial drug resistance. These gene classes are potentially involved in bacterial communication, bacterial-host and bacterial-pathogen interactions among other functions. We found that C. fitzingeri metagenomes have a wide array of genes that code for secondary metabolites, including antibiotics and bacterial toxins, which may be involved in bacterial communication, but could also have a defensive role against pathogens. Several genes involved in bacterial communication and bacterial-host interactions, such as biofilm formation and bacterial secretion systems were found. We identified specific genes and pathways enriched at the different sites and determined that gene co-occurrence networks differed between sites. Our results suggest that skin microbiomes are composed of distinct bacterial taxa with a wide range of metabolic capabilities involved in bacterial defense and communication. Differences in taxonomic composition and pathway enrichments suggest that skin microbiomes from different sites have unique functional properties. This study strongly supports the need for shotgun metagenomic analyses to describe the functional capacities of skin microbiomes and to tease apart their role in host defense against pathogens.
- Published
- 2017
38. Unveiling microbial interactions in stratified mat communities from a warm saline shallow pond
- Author
-
Saghaï, Aurélien, Gutiérrez-Preciado, Ana, Deschamps, Philippe, Moreira, David, Bertolino, Paola, Ragon, Marie, and López-García, Purificación
- Subjects
Salinity ,Bacteria ,Biodiversity ,Archaea ,Article ,Phototrophic Processes ,Biofilms ,RNA, Ribosomal, 16S ,RNA, Ribosomal, 18S ,Animals ,Microbial Interactions ,Parasites ,Chile ,Ponds ,Ecosystem ,Phylogeny - Abstract
Modern phototrophic microbial mats are complex communities often used as analogs of major Precambrian ecosystems. Characterizing biotic, notably metabolic, interactions among different microbial mat members is essential to gain insights into the ecology and biogeochemistry of these systems. We applied 16S/18S rRNA metabarcoding approaches to characterize the structure of archaea, bacteria and protist communities from microbial mats collected along strong physicochemical (oxygen, salinity, temperature, depth) gradients in a shallow pond at the salar de Llamara (Chile). All mats were highly diverse, including members of virtually all known high-rank eukaryotic and prokaryotic taxa but also many novel lineages. Bacterial candidate divisions accounted for almost 50% of sequences in deeper mats, while Archaea represented up to 40% of sequences in some mat layers. Molecular phylogenetic analyses revealed six novel deeply divergent archaeal groups, along abundant and diverse Pacearchaeota and Woesearchaeota. Multivariate statistical analyses showed that local environmental conditions strongly influenced community composition. Co-occurrence network structure was markedly different between surface mats located in the oxygenated zone and mats located in transition and anoxic water layers. We identified potential biotic interactions between various high- and low-rank taxa. Notably, a strong positive correlation was observed between Lokiarchaeota and the poorly known candidate bacterial division TA06.
- Published
- 2017
39. The Skin Microbiome of the Neotropical Frog Craugastor fitzingeri: Inferring Potential Bacterial-Host-Pathogen Interactions From Metagenomic Data
- Author
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Rebollar, Eria A., primary, Gutiérrez-Preciado, Ana, additional, Noecker, Cecilia, additional, Eng, Alexander, additional, Hughey, Myra C., additional, Medina, Daniel, additional, Walke, Jenifer B., additional, Borenstein, Elhanan, additional, Jensen, Roderick V., additional, Belden, Lisa K., additional, and Harris, Reid N., additional
