Browsing by Author "Almonacid, L. I."

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    Assessment of Mutations Associated With Genomic Variants of SARS-CoV-2: RT-qPCR as a Rapid and Affordable Tool to Monitoring Known Circulating Variants in Chile, 2021
    (2022) Angulo, J.; Martinez Valdebenito, C.; Pardo Roa, C.; Almonacid, L. I.; Fuentes Luppichini, E.; Contreras, A. M.; Maldonado, C.; Le Corre, N.; Melo Ledermann, Francisco Javier; Medina, R. A.; Ferrés, M.
    Since the first report of SARS-CoV-2 infection in humans, the virus has mutated to develop new viral variants with higher infection rates and more resistance to neutralization by antibodies elicited after natural SARS-CoV-2 infection or by vaccines. Therefore, rapid identification of viral variants circulating in the population is crucial for epidemiological assessment and efforts to contain the resurgence of the pandemic. Between January and November 2021, we performed a large variant RT-qPCR-based screening of mutations in the spike protein of 1851 SARS-CoV-2-positive samples derived from outpatients from the UC-Christus Health Network in Chile. In a portion of samples (n = 636), we validated our RT-qPCR-pipeline by WGS, obtaining a 99.2% concordance. Our results indicate that from January to March 2021 there was a dominance of non-identifiable variants by the RT-qPCR-based screening; however, throughout WGS we were able to identify the Lambda (C.37) variant of interest (VOI). From March to July, we observed the rapid emergence of mutations associated with the Gamma variant (P.1), which was quickly replaced by the appearance of a combination of samples harboring mutations associated with the Delta variant (B.1.617.2), which predominated until the end of the study. Our results highlight the applicability of cost-effective RT-qPCR-based screening of mutations associated with known variants of concern (VOC), VOI and variants under monitoring (VUM) of SARS-CoV-2, being a rapid and reliable tool that complements WGS-based surveillance.
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    Characterization of small RNAs in X. tropicalis gastrulae
    (2012) Faunes Quinteros, Fernando Emerson; Almonacid, L. I.; Melo Ledermann, Francisco Javier; Larraín Correa, Juan Agustín
    Here, we report and characterize deep sequencing data and bioinformatics analysis of small RNAs from X. tropicalis gastrula. A total of 17,553,124 reads with perfect match to the genome derived from 2,616,053 unique sequences were identified. Seventy-seven percent of theses sequences were not found in previous reports from X. tropicalis oocytes and somatic tissues. Bioinformatics analyses indicate that a large fraction of the small RNAs are PIWI-interacting RNAs. Up to 23.9% of small RNAs mapped to transposable elements and 27% to genic regions. Most of the abundant transposon-derived small RNAs are found in oocyte and gastrula libraries, suggesting that transposons also need to be silenced during early embryonic development. Importantly, novel clusters of piRNAs whose expression is activated after zygotic transcription begins were identified in the genome of X. tropicalis. Additionally, miRNAs were also identified and many of them are not present in oocytes, suggesting that miRNA expression is stage-specific. To the best of our knowledge, this is the first high throughput data release and bioinformatics characterization of small RNAs during Xenopus early embryonic development. genesis 50:572–58, 2012. © 2012 Wiley Periodicals, Inc.
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    Computer-based annotation of putative AraC/XylS-family transcription factors of known structure but unknown function
    (2012) Schüller, Andreas; Slater, A. W.; Norambuena, T.; Cifuentes, J. J.; Almonacid, L. I.; Melo Ledermann, Francisco Javier
    Currently, about 20 crystal structures per day are released and deposited in the Protein Data Bank. A significant fraction of these structures is produced by research groups associated with the structural genomics consortium. The biological function of many of these proteins is generally unknown or not validated by experiment. Therefore, a growing need for functional prediction of protein structures has emerged. Here we present an integrated bioinformatics method that combines sequence-based relationships and three-dimensional (3D) structural similarity of transcriptional regulators with computer prediction of their cognate DNA binding sequences. We applied this method to the AraC/XylS family of transcription factors, which is a large family of transcriptional regulators found in many bacteria controlling the expression of genes involved in diverse biological functions. Three putative new members of this family with known 3D structure but unknown function were identified for which a probable functional classification is provided. Our bioinformatics analyses suggest that they could be involved in plant cell wall degradation (Lin2118 protein from Listeria innocua, PDB code 3oou), symbiotic nitrogen fixation (protein from Chromobacterium violaceum, PDB code 3oio), and either metabolism of plant-derived biomass or nitrogen fixation (protein from Rhodopseudomonas palustris, PDB code 3mn2).
