DSpace Angular :: Browsing by Author "Allende, Miguel L."

Browsing by Author "Allende, Miguel L."

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A Novel In Vivo Model to Study Impaired Tissue Regeneration Mediated by Cigarette Smoke
(2018) Alvarez, Marjorie ; Chávez, Myra N. ; Miranda, Miguel ; Aedo, Geraldine ; Allende, Miguel L. ; Egaña, José T.
Abrogation of prostaglandin E₂/EP4 signaling impairs the development of rag1⁺ lymphoid precursors in the thymus of zebrafish embryos
(2007) Villablanca, Eduardo J.; Pistocchi, Anna; Court, Felipe A.; Cotelli, Franco; Bordignon, Claudio; Allende, Miguel L.; Traversari, Catia; Russo, Vincenzo
PGE(2) is involved in a wide variety of physiological and pathological processes; however, deciphering its role in early Mammalian development has been difficult due to the maternal contribution of PGE(2). To overcome this limitation we have investigated the role of PGE(2) during T cell development in zebrafish. In this study, we show that zebrafish ep4a, a PGE(2) receptor isoform of EP4, is expressed at 26 h postfertilization in the dorsal aorta-posterior cardinal vein joint region, which has a high homology with the mammal aorta-gonad-mesonephros area and where definitive hemopoiesis arises. Furthermore, it is expressed in the presumptive thymus rudiment by 48 h postfertilization. Supplementation of PGE(2), results in a strong increase in rag 1 levels and cell proliferation in the thymus. In contrast, the inhibition of PGE(2) production, as well as EP4 blockade, abrogates the expression of rag1 in the thymus and that of the lymphoid precursor marker ikaros, not only in the dorsal aorta-posterior cardinal vein joint region but also in the newly identified caudal hemopoietic tissue without affecting early hemopoietic (scl, gata2) and erythropoietic (gatal1) markers. These results identify ep4a as the earliest thymus marker and define a novel role for the PGE(2)/EP4 pathway in controlling T cell precursor development in zebrafish.
Antiangiogenic, antimigratory and antiinflammatory effects of 2-methoxyestradiol in zebrafish larvae
(2013) Quezada, Marisol; Alvarez, Marjorie; Peña, Oscar A.; Henríquez, Soledad; D' Alencon, Claudia A.; Lange, Soledad; Oliva, Barbara; Owen, Gareth Ivor; Allende, Miguel L.
Autophagy Activation in Zebrafish Heart Regeneration
(2020) Chavez, Myra N.; Morales, Rodrigo A.; Lopez-Crisosto, Camila; Carlos Roa, Juan; Allende, Miguel L.; Lavandero, Sergio
Autophagy is an evolutionarily conserved process that plays a key role in the maintenance of overall cellular health. While it has been suggested that autophagy may elicit cardioprotective and pro-survival modulating functions, excessive activation of autophagy can also be detrimental. In this regard, the zebrafish is considered a hallmark model for vertebrate regeneration, since contrary to adult mammals, it is able to faithfully regenerate cardiac tissue. Interestingly, the role that autophagy may play in zebrafish heart regeneration has not been studied yet. In the present work, we hypothesize that, in the context of a well-established injury model of ventricular apex resection, autophagy plays a critical role during cardiac regeneration and its regulation can directly affect the zebrafish regenerative potential. We studied the autophagy events occurring upon injury using electron microscopy, in vivo tracking of autophagy markers, and protein analysis. Additionally, using pharmacological tools, we investigated how rapamycin, an inducer of autophagy, affects regeneration relevant processes. Our results show that a tightly regulated autophagic response is triggered upon injury and during the early stages of the regeneration process. Furthermore, treatment with rapamycin caused an impairment in the cardiac regeneration outcome. These findings are reminiscent of the pathophysiological description of an injured human heart and hence put forward the zebrafish as a model to study the poorly understood double-sword effect that autophagy has in cardiac homeostasis.
