Browsing by Author "Altimiras, Francisco"
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Item Genome Sequencing Variations in the Octodon degus, an Unconventional Natural Model of Aging and Alzheimer's Disease(2022) Hurley, Michael; Urra, Claudio; Garduno, Maximiliano; Bruno, Agostino; Kimbell, Allison; Wilkinson, Brent; Marino, Cristina; Ezquer, Marcelo; Ezquer, Fernando; Aburto, Pedro; Poulin, Elie; Vasquez, Rodrigo; Deacon, Robert; Avila, Ariel; Altimiras, Francisco; Whitney, Peter; Zampieri, Guido; Angione, Claudio; Constantino, Gabriele; Holmes, Todd; Coba, Marcelo; Xu, Xiangmin; Cogram, PatriciaThe degu (Octodon degus) is a diurnal long-lived rodent that can spontaneously develop molecular and behavioral changes that mirror those seen in human aging. With age some degu, but not all individuals, develop cognitive decline and brain pathology like that observed in Alzheimer’s disease including neuroinflammation, hyperphosphorylated tau and amyloid plaques, together with other co-morbidities associated with aging such as macular degeneration, cataracts, alterations in circadian rhythm, diabetes and atherosclerosis. Here we report the whole-genome sequencing and analysis of the degu genome, which revealed unique features and molecular adaptations consistent with aging and Alzheimer’s disease. We identified single nucleotide polymorphisms in genes associated with Alzheimer’s disease including a novel apolipoprotein E (Apoe) gene variant that correlated with an increase in amyloid plaques in brain and modified the in silico predicted degu APOE protein structure and functionality. The reported genome of an unconventional long-lived animal model of aging and Alzheimer’s disease offers the opportunity for understanding molecular pathways involved in aging and should help advance biomedical research into treatments for Alzheimer’s diseasePublication Transcriptome Data Analysis Applied to Grapevine Growth Stage Identification(2024) Altimiras, Francisco; Pavéz, Leonardo; Pourreza, Alireza; Yañez, Osvaldo; González-Rodríguez, Lisdelys; García, José; Galaz, Claudio; Leiva-Araos, Andres; Allende-Cid, HéctorIn agricultural production, it is fundamental to characterize the phenological stage of plants to ensure a good evaluation of the development, growth and health of crops. Phenological characterization allows for the early detection of nutritional deficiencies in plants that diminish the growth and productive yield and drastically affect the quality of their fruits. Currently, the phenological estimation of development in grapevine (Vitis vinifera) is carried out using four different schemes: Baillod and Baggiolini, Extended BBCH, Eichhorn and Lorenz, and Modified E-L. Phenological estimation requires the exhaustive evaluation of crops, which makes it intensive in terms of labor, personnel, and the time required for its application. In this work, we propose a new phenological classification based on transcriptional measures of certain genes to accurately estimate the stage of development of grapevine. There are several genomic information databases for Vitis vinifera, and the function of thousands of their genes has been widely characterized. The application of advanced molecular biology, including the massive parallel sequencing of RNA (RNA-seq), and the handling of large volumes of data provide state-of-the-art tools for the determination of phenological stages, on a global scale, of the molecular functions and processes of plants. With this aim, we applied a bioinformatic pipeline for the high-throughput quantification of RNA-seq datasets and further analysis of gene ontology terms. We identified differentially expressed genes in several datasets, and then, we associated them with the corresponding phenological stage of development. Differentially expressed genes were classified using count-based expression analysis and clustering and annotated using gene ontology data. This work contributes to the use of transcriptome data and gene expression analysis for the classification of development in plants, with a wide range of industrial applications in agriculture.