- Published
- 2018
- Full Text
- View/download PDF
40. The genomic sequence of Exiguobacterium chiriqhucha str. N139 reveals a species that thrives in cold waters and extreme environmental conditions
- Author
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Gutiérrez-Preciado A, Vargas-Chávez C, Reyes-Prieto M, Ordoñez OF, Santos-García D, Rosas-Pérez T, Valdivia-Anistro J, Rebollar EA, Saralegui A, Moya A, Merino E, Farías ME, Latorre A, and Souza V
- Subjects
Arsenic resistance, Bacterial metabolism, Exiguobacterium, Extremophiles, High altitude Andean lakes, Metals or metalloids, Tryptophan biosynthesis, UV resistance ,High altitude Andean lakes ,Extremophiles ,Arsenic resistance ,Exiguobacterium ,UV resistance ,Tryptophan biosynthesis ,Bacterial metabolism ,Metals or metalloids - Abstract
We report the genome sequence of Exiguobacterium chiriqhucha str. N139, isolated from a high-altitude Andean lake. Comparative genomic analyses of the Exiguobacterium genomes available suggest that our strain belongs to the same species as the previously reported E. pavilionensis str. RW-2 and Exiguobacterium str. GIC 31. We describe this species and propose the chiriqhucha name to group them. 'Chiri qhucha' in Quechua means 'cold lake', which is a common origin of these three cosmopolitan Exiguobacteria. The 2,952,588-bp E. chiriqhucha str. N139 genome contains one chromosome and three megaplasmids. The genome analysis of the Andean strain suggests the presence of enzymes that confer E. chiriqhucha str. N139 the ability to grow under multiple environmental extreme conditions, including high concentrations of different metals, high ultraviolet B radiation, scavenging for phosphorous and coping with high salinity. Moreover, the regulation of its tryptophan biosynthesis suggests that novel pathways remain to be discovered, and that these pathways might be fundamental in the amino acid metabolism of the microbial community from Laguna Negra, Argentina.
- Published
- 2017
41. The genomic sequence of Exiguobacterium chiriqhucha str. N139 reveals a species that thrives in cold waters and extreme environmental conditions
- Author
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Enrique Merino, Mariana Reyes-Prieto, Andrés Moya, Ana Gutiérrez-Preciado, Amparo Latorre, Jorge Valdivia-Anistro, Valeria Souza, Andrés Saralegui, Maria Eugenia Farias, Diego Santos-Garcia, Tania Rosas-Pérez, Omar Federico Ordoñez, Eria A. Rebollar, Carlos Vargas-Chávez, AgroParisTech, Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), and Universitat de València (UV)
- Subjects
0301 basic medicine ,megaplasmid ,Bioinformatics ,Otras Ciencias Biológicas ,[SDV]Life Sciences [q-bio] ,Microbial metabolism ,Biodiversity ,lcsh:Medicine ,Genomics ,Tryptophan biosynthesis ,Microbiology High altitude Andean lakes ,Biology ,Subjects Biochemistry ,Genome ,Biochemistry ,Microbiology ,General Biochemistry, Genetics and Molecular Biology ,Ciencias Biológicas ,purl.org/becyt/ford/1 [https] ,03 medical and health sciences ,Extremophiles ,Arsenic resistance ,Exiguobacterium ,Botany ,Extremophile ,purl.org/becyt/ford/1.6 [https] ,genome ,2. Zero hunger ,Whole genome sequencing ,Genetics ,General Neuroscience ,lcsh:R ,General Medicine ,Metals or metalloids ,biology.organism_classification ,High altitude Andean lakes ,030104 developmental biology ,Microbial population biology ,13. Climate action ,UV resistance ,Bacterial metabolism ,General Agricultural and Biological Sciences ,CIENCIAS NATURALES Y EXACTAS - Abstract