DNA sequencing in the classroom: complete genome sequence of two earwig (Dermaptera; Insecta) species
(2023) Kobayashi, Sanae; Maldonado, Jonathan E.; Gaete, Alexis; Araya, Ingrid; Aguado-Norese, Constanza; Cumplido, Nicolás; Díaz, Sebastián; Espinoza, Alonso; Fernández, Edelmira; Gajardo, Felipe; González-Ordenes, Felipe; Hauyon, Khantati; Maldonado, Piedad; Maldonado, Rodrigo; Pochet, Isabel; Riveros, Aníbal; Sandoval, Paula; Sepúlveda-González, Ailynne; Stuardo, Camila; Tapia-Reyes, Patricio; Thornton, Carolina; Undurraga, Soledad; Varas, Macarena; Valdivieso, Camilo; Gutiérrez Ilabaca, Rodrigo Antonio; Orellana, Ariel; Montecino, Martín; Maass, Alejandro; González, Mauricio; Allende, Miguel L.; Hodar, Christian; Irles, Paula
Background Despite representing the largest fraction of animal life, the number of insect species whose genome has been sequenced is barely in the hundreds. The order Dermaptera (the earwigs) suffers from a lack of genomic information despite its unique position as one of the basally derived insect groups and its importance in agroecosystems. As part of a national educational and outreach program in genomics, a plan was formulated to engage the participation of high school students in a genome sequencing project. Students from twelve schools across Chile were instructed to capture earwig specimens in their geographical area, to identify them and to provide material for genome sequencing to be carried out by themselves in their schools. Results The school students collected specimens from two cosmopolitan earwig species: Euborellia annulipes (Fam. Anisolabididae) and Forficula auricularia (Fam. Forficulidae). Genomic DNA was extracted and, with the help of scientific teams that traveled to the schools, was sequenced using nanopore sequencers. The sequence data obtained for both species was assembled and annotated. We obtained genome sizes of 1.18 Gb (F. auricularia) and 0.94 Gb (E. annulipes) with the number of predicted protein coding genes being 31,800 and 40,000, respectively. Our analysis showed that we were able to capture a high percentage (≥ 93%) of conserved proteins indicating genomes that are useful for comparative and functional analysis. We were also able to characterize structural elements such as repetitive sequences and non-coding RNA genes. Finally, functional categories of genes that are overrepresented in each species suggest important differences in the process underlying the formation of germ cells, and modes of reproduction between them, features that are one of the distinguishing biological properties that characterize these two distant families of Dermaptera. Conclusions This work represents an unprecedented instance where the scientific and lay community have come together to collaborate in a genome sequencing project. The versatility and accessibility of nanopore sequencers was key to the success of the initiative. We were able to obtain full genome sequences of two important and widely distributed species of insects which had not been analyzed at this level previously. The data made available by the project should illuminate future studies on the Dermaptera.
Genome sequencing and transcriptomic analysis of the Andean killifish Orestias ascotanensis reveals adaptation to high-altitude aquatic life
(2022) Di Genova, Alex; Nardocci, Gino; Maldonado-Agurto, Rodrigo; Hodar, Christian; Valdivieso, Camilo; Morales, Pamela; Gajardo, Felipe; Marina, Raquel; Gutierrez, Rodrigo A.; Orellana, Ariel; Cambiazo, Veronica; Gonzalez, Mauricio; Glavic, Alvaro; Mendez, Marco A.; Maass, Alejandro; Allende, Miguel L.; Montecino, Martin A.
Orestias ascotanensis (Cyprinodontidae) is a teleost pupfish endemic to springs feeding into the Ascotan saltpan in the Chilean Altiplano (3,700 m.a.s.l.) and represents an opportunity to study adaptations to high-altitude aquatic environments. We have de novo assembled the genome of O. ascotanensis at high coverage. Comparative analysis of the O. ascotanensis genome showed an overall process of contraction, including loss of genes related to Gprotein signaling, chemotaxis and signal transduction, while there was expansion of gene families associated with microtubule-based movement and protein ubiquitination. We identified 818 genes under positive selection, many of which are involved in DNA repair. Additionally, we identified novel and conserved microRNAs expressed in O. ascotanensis and its closely-related species, Orestias gloriae. Our analysis suggests that positive selection and expansion of genes that preserve genome stability are a potential adaptive mechanism to cope with the increased solar UV radiation to which high-altitude animals are exposed to.
Genomes of the Orestias pupfish from the Andean Altiplano shed light on their evolutionary history and phylogenetic relationships within Cyprinodontiformes
(2024) Morales, Pamela; Gajardo, Felipe; Valdivieso, Camilo; Valladares, Moises A.; Di Genova, Alex; Orellana, Ariel; Gutierrez, Rodrigo A.; Gonzalez, Mauricio; Montecino, Martin; Maass, Alejandro; Mendez, Marco A.; Allende, Miguel L.
