Browsing by Author "Gutiérrez Ilabaca, Rodrigo Antonio"

Now showing 1 - 20 of 103
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    2020 vision for biology: the role of plants in addressing grand challenges in biology
    (2008) Bender, J.; Gutiérrez Ilabaca, Rodrigo Antonio
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    A framework integrating plant growth with hormones and nutrients
    (2011) Krouk, G.; Gutiérrez Ilabaca, Rodrigo Antonio
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    A holistic view of nitrogen acquisition in plants
    (2011) Kraiser Miranda, Tatiana Diannela; Gutiérrez Ilabaca, Rodrigo Antonio
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    A machine learning approach to predict gene expression signatures, local gene networks, and key genes for biological functions of interest.
    (2015) Puelma Peters, Tomás Francisco; Gutiérrez Ilabaca, Rodrigo Antonio; Pontificia Universidad Católica de Chile. Escuela de Ingeniería
    Un objetivo importante en la investigación biológica es descubrir genes relevantes para funciones biológicas de interés. Estas funciones pueden tener distintos grados de complejidad, desde procesos biológicos específicos a características complejas como “enfermedades metabólicas” en humanos o “tiempo de floración” en plantas. Esta tesis presenta “Discriminative Local Subspaces” (DLS), un método computacional que combina técnicas de aprendizaje de máquina supervisado y coexpresión para predecir redes de genes capaces de exponer nuevos genes y señalar cuáles son importantes para una función biológica de interés. Además presenta GENIUS, un servidor web que permite a la comunidad científica aprovechar las capacidades de DLS a través de una interfaz amistosa. En contraste con las redes de coexpresión tradicionales, DLS usa el conocimiento disponible en GeneOntology (GO) para generar conjuntos de entrenamiento informativos y guiar la búsqueda de “firmas de expresión”: patrones de expresión distintivos para los genes que participan en una función biológica de interés. Luego, DLS une los genes que se coexpresan con estas firmas para formar una red génica que contiene tanto genes conocidos como nuevos, para la función biológica de interés. Nuestras evaluaciones sistemáticas demuestran que DLS puede predecir genes nuevos con precisiones comparables a los métodos altamente discriminativos “Support Vector Maquines” (SVM), pero manteniendo la representación intuitiva e informativa que proveenlas redes de coexpresión. Más aún, nuestras evaluaciones muestran que, en contraste con estos métodos, DLS mejora su precisión sistemáticamente al aumentar la cantidad de datos experimentales disponibles. Además, nuestras evaluaciones en escenarios reales muestran que GENIUS puede realizar nuevos descubrimientos de manera efectiva. En particular,GENIUS predijo un nuevo gen, clave para mejorar la eficiencia del uso del nitrógeno en plantas, lo cual fue validado experimentalmente. Por lo tanto, creemos que GENIUS puede ayudar a generar hipótesis concretas a partir de conocimiento previo, realizar nuevos descubrimientos y, por lo tanto, mejorar nuestra comprensión molecular sobre los sistemas biológicos. GENIUS actualmente puede ser utilizado en ocho importantes organismos y es de libre acceso en http://networks.bio.puc.cl/genius.
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    A simple RNA preparation method for SARS-CoV-2 detection by RT-qPCR
    (2020) Wozniak Banchero, Aniela; Cerda Rojas, Ariel Patricio; Lamig Giannini, Liliana Andrea; Solari Gajardo, Sandra; Guzmán Durán, Ana María; Riveras Hernández, Eleodoro Javier; Ferres Garrido, Marcela Viviana; Gutiérrez Ilabaca, Rodrigo Antonio; García Cañete, Patricia; Ibarra Henriquez, C.; Sebastian, V.; Armijo, G.; Lamig, L.; Miranda, C.; Lagos, M.; Quiroga, T.; Hitschfeld, S.
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    A systems view of nitrogen nutrient and metabolite responses in Arabidopsis
    (2008) Vidal Olate, Elena Alejandra; Gutiérrez Ilabaca, Rodrigo Antonio
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    An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis
    (2008) Thum, Karen E.; Shin, Michael J.; Gutiérrez Ilabaca, Rodrigo Antonio; Mukherjee, Indrani; Katari, Manpreet S.; Nero, Damion; Shasha, Dennis; Coruzzi, Gloria M.
