PUBLICATIONS

Featured Publications

Here, we report that negative clinical outcomes caused by SARS-Cov2 were associated with divergent transcriptome profiles in peripheral immune cells compared with mild cases during the first weeks after disease onset. Protein-protein interaction analysis indicated that early-responding cytotoxic NK cells were associated with an effective clearance of the virus and a less severe outcome. This innate immune response is associated with the cytokine-cytokine receptor pathways and Th1/Th2 cell differentiation profiles. This knowledge forms the basis of clinical triage that may be used to detect high-risk patients before life-threatening outcomes ensue, giving new insights into the COVID-19 disease.

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By using an integrative approach including biochemical and transcriptomic

analyses, we evaluate the effect of feeding diets containing inulin, β-glucan, and chitosan on the physiological performance of Totoaba macdonaldi juveniles. After 60 days, each dietary prebiotic produces unique physiological responses and transcriptomic profiles in juvenile totoaba. These profiles indicate possible causative mechanisms and reveal hitherto unrecognized processes linked to the immune system and growth. Based on our results, we propose the inclusion of 1% dietary inulin to improve the digestibility and the addition of 0.5% chitosan to stimulate the immune system of T. macdonaldi juveniles.

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Due to ocean acidification, most mollusks have difficulties in fabricating the shell. Here, we evaluate histological, secretory, and transcriptional changes in the mantle tissue of adult oysters exposed to ambient and reduced pH conditions. We found no differences in mantle morphology, but there are differences in the mantle cells' secretory activity, affecting the shell's fabrication. Transcriptomic analysis revealed that genes involved in cellular response to stimulus and stress are the most affected by low pH. This study demonstrates that histology and gene expression profiling can advance our understanding of the cellular and molecular mechanisms underlying adult oyster tolerance to ocean acidification.

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All Publications

2024

Medina MA, Fuentes-Villalobos F, Quevedo C, Aguilera F, Riquelme R, Rioseco ML, Barria S, Pinos Y, Calvo M, Burbulis I, Alvarez RA, Garrido JL, Barria MI. Longitudinal transcriptional changes reveal genes from the natural killer cell-mediated cytotoxicity pathway as critical players underlying COVID-19 progression. eLife (doi: 10.7554/eLife.94242.1) PDF
Juárez OE, Galindo-Sánchez CE, Enciso S, López-Lavandery EA, Muñoz C*, Aguilera F, Lazo JP, Lafarga-De la Cruz F. Physiological and transcriptomic effects of formulated diets including the prebiotics chitosan, inulin, and ß-glucan on juveniles of Totoaba macdonaldi. Aquaculture International 32:61-85 (doi: 10.1007/s10499-023-01144-1) PDF

2023

Canales-Aguirre C, Ferrada-Fuentes S, Herrera-Yañez V, Aguilera F, Araya C, Lam N, Galleguillos R. Heterogametic females reveal a ZW sex-determination system and a putative sex chromosome for the Chilean jack mackerel, Trachurus murphyi. Molecular Ecology Resources Submitted.
Decker SH, Saadi AJ, Baranyi C, Hirose M, Lemer S, Sombke A, Aguilera F, Vieira LM, Smith AM, Waeschenbach A, Schwaha T. Boring systematics: a skimmed phylogeny of ctenostome bryozoans and their endolithic family Penetrantiidae with the description of one new species. Ecology and Evolution Submitted PDF.
Castillo H, Hanna P, Sachs L, Buisine N, Godoy F, Gilbert C, Aguilera F, Muñoz D, Boisvert C, Debiais-Thibaud M, Spicuglia S, Marcellini S. Cross-validation of conserved osteoblast-specific enhancers illuminates bone disease and early skeletal evolution. PLoS Biology Submitted.
Morales-León F, Matus-Köhler M, Araya-Vega P, Aguilera F, Torres I*, Vera R, Ibarra C, Venegas S, Bello-Toledo H, González-Rocha G, Opazo-Capurro A. Molecular characterisation of convergent carbapenem-resistant and hypervirulent Klebsiella pneumoniae K1-ST23 collected in Chile during COVID-19 pandemic. Microbiology Spectrum 11:e00540-23 (doi: 10.1128/spectrum.00540-23) PDF
Zúñiga-Soto N*, Pinto-Borguero I*, Quevedo C*, Aguilera F. Secretory and transcriptomic responses of mantle cells to low pH in the Pacific oyster (Crassostrea gigas). Frontiers in Marine Science 10:1156831 (doi: 10.3389/fmars.2023.1156831) PDF
Aguilera F. In the Spotlight – Early career researcher. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 340:341 (doi: 10.1002/jez.b.23179) PDF

*Aguilera lab student or research assistant

2022

Mongiardino Koch N, Thompson JR, Hatch AS, McCowin MF, Armstrong AF, Coppard SE, Aguilera F, Bronstein O, Kroh A, Mooi R, Rouse GW. Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record. eLife 11:e72460 (doi: 10.7554/eLife.72460) PDF
Muñoz C*, Romero A, Sepúlveda V, Vira MA, Fehrmann-Cartes K, Marcellini S, Aguilera F, Caprile T, Fuentes R. (2022). Turning the curve into straight: phenogenetics of the spine morphology and coordinate maintenance in the zebrafish. Frontiers in Cell and Developmental Biology 9:801652 (doi: 10.3389/fcell.2021.801652) PDF