Background To unravel the evolutionary history of a complex group, a comprehensive reconstruction of its phylogenetic relationships is crucial. This requires meticulous taxon sampling and careful consideration of multiple characters to ensure a complete and accurate reconstruction. The phylogenetic position of the Orestias genus has been estimated partly on unavailable or incomplete information. As a consequence, it was assigned to the family Cyprindontidae, relating this Andean fish to other geographically distant genera distributed in the Mediterranean, Middle East and North and Central America. In this study, using complete genome sequencing, we aim to clarify the phylogenetic position of Orestias within the Cyprinodontiformes order.
Genomes of the Orestias pupfish from the Andean Altiplano shed light on their evolutionary history and phylogenetic relationships within Cyprinodontiformes
(2024) Morales, Pamela; Gajardo, Felipe; Valdivieso, Camilo; Valladares, Moisés A.; Di Genova, Alex; Orellana, Ariel; Gutiérrez Ilabaca, Rodrigo Antonio; González, Mauricio; Montecino, Martin; Maass, Alejandro; Méndez, Marco A.; Allende, Miguel L.
To unravel the evolutionary history of a complex group, a comprehensive reconstruction of its phylogenetic relationships is crucial. This requires meticulous taxon sampling and careful consideration of multiple characters to ensure a complete and accurate reconstruction. The phylogenetic position of the Orestias genus has been estimated partly on unavailable or incomplete information. As a consequence, it was assigned to the family Cyprindontidae, relating this Andean fish to other geographically distant genera distributed in the Mediterranean, Middle East and North and Central America. In this study, using complete genome sequencing, we aim to clarify the phylogenetic position of Orestias within the Cyprinodontiformes order. Results We sequenced the genome of three Orestias species from the Andean Altiplano. Our analysis revealed that the small genome size in this genus (~ 0.7 Gb) was caused by a contraction in transposable element (TE) content, particularly in DNA elements and short interspersed nuclear elements (SINEs). Using predicted gene sequences, we generated a phylogenetic tree of Cyprinodontiformes using 902 orthologs extracted from all 32 available genomes as well as three outgroup species. We complemented this analysis with a phylogenetic reconstruction and time calibration considering 12 molecular markers (eight nuclear and four mitochondrial genes) and a stratified taxon sampling to consider 198 species of nearly all families and genera of this order. Overall, our results show that phylogenetic closeness is directly related to geographical distance. Importantly, we found that Orestias is not part of the Cyprinodontidae family, and that it is more closely related to the South American fish fauna, being the Fluviphylacidae the closest sister group. Conclusions The evolutionary history of the Orestias genus is linked to the South American ichthyofauna and it should no longer be considered a member of the Cyprinodontidae family. Instead, we submit that Orestias belongs to the Orestiidae family, as suggested by Freyhof et al. (2017), and that it is the sister group of the Fluviphylacidae family, distributed in the Amazonian and Orinoco basins. These two groups likely diverged during the Late Eocene concomitant with hydrogeological changes in the South American landscape.
Drosophila DAxud1 Has a Repressive Transcription Activity on Hsp70 and Other Heat Shock Genes
(2023) Zuniga-Hernandez, Jorge; Meneses, Claudio; Bastias, Macarena; Allende, Miguel L.; Glavic, Alvaro
Drosophila melanogaster DAxud1 is a transcription factor that belongs to the Cysteine Serine Rich Nuclear Protein (CSRNP) family, conserved in metazoans, with a transcriptional transactivation activity. According to previous studies, this protein promotes apoptosis and Wnt signaling-mediated neural crest differentiation in vertebrates. However, no analysis has been conducted to determine what other genes it might control, especially in connection with cell survival and apoptosis. To partly answer this question, this work analyzes the role of Drosophila DAxud1 using Targeted-DamID-seq (TaDa-seq), which allows whole genome screening to determine in which regions it is most frequently found. This analysis confirmed the presence of DAxud1 in groups of pro-apoptotic and Wnt pathway genes, as previously described; furthermore, stress resistance genes that coding heat shock protein (HSP) family genes were found as hsp70, hsp67, and hsp26. The enrichment of DAxud1 also identified a DNA-binding motif (AYATACATAYATA) that is frequently found in the promoters of these genes. Surprisingly, the following analyses demonstrated that DAxud1 exerts a repressive role on these genes, which are necessary for cell survival. This is coupled with the pro-apoptotic and cell cycle arrest roles of DAxud1, in which repression of hsp70 complements the maintenance of tissue homeostasis through cell survival modulation.