    Abstract Background Light and carbon are two important interacting signals affecting plant growth and development. The mechanism(s) and/or genes involved in sensing and/or mediating the signaling pathways involving these interactions are unknown. This study integrates genetic, genomic and systems approaches to identify a genetically perturbed gene network that is regulated by the interaction of carbon and light signaling in Arabidopsis. Results C arbon and l ight i nsensitive (cli) mutants were isolated. Microarray data from cli186 is analyzed to identify the genes, biological processes and gene networks affected by the integration of light and carbon pathways. Analysis of this data reveals 966 genes regulated by light and/or carbon signaling in wild-type. In cli186, 216 of these light/carbon regulated genes are misregulated in response to light and/or carbon treatments where 78% are misregulated in response to light and carbon interactions. Analysis of the gene lists show that genes in the biological processes "energy" and "metabolism" are over-represented among the 966 genes regulated by carbon and/or light in wild-type, and the 216 misregulated genes in cli186. To understand connections among carbon and/or light regulated genes in wild-type and the misregulated genes in cli186, the microarray data is interpreted in the context of metabolic and regulatory networks. The network created from the 966 light/carbon regulated genes in wild-type, reveals that cli186 is affected in the light and/or carbon regulation of a network of 60 connected genes, including six transcription factors. One transcription factor, HAT22 appears to be a regulatory "hub" in the cli186 network as it shows regulatory connections linking a metabolic network of genes involved in "amino acid metabolism", "C-compound/carbohydrate metabolism" and "glycolysis/gluconeogenesis". Conclusion The global misregulation of gene networks controlled by light and carbon signaling in cli186 indicates that it represents one of the first Arabidopsis mutants isolated that is specifically disrupted in the integration of both carbon and light signals to control the regulation of metabolic, developmental and regulatory genes. The network analysis of misregulated genes suggests that CLI186 acts to integrate light and carbon signaling interactions and is a master regulator connecting the regulation of a host of downstream metabolic and regulatory processes.
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    An International Bioinformatics Infrastructure to Underpin the Arabidopsis Community
    (2010) Bastow, R.; Gutiérrez Ilabaca, Rodrigo Antonio
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    Analysis of the metabolic features of plant extremophile species from the Atacama desert
    (2022) Dussarrat, Thomas; Gutiérrez Ilabaca, Rodrigo Antonio; Pontificia Universidad Católica de Chile. Facultad de Ciencias Biológicas; Pontificia Universidad Católica de Chile. Facultad de Agronomía e Ingeniería Forestal
    Los sitios extremos situados en los márgenes de al menos un gradiente abiótico permiten la supervivencia de muy pocas especies. Estas especies denominadas extremófilas (literalmente que aman los extremos) albergan una reserva única de adaptaciones genéticas y bioquímicas que siempre han atraído la curiosidad humana. Estudios anteriores han demostrado un alto grado de especificidad para la adaptación de las especies de plantas a biomas hostiles, lo que explica que las transferencias exitosas de esas adaptaciones a los cultivos sigan siendo escasas. Sin embargo, también pueden existir estrategias adaptativas genéricas o más generales. En este contexto, me propongo utilizar un enfoque integral desde el ecosistema hasta los metabolitos para investigar las adaptaciones bioquímicas de las especies vegetales extremófilas del desierto de Atacama, el desierto no polar más seco del planeta. Las plantas se recogieron en su entorno natural, que abarca un gradiente de altitud de 2500 a 4500m. Se combinaron múltiples enfoques metabolómicos con el aprendizaje automático o “machine learning” para develar una serie de herramientas genéricas para la resistencia de las plantas a las duras condiciones del Atacama. Posteriormente, los análisis de enriquecimiento de reacciones y vías metabólicas identificaron los legados genéticos subyacentes a las estrategias bioquímicas convergentes seleccionadas evolutivamente. Por último, se exploró el rol de las interacciones positivas con el cactus Maihueniopsis camachoi en la adaptación de varias especies a las extremas condiciones ambientales. Los resultados permitieron comprender mejor los procesos de facilitación y descubrir un novedoso conjunto de metabolitos capaces de predecir el estado de la interacción. Finalmente, este estudio aporta información importante para comprender los mecanismos de adaptación que subyacen a la resistencia de las plantas a los climas extremos, y nuestro enfoque multiespecífico presagia estudios y descubrimientos prometedores en agronomía y ecología.