We report the genome sequence of Exiguobacterium chiriqhucha str. N139, isolated from a high-altitude Andean lake. Comparative genomic analyses of the Exiguobacterium genomes available suggest that our strain belongs to the same species as the previously reported E. pavilionensis str. RW-2 and Exiguobacterium str. GIC 31. We describe this species and propose the chiriqhucha name to group them. ‘Chiri qhucha’ in Quechua means ‘cold lake’, which is a common origin of these three cosmopolitan Exiguobacteria. The 2,952,588-bp E. chiriqhucha str. N139 genome contains one chromosome and three megaplasmids. The genome analysis of the Andean strain suggests the presence of enzymes that confer E. chiriqhucha str. N139 the ability to grow under multiple environmental extreme conditions, including high concentrations of different metals, high ultraviolet B radiation, scavenging for phosphorous and coping with high salinity. Moreover, the regulation of its tryptophan biosynthesis suggests that novel pathways remain to be discovered, and that these pathways might be fundamental in the amino acid metabolism of the microbial community from Laguna Negra, Argentina. Fil: Gutierrez, Ana. Universidad de Valencia; España Fil: Vargas Chaves, Carlos. Universidad de Valencia; España Fil: Reyes Prieto, Mariana. Universidad de Valencia; España Fil: Ordoñez, Omar Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Planta Piloto de Procesos Industriales Microbiologicos; Argentina Fil: Santos-García, Diego. Universidad de Valencia; España Fil: Rosas-Pérez, Tania. Universidad de Valencia; España Fil: Valdivia-Anistro, Jorge. Universidad de Valencia; España Fil: Rebollar, Eria A.. Universidad Nacional Autónoma de México; México Fil: Saralegui, Andrés. Universidad Nacional Autónoma de México; México Fil: Moya, Andrés. Universidad de Valencia; España Fil: Merino, Enrique. Universidad Nacional Autónoma de México; México Fil: Farias, Maria Eugenia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Planta Piloto de Procesos Industriales Microbiologicos; Argentina Fil: Latorre, Amparo. Universidad de Valencia; España Fil: Souza, Valeria. Universidad Nacional Autónoma de México; México
- Published
- 2017
- Full Text
- View/download PDF
42. Exiguobacterium pavilionensis str. N139, a halotolerant, UV-B and metal resistant bacteria from a high-altitude Andean lake
- Author
-
Maria Eugenia Farias, Diego Santos-Garcia, Carlos Vargas-Chávez, Valeria Souza, Andrés Saralegui, Andrés Moya, Enrique Merino, Ana Gutiérrez-Preciado, Amparo Latorre, Mariana Reyes-Prieto, Eria A. Rebollar, Tania Rosas-Pérez, Omar Federico Ordoñez, and Jorge Valdivia-Anistro
- Subjects
UV resistance ,Resistant bacteria ,Altitude ,biology ,Tryptophan biosynthesis ,Botany ,Microbial metabolism ,Halotolerance ,Extremophile ,Exiguobacterium ,biology.organism_classification ,Microbiology - Abstract
We report the genome sequence of Exiguobacterium pavilionensis str. N139, isolated from a high-altitude Andean lake. The 2,952,588-bp genome contains one chromosome and three megaplasmids. The genome analysis suggests the presence of enzymes that confer E. pavilionensis str. N139 the ability to grow under multiple environmental extreme conditions, including high concentrations of different metals and high ultraviolet B radiation. Moreover, the regulation of its tryptophan biosynthesis suggests that novel pathways remain to be discovered, and that these pathways might be fundamental in the amino acid metabolism of the microbial community from Laguna Negra, Argentina .
- Published
- 2016
- Full Text
- View/download PDF
43. Genome Sequence Databases: Types of Data and Bioinformatic Tools
- Author
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Gutiérrez-Preciado, Ana, Deschamps, Philippe, Delmont, Tom O., Chica, Claudia, Chrismas, Nathan A.M., and Rodríguez de la Vega, Ricardo C.