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    Genome-wide expression profile of the response to spinal cord injury in Xenopus laevis reveals extensive differences between regenerative and non-regenerative stages
    (2014) Lee Liu, D.; Moreno, M.; Almonacid, L. I.; Tapia, V. S.; Muñoz, R.; von Marées, J.; Gaete Carrasco, Marcia; Melo Ledermann, Francisco Javier; Larraín Correa, Juan Agustín
    Background Xenopus laevis has regenerative and non-regenerative stages. As a tadpole, it is fully capable of functional recovery after a spinal cord injury, while its juvenile form (froglet) loses this capability during metamorphosis. We envision that comparative studies between regenerative and non-regenerative stages in Xenopus could aid in understanding why spinal cord regeneration fails in human beings. Results To identify the mechanisms that allow the tadpole to regenerate and inhibit regeneration in the froglet, we obtained a transcriptome-wide profile of the response to spinal cord injury in Xenopus regenerative and non-regenerative stages. We found extensive transcriptome changes in regenerative tadpoles at 1 day after injury, while this was only observed by 6 days after injury in non-regenerative froglets. In addition, when comparing both stages, we found that they deployed a very different repertoire of transcripts, with more than 80% of them regulated in only one stage, including previously unannotated transcripts. This was supported by gene ontology enrichment analysis and validated by RT-qPCR, which showed that transcripts involved in metabolism, response to stress, cell cycle, development, immune response and inflammation, neurogenesis, and axonal regeneration were regulated differentially between regenerative and non-regenerative stages. Conclusions We identified differences in the timing of the transcriptional response and in the inventory of regulated transcripts and biological processes activated in response to spinal cord injury when comparing regenerative and non-regenerative stages. These genes and biological processes provide an entry point to understand why regeneration fails in mammals. Furthermore, our results introduce Xenopus laevis as a genetic model organism to study spinal cord regeneration.
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    Metabolic and transcriptomic response of the wine yeast Saccharomyces cerevisiae strain EC1118 after an oxygen impulse under carbon-sufficient, nitrogen-limited fermentative conditions
    (2014) Orellana, M.; Aceituno, F. F.; Slater, A. W.; Almonacid, L. I.; Melo Ledermann, Francisco Javier; Agosin T., Eduardo
    During alcoholic fermentation, Saccharomyces cerevisiae is exposed to continuously changing environmental conditions, such as decreasing sugar and increasing ethanol concentrations. Oxygen, a critical nutrient to avoid stuck and sluggish fermentations, is only discretely available throughout the process after pump-over operation. In this work, we studied the physiological response of the wine yeast S. cerevisiae strain EC1118 to a sudden increase in dissolved oxygen, simulating pump-over operation. With this aim, an impulse of dissolved oxygen was added to carbon-sufficient, nitrogen-limited anaerobic continuous cultures. Results showed that genes related to mitochondrial respiration, ergosterol biosynthesis, and oxidative stress, among other metabolic pathways, were induced after the oxygen impulse. On the other hand, mannoprotein coding genes were repressed. The changes in the expression of these genes are coordinated responses that share common elements at the level of transcriptional regulation. Beneficial and detrimental effects of these physiological processes on wine quality highlight the dual role of oxygen in ‘making or breaking wines’. These findings will facilitate the development of oxygen addition strategies to optimize yeast performance in industrial fermentations.
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    Transcriptomics using next generation sequencing technologies
    (2012) Lee Liu, D.; Almonacid, L. I.; Faunes Quinteros, Fernando Emerson; Melo Ledermann, Francisco Javier; Larraín Correa, Juan Agustín
    Next generation sequencing technologies may now be applied to the study of transcriptomics. RNA-Seq or RNA sequencing employs high-throughput sequencing of complementary DNA fragments delivering a transcriptional profile. In this chapter, we aim to provide a starting point for Xenopus researchers planning on starting an RNA-Seq transcriptomics study. We begin by providing a section on template isolation and library preparation. The next section comprises the main bioinformatics procedures that need to be performed for raw data processing, normalization, and differential gene expression. Finally, we have included a section on studying deep sequencing results in Xenopus, which offers general guidance as to what can be done in this model.