Browsing by Author "Vidal, Gonzalo"

Now showing 1 - 7 of 7
  • No Thumbnail Available
    Item
    Accurate characterization of dynamic microbial gene expression and growth rate profiles
    (2022) Vidal, Gonzalo; Vidal-Cespedes, Carlos; Silva, Macarena Munoz; Castillo-Passi, Carlos; Feliu, Guillermo Yanez; Federici, Fernan; Rudge, Timothy J.
    Genetic circuits are subject to variability due to cellular and compositional contexts. Cells face changing internal states and environments, the cellular context, to which they sense and respond by changing their gene expression and growth rates. Furthermore, each gene in a genetic circuit operates in a compositional context of genes which may interact with each other and the host cell in complex ways. The context of genetic circuits can, therefore, change gene expression and growth rates, and measuring their dynamics is essential to understanding natural and synthetic regulatory networks that give rise to functional phenotypes. However, reconstruction of microbial gene expression and growth rate profiles from typical noisy measurements of cell populations is difficult due to the effects of noise at low cell densities among other factors. We present here a method for the estimation of dynamic microbial gene expression rates and growth rates from noisy measurement data. Compared to the current state-of-the-art, our method significantly reduced the mean squared error of reconstructions from simulated data of growth and gene expression rates, improving the estimation of timing and magnitude of relevant shapes of profiles. We applied our method to characterize a triple-reporter plasmid library combining multiple transcription units in different compositional and cellular contexts in Escherichia coli. Our analysis reveals cellular and compositional context effects on microbial growth and gene expression rate dynamics and suggests a method for the dynamic ratiometric characterization of constitutive promoters relative to an in vivo reference.
  • No Thumbnail Available
    Item
    LOICA: Integrating Models with Data for Genetic Network Design Automation
    (2022) Vidal, Gonzalo; Vidal-Cespedes, Carlos; Rudge, Timothy J.
    Genetic design automation tools are necessary to expand the scale and complexity of possible synthetic genetic networks. These tools are enabled by abstraction of a hierarchy of standardized components and devices. Abstracted elements must be parametrized from data derived from relevant experiments, and these experiments must be related to the part composition of the abstract components. Here we present Logical Operators for Integrated Cell Algorithms (LOICA), a Python package for designing, modeling, and characterizing genetic networks based on a simple object-oriented design abstraction. LOICA uses classes to represent different biological and experimental components, which generate models through their interactions. These models can be parametrized by direct connection to data contained in Flapjack so that abstracted components of designs can characterize themselves. Models can be simulated using continuous or stochastic methods and the data published and managed using Flapjack. LOICA also outputs SBOL3 descriptions and generates graph representations of genetic network designs.
  • Thumbnail Image
    Item
    Mitochondrial nucleoid dynamics perturbation by OPA1 disease-causing mutants
    (CELL PRESS, 2022) Eisner, Veronica; Macuada, Josefa; Vidal, Gonzalo; Aedo, Geraldine; Cartes-Saavedra, Benjamin; Rudge, Timothy
  • Thumbnail Image
    Item
    OPA1 and disease-causing mutants perturb mitochondrial nucleoid distribution
    (2024) Macuada Alvarado, Josefa Pilar; Molina Riquelme, Isidora Elvira; Vidal, Gonzalo; Pérez Bravo, N.; Vásquez-Trincado, C.; Aedo, G.; Lagos, D.; Horvath, R.; Rudge Timothy, James; Cartes Saavedra, Benjamín Tomas; Eisner Sagues, Verónica Raquel
    Optic atrophy protein 1 (OPA1) mediates inner mitochondrial membrane (IMM) fusion and cristae organization. Mutations in OPA1 cause autosomal dominant optic atrophy (ADOA), a leading cause of blindness. Cells from ADOA patients show impaired mitochondrial fusion, cristae structure, bioenergetic function, and mitochondrial DNA (mtDNA) integrity. The mtDNA encodes electron transport chain subunits and is packaged into nucleoids spread within the mitochondrial population. Nucleoids interact with the IMM, and their distribution is tightly linked to mitochondrial fusion and cristae shaping. Yet, little is known about the physio-pathological relevance of nucleoid distribution. We studied the effect of OPA1 and ADOA-associated mutants on nucleoid distribution using high-resolution confocal microscopy. We applied a novel model incorporating the mitochondrial context, separating nucleoid distribution into the array in the mitochondrial population and intramitochondrial longitudinal distribution. Opa1-null cells showed decreased mtDNA levels and nucleoid abundance. Also, loss of Opa1 lead to an altered distribution of nucleoids in the mitochondrial population, loss of cristae periodicity, and altered nucleoids to cristae proximity partly rescued by OPA1 isoform 1. Overexpression of WT OPA1 or ADOA-causing mutants c.870+5G>A or c.2713C>T in WT cells, showed perturbed nucleoid array in the mitochondria population associated with cristae disorganization. Opa1-null and cells overexpressing ADOA mutants accumulated mitochondria without nucleoids. Interestingly, intramitochondrial nucleoid distribution was only altered in Opa1-null cells. Altogether, our results highlight the relevance of OPA1 in nucleoid distribution in the mitochondrial landscape and at a single-organelle level and shed light on new components of ADOA etiology. The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
  • Thumbnail Image
    Item
    OPA1 disease-causing mutants perturb mitochondrial nucleoid cluster distribution
    (ELSEVIER, 2022) Eisner, Veronica; Macuada, Josefa; Vidal, Gonzalo; Molina-Riquelme, Isidora; Aedo, Geraldine; Lagos, Daniel; Perez, Nicolas; Rudge, Timothy; Cartes-Saavedra, Benjamin
  • No Thumbnail Available
    Item
    Role of OPA1 ADOA-Causing Mutants in Mitochondrial Nucleoid Distribution
    (CELL PRESS, 2021) Macuada, Josefa; Aedo, Geraldine; Vidal, Gonzalo; Rudge, Timothy; Cartes Saavedra, Benjamin; Eisner, Veronica
  • Thumbnail Image
    Item
    Semi-Automated Method for Image Analysis of mtDNA Nucleoids Dynamics
    (CELL PRESS, 2021) Aedo, Geraldine; Macuada, Josefa; Cartes Saavedra, Benjamin; Vidal, Gonzalo; Rudge, Timothy; Eisner, Veronica