- Published
- 2015
- Full Text
- View/download PDF
44. An educational software for teaching database normalization
- Author
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Piza-Dávila, Hugo I., primary, Gutiérrez-Preciado, Luis F., additional, and Ortega-Guzmán, Víctor H., additional
- Published
- 2017
- Full Text
- View/download PDF
45. Unveiling microbial interactions in stratified mat communities from a warm saline shallow pond
- Author
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Saghaï, Aurélien, primary, Gutiérrez-Preciado, Ana, additional, Deschamps, Philippe, additional, Moreira, David, additional, Bertolino, Paola, additional, Ragon, Marie, additional, and López-García, Purificación, additional
- Published
- 2017
- Full Text
- View/download PDF
46. The genomic sequence ofExiguobacterium chiriqhuchastr. N139 reveals a species that thrives in cold waters and extreme environmental conditions
- Author
-
Gutiérrez-Preciado, Ana, primary, Vargas-Chávez, Carlos, additional, Reyes-Prieto, Mariana, additional, Ordoñez, Omar F., additional, Santos-García, Diego, additional, Rosas-Pérez, Tania, additional, Valdivia-Anistro, Jorge, additional, Rebollar, Eria A., additional, Saralegui, Andrés, additional, Moya, Andrés, additional, Merino, Enrique, additional, Farías, María Eugenia, additional, Latorre, Amparo, additional, and Souza, Valeria, additional
- Published
- 2017
- Full Text
- View/download PDF
47. Exiguobacterium pavilionensis str. N139, a halotolerant, UV-B and metal resistant bacteria from a high-altitude Andean lake
- Author
-
Gutiérrez-Preciado, Ana, primary, Vargas-Chávez, Carlos, additional, Reyes-Prieto, Mariana, additional, Ordoñez, Omar F, additional, Santos-García, Diego, additional, Rosas-Pérez, Tania, additional, Valdivia-Anistro, Jorge, additional, Rebollar, Eria A, additional, Saralegui, Andrés, additional, Moya, Andrés, additional, Merino, Enrique, additional, Farías, María Eugenia, additional, Latorre, Amparo, additional, and Souza, Valeria, additional
- Published
- 2016
- Full Text
- View/download PDF
48. Extensive Identification of Bacterial Riboflavin Transporters and Their Distribution across Bacterial Species
- Author
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Gutiérrez-Preciado, Ana, primary, Torres, Alfredo Gabriel, additional, Merino, Enrique, additional, Bonomi, Hernán Ruy, additional, Goldbaum, Fernando Alberto, additional, and García-Angulo, Víctor Antonio, additional
- Published
- 2015
- Full Text
- View/download PDF
49. Biochemical Features and Functional Implications of the RNA-Based T-Box Regulatory Mechanism
- Author
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Ana Gutiérrez-Preciado, Tina M. Henkin, Frank J. Grundy, Charles Yanofsky, and Enrique Merino
- Subjects
Deltaproteobacteria ,Gene Transfer, Horizontal ,Operon ,Reviews ,Biology ,Regulatory Sequences, Nucleic Acid ,Gram-Positive Bacteria ,Microbiology ,Regulon ,Amino Acyl-tRNA Synthetases ,Evolution, Molecular ,Transcription (biology) ,Amino Acids ,Molecular Biology ,Gene ,Regulation of gene expression ,Genetics ,Gene Expression Regulation, Bacterial ,Repressor Proteins ,Infectious Diseases ,Terminator (genetics) ,Regulatory sequence ,Transfer RNA ,bacteria ,T-Box Domain Proteins - Abstract
SUMMARY The T-box mechanism is a common regulatory strategy used for modulating the expression of genes of amino acid metabolism-related operons in gram-positive bacteria, especially members of the Firmicutes. T-box regulation is usually based on a transcription attenuation mechanism in which an interaction between a specific uncharged tRNA and the 5′ region of the transcript stabilizes an antiterminator structure in preference to a terminator structure, thereby preventing transcription termination. Although single T-box regulatory elements are common, double or triple T-box arrangements are also observed, expanding the regulatory range of these elements. In the present study, we predict the functional implications of T-box regulation in genes encoding aminoacyl-tRNA synthetases, proteins of amino acid biosynthetic pathways, transporters, and regulatory proteins. We also consider the global impact of the use of this regulatory mechanism on cell physiology. Novel biochemical relationships between regulated genes and their corresponding metabolic pathways were revealed. Some of the genes identified, such as the quorum-sensing gene luxS, in members of the Lactobacillaceae were not previously predicted to be regulated by the T-box mechanism. Our analyses also predict an imbalance in tRNA sensing during the regulation of operons containing multiple aminoacyl-tRNA synthetase genes or biosynthetic genes involved in pathways common to more than one amino acid. Based on the distribution of T-box regulatory elements, we propose that this regulatory mechanism originated in a common ancestor of members of the Firmicutes, Chloroflexi, Deinococcus-Thermus group, and Actinobacteria and was transferred into the Deltaproteobacteria by horizontal gene transfer.
- Published
- 2009
50. Biochemical Features and Functional Implications of the RNA-Based T-Box Regulatory Mechanism
- Author
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Gutiérrez-Preciado, Ana, primary, Henkin, Tina M., additional, Grundy, Frank J., additional, Yanofsky, Charles, additional, and Merino, Enrique, additional
- Published
- 2009
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