Hox genes control homocercal caudal fin development and evolution
(2024) Cumplido, Nicolas; Arratia, Gloria; Desvignes, Thomas; Munoz-Sanchez, Salome; Postlethwait, John H.; Allende, Miguel L.
Ancient bony fishes had heterocercal tails, like modern sharks and sturgeons, with asymmetric caudal fins and a vertebral column extending into an elongated upper lobe. Teleost fishes, in contrast, developed a homocercal tail characterized by two separate equal-sized fin lobes and the body axis not extending into the caudal fin. A similar heterocercal-to-homocercal transition occurs during teleost ontogeny, although the underlying genetic and developmental mechanisms for either transition remain unresolved. Here, we investigated the role of hox13 genes in caudal fin formation as these genes control posterior identity in animals. Analysis of expression profiles of zebrafish hox13 paralogs and phenotypes of CRISPR/Cas9-induced mutants showed that double hoxb13a and hoxc13a mutants fail to form a caudal fin. Furthermore, single mutants display heterocercal-like morphologies not seen since Mesozoic fossil teleosteomorphs. Relaxation of functional constraints after the teleost genome duplication may have allowed hox13 duplicates to neo- or subfunctionalize, ultimately contributing to the evolution of a homocercal tail in teleost fishes.
Plant ecological genomics at the limits of life in the Atacama Desert
(2021) Eshel, Gil; Araus, Viviana; Undurraga, Soledad; Soto, Daniela C.; Moraga, Carol; Montecinos, Alejandro; Moyano, Tomas; Maldonado, Jonathan; Diaz, Francisca P.; Varala, Kranthi; Nelson, Chase W.; Contreras-Lopez, Orlando; Pal-Gabor, Henrietta; Kraiser, Tatiana; Carrasco-Puga, Gabriela; Nilo-Poyanco, Ricardo; Zegar, Charles M.; Orellana, Ariel; Montecino, Martin; Maass, Alejandro; Allende, Miguel L.; DeSalle, Robert; Stevenson, Dennis W.; Gonzalez, Mauricio; Latorre, Claudio; Coruzzi, Gloria M.; Gutierrez, Rodrigo A.
The Atacama Desert in Chile-hyperarid and with high-ultraviolet irradiance levels-is one of the harshest environments on Earth. Yet, dozens of species grow there, including Atacama-endemic plants. Herein, we establish the Talabre-Leji = a transect (TLT) in the Atacama as an unparalleled natural laboratory to study plant adaptation to extreme environmental conditions. We characterized climate, soil, plant, and soil-microbe diversity at 22 sites (every 100 m of altitude) along the TLT over a 10-y period. We quantified drought, nutrient deficiencies, large diurnal temperature oscillations, and pH gradients that define three distinct vegetational belts along the altitudinal cline. We deep-sequenced transcriptomes of 32 dominant plant species spanning the major plant clades, and assessed soil microbes by metabarcoding sequencing. The top-expressed genes in the 32 Atacama species are enriched in stress responses, metabolism, and energy production. Moreover, their root-associated soils are enriched in growthpromoting bacteria, including nitrogen fixers. To identify genes associated with plant adaptation to harsh environments, we compared 32 Atacama species with the 32 closest sequenced species, comprising 70 taxa and 1,686,950 proteins. To perform phylogenomic reconstruction, we concatenated 15,972 ortholog groups into a supermatrix of 8,599,764 amino acids. Using two codonbased methods, we identified 265 candidate positively selected genes (PSGs) in the Atacama plants, 64% of which are located in Pfam domains, supporting their functional relevance. For 59/184 PSGs with an Arabidopsis ortholog, we uncovered functional evidence linking them to plant resilience. As some Atacama plants are closely related to staple crops, these candidate PSGs are a "genetic goldmine" to engineer crop resilience to face climate change.

Browsing by Author "Allende, Miguel L."

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