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    Ancient parasite DNA from late Quaternary Atacama Desert rodent middens
    (2019) Wood, Jamie R.; Díaz Aguirre, Francisca Paulina; Latorre H., Claudio; Wilmshurst, Janet M.; Burge, Olivia R.; González Pinilla, Francisco J.; Gutiérrez Ilabaca, Rodrigo Antonio
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    Arabidopsis TCP20 links regulation of growth and cell division control pathways
    (2005) Li, C.; Gutiérrez Ilabaca, Rodrigo Antonio
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    Bacterial communities associated to Chilean altiplanic native plants from the Andean grasslands soils
    (2019) Fernandez-Gomez, Beatriz; Maldonado, Jonathan; Mandakovic, Dinka; Gaete, Alexis; Gutiérrez Ilabaca, Rodrigo Antonio; Maass, Alejandro; Cambiazo, Verónica; González, Mauricio
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    BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data
    (2020) Moraga, Carol; Sanchez, Evelyn; Ferrarini, Mariana Galvão; Gutiérrez Ilabaca, Rodrigo Antonio; Vidal, Elena A.; Sagot, Marie-France
    MicroRNAs (miRNAs) are small non-coding RNAs that are key players in the regulation of gene expression. In the last decade, with the increasing accessibility of high-throughput sequencing technologies, different methods have been developed to identify miRNAs, most of which rely on pre-existing reference genomes. However, when a reference genome is absent or is not of high quality, such identification becomes more difficult. In this context, we developed BrumiR, an algorithm that is able to discover miRNAs directly and exclusively from sRNA-seq data. We benchmarked BrumiR with datasets encompassing animal and plant species using real and simulated sRNA-seq experiments. The results demonstrate that BrumiR reaches the highest recall for miRNA discovery, while at the same time being much faster and more efficient than the state-of-the-art tools evaluated. The latter allows BrumiR to analyze a large number of sRNA-seq experiments, from plants or animals species. Moreover, BrumiR detects additional information regarding other expressed sequences (sRNAs, isomiRs, etc.), thus maximizing the biological insight gained from sRNA-seq experiments. Finally, when a reference genome is available, BrumiR provides a new mapping tool (BrumiR2ref) that performs an a posteriori exhaustive search to identify the precursor sequences. The code of BrumiR is freely available at https://github.com/camoragaq/BrumiR.
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    Cell-specific nitrogen responses mediate developmental plasticity
    (2008) Gifford, M.; Gutiérrez Ilabaca, Rodrigo Antonio
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    Characterization of crystals of Penicillium purpurogenum acetyl xylan esterase from high-resolution X-ray diffraction
    (1996) Pangborn, Walter; Erman, Mary; Li, Naiyin; Burkhart, Brian M.; Pletnev, Vladimir Z.; Duax, William L.; Gutiérrez Ilabaca, Rodrigo Antonio; Peirano, Alessandra; Eyzaguirre, Jaime; Thiel, Daniel J.; Ghosh, Debashis
    Acetyl xylan esterase from Penicillium purpurogenum, a single-chain 23 kDa member of a newly characterized family of esterases that cleaves side chain ester linkages in xylan, has been crystallized. The crystals diffract to better than 1 Å resolution at the Cornell High Energy Synchrotron Source (CHESS) and are highly stable in the synchrotron radiation. The space group is P212121 and cell dimensions are a = 34.9 Å, b = 61.0 Å, c = 72.5 Å.
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    Common variants in ABCG8 and TRAF3 genes confer risk for gallstone disease and gallbladder cancer in admixed Latinos with Mapuche Native American ancestry
    (2018) Bustos, Bernabé I.; Pérez Palma, Eduardo; Buch, Stephan; Azócar, Lorena; Riveras, Eleodoro; Ugarte, Giorgia D.; Toliat, Mohammad; Nürnberg, Peter; Lieb, Wolfgang; Franke, Andre; Hinz, Sebastian; Burmeister, Greta; von Schönfels, Witigo; Schafmayer, Clemens; Völzke, Henry; Völker, Uwe; Homuth, Georg; Lerch, Markus M.; Santos Martín, José Luis; Puschel Illanes, Klaus; Bambs S., Claudia; Gutiérrez Ilabaca, Rodrigo Antonio; Hampe, Jochen; de Ferrari, Giancarlo V.; Miquel, Juan Francisco
    Background Latin Americans and Chilean Amerindians have the highest prevalence of cholesterol gallstone disease (GSD) and gallbladder cancer (GBC) in the world. A handful of loci have been associated with GSD in populations of predominantly European ancestry, however they only explain a small portion of the population-attributable risk of the disease.Methods We performed a genome-wide association study (GWAS) for GSD in 1,095 admixed Latinos with Mapuche Native American Ancestry, followed by a replication analysis of 10 candidate single nucleotide polymorphisms (SNPs) with suggestive genome-wide significance (P<1×10−5) in 1,643 individuals. Disease status was assessed by cholecystectomy or abdominal ultrasonography. Logistic regression analyses were adjusted for age, sex, BMI, Type 2 Diabetes and Amerindian ancestry. Associated variants were further examined in two large GSD European populations and in a Chilean gallbladder cancer (GBC) cohort. We determined the expression levels of a novel GSD-candidate gene in normal and GSD-tissue samples.Results We consistently replicated the ABCG8 gene (rs11887534; P=3.24×10−8, OR=1.74) associated with GSD in admixed Latinos and identified a novel candidate signal within the TRAF3 gene on chromosome 14 (rs12882491; P=1.11×10−7, OR=1.40). ABCG8 and TRAF3 variants also conferred risk to GBC. Gene expression analyses indicated that TRAF3 levels were significantly decreased in the gallbladder (P=0.015) and the duodenal mucosa (P=0.001) of affected GSD individuals compared to healthy controls.Conclusions We confirmed ABCG8 and identified TRAF3 both associated with GSD and GBC in admixed Latinos. Decreased TRAF3 expression levels could enhance gallbladder inflammation as is observed in GSD and GSD-associated GBC.