*Aguilera lab student or research assistant

2021

Rojas J*, Hinostroza F, Vergara S, Pinto-Borguero I*, Aguilera F, Fuentes R, Carvacho I. Knockin´on egg´s door: Gains N’ Losses during egg activation that influence cortical granules exocytosis and fertilization in animal species. Frontiers in Cell and Developmental Biology 9:704867 (doi: 10.3389/fcell.2021.704867) PDF
McDougall C, Aguilera F, Shokoohmand A, Moase P, Degnan BM. Pearl sac gene expression profiles associated with pearl attributes in the silver-lip pearl oyster, Pinctada maxima. Frontiers in Genetics 11:597459 (doi: 10.3389/fgene.2020.597459) PDF
Martínez-Porchas M, Lafarga F, Aguilera F, Cicala F, Lago-Lestón A. Water microbiota is not affected by stocking density of the yellowtail kingfish (Seriola lalandi) in a recirculating aquaculture system. Aquaculture Research 52:410-414 (doi:10.1111/are.14883) PDF

*Aguilera lab student or research assistant

2020

González G, Aguilera F, D’Afonseca V. Transcriptome profiling of raspberry (Rubus idaeus Var. Amira) in response to infection by tomato ringspot virus (ToRSV). Heliyon 6:e04518 (doi:10.1016/j.heliyon.2020.e04518) PDF
Ruiz P, Sepúlveda D, Torres C, Vidal JM, Villouta G, Carrasco C, Aguilera F, Ruiz-Tagle N, Urrutia H. Overview and future perspectives of nitrifying bacteria on biofilters for recirculating aquaculture systems. Reviews in Aquaculture 12:1478-1494 (doi:10.1111/raq.12392) PDF

2019

Fromm B, Tosar JP, Aguilera F, Friedländer MR, Bachmann L, Hejnol A. Evolutionary implications of the first microRNA- and piRNA complement of Lepidodermella squamata (Gastrotricha). Non-Coding RNA 5: 19 (doi:10.3390/ncrna5010019) (Cover Image) PDF

2018

Thiel D, Franz-Wachtel M, Aguilera F, Hejnol A. Xenacoelomorph neuropeptidomes reveal a major expansion of neuropeptide systems during early bilaterian evolution. Molecular Biology and Evolution 35:2528-2543 (doi:10.1093/molbev/msy160) (Cover Image) PDF
Fernandez-Valverde SL, Aguilera F, Ramoz-Diaz RA. Inference of developmental gene regulatory networks beyond classical model systems: new approaches in the post-genomic era. Integrative and Comparative Biology 58:640-653 (doi:10.1093/icb/icy061) PDF

2017

Aguilera F. Neoplasia in mollusks: What does it tell us about cancer in humans? A Review. Journal of Genetic Disorders 1:07 PDF
Lim DKY, Schuhmann H, Thomas-Hall SR, Chan KCK, Wass JT, Aguilera F, Adarme-Vega CT, Dal’Molin CGO, Thorpe GJ, Batley J, Edwards D, Schenk PM. (2017). RNA-Seq and metabolic flux analysis of Tetraselmis sp. M8 during nitrogen starvation reveals a two-stage lipid accumulation mechanism. Bioresource Technology 244:1281-1293 (doi:10.1016/j.biortech.2017.06.003) PDF
Aguilera F, McDougall C, Degnan BM. Co-option and de novo gene evolution underlie molluscan shell diversity. Molecular Biology and Evolution 34:779-792 (doi:10.1093/molbev/msw294) PDF

2016

Kocot KM, Aguilera F, McDougall C, Jackson DJ, Degnan BM. Sea shell diversity and rapidly evolving secretomes: insights into the evolution of biomineralization. Frontiers in Zoology 13:23 (doi:10.1186/s12983-016-0155-z) PDF

2014

Aguilera F, McDougall C, Degnan BM. Evolution of the tyrosinase gene family in bivalve molluscs: independent expansion of the mantle gene repertoire. Acta Biomaterialia 10:3855-3865 (doi:10.1016/j.actbio.2014.03.031) PDF

2013

McDougall C, Aguilera F, Moase P, Lucas JS, Degnan BM. Pearls. Current Biology 23:R671-R673 (doi:10.1016/j.cub.2013.05.042) PDF
Aguilera F, McDougall C, Degnan BM. Origin, evolution and classification of type-3 copper proteins: lineage-specific gene expansions and losses across the Metazoa. BMC Evolutionary Biology 13:96 (doi:10.1186/1471-2148-13-96) PDF
McDougall C, Aguilera F, Degnan BM. Rapid evolution of pearl oyster proteins with repetitive, low-complexity domains. Journal of the Royal Society Interface 10:20130041 (doi:10.1098/rsif.2013.0041) (Cover Image) PDF

2009

Aguilera F, Lafarga-De la Cruz F, Gallardo-Escarate C. Molecular analysis in Chilean commercial gastropods based on DNA sequences of 16S rRNA, COI and ITS1-5.8S rDNA-ITS2 sequences. Gayana 73:17-27 (doi:10.4067/S0717-65382009000100003) PDF

2008

Aguilera F, Valenzuela-Muñoz V, Gallardo-Escarate C. Authentication of commercial Chilean molluscs using ribosomal internal transcribed spacer (ITS) as species-specific DNA marker. Gayana 72:186-195 (doi:10.4067/S0717-65382008000200007) PDF