Mariana Gomez Schiavon

Universidad Nacional Autónoma de México | UNAM · Laboratorio Internacional de Investigación sobre el Genoma Humano (LIIGH)

Feedback control is a fundamental underpinning of life, underlying homeostasis of biological processes at every scale of organization, from cells to ecosystems. The ability to evaluate the contribution and limitations of feedback control mechanisms operating in cells is a critical step for understanding and ultimately designing feedback control sys...

Mathematical models can aid the design of genetic circuits, but may yield inaccurate results if individual parts are not modeled at the appropriate resolution. To illustrate the importance of this concept, we study transcriptional cascades consisting of two inducible synthetic transcription factors connected in series. Despite the simplicity of thi...

Feedback control is a fundamental underpinning of life, underlying homeostasis of biological processes at every scale of organization, from cells to ecosystems. The ability to evaluate the contribution and limitations of feedback control mechanisms operating in cells is a critical step for understanding and ultimately designing feedback control sys...

Mathematical models can aid the design of genetic circuits, but may yield inaccurate results if individual parts are not modeled at the appropriate resolution. To illustrate the importance of this concept, we study transcriptional cascades consisting of two inducible synthetic transcription factors connected in series. Despite the simplicity of thi...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Epigenetic switches are bistable, molecular systems built from self-reinforcing feedback loops that can spontaneously switch between heritable phenotypes in the absence of DNA mutation. It has been hypothesized that epigenetic switches first evolved as a mechanism of bet-hedging and adaptation, but the evolutionary trajectories and conditions by wh...

The capability to engineer de novo feedback control with biological molecules is ushering in an era of robust functionality for many applications in biotechnology and medicine. To fulfill their potential, these control strategies need to be generalizable, modular, and operationally predictable. Proportional-integral-derivative (PID) control fulfill...

De novo-designed proteins1–3 hold great promise as building blocks for synthetic circuits, and can complement the use of engineered variants of natural proteins4–7. One such designer protein—degronLOCKR, which is based on ‘latching orthogonal cage–key proteins’ (LOCKR) technology⁸—is a switch that degrades a protein of interest in vivo upon inducti...

Neuronal activity-inducible gene transcription correlates with rapid and transient increases in histone acetylation at promoters and enhancers of activity-regulated genes. Exactly how histone acetylation modulates transcription of these genes has remained unknown. We used single-cell in situ transcriptional analysis to show that Fos and Npas4 are t...

The ability of cells to regulate their function through feedback control is a fundamental underpinning of life. The capability to engineer de novo feedback control with biological molecules is ushering in an era of robust functionality for many applications in biotechnology and medicine. To fulfill their potential, feedback control strategies imple...

Mathematical models continue to be essential for deepening our understanding of biology. On one extreme, simple or small-scale models help delineate general biological principles. However, the parsimony of detail in these models as well as their assumption of modularity and insulation make them inaccurate for describing quantitative features. On th...

Mathematical models continue to be essential for deepening our understanding of biology. On one extreme, simple or small-scale models help delineate general biological principles. However, the parsimony of detail in these models as well as their assumption of modularity and insulation make them inaccurate for describing quantitative features. On th...

Single-molecule RNA fluorescence in situ hybridization (smFISH) provides unparalleled resolution in the measurement of the abundance and localization of nascent and mature RNA transcripts in fixed, single cells. We developed a computational pipeline (BayFish) to infer the kinetic parameters of gene expression from smFISH data at multiple time point...

Single-molecule RNA fluorescence in situ hybridization (smFISH) provides unparalleled resolution on the abundance and localization of nascent and mature transcripts in fixed, single cells. We developed a computational pipeline —BayFish— to infer kinetic parameters of gene expression from smFISH data at multiple time points after induction. Given an...

Single-molecule RNA fluorescence in situ hybridization (smFISH) provides unparalleled resolution on the abundance and localization of nascent and mature transcripts in single cells. Gene expression dynamics are typically inferred by measuring mRNA abundance in small numbers of fixed cells sampled from a population at multiple time-points after indu...

Adaptation and survival in fluctuating environments is an evolutionary challenge faced by organisms. Epigenetic switches (bistable, molecular systems built from self-reinforcing feedback loops) have been suggested as a mechanism of bet-hedging and adaptation to fluctuating environments. These epigenetic systems are capable of spontaneously switchin...

Adaptation and survival in fluctuating environments is a challenge faced by living organisms. Genetic adaptation and bistable stochastic switching are two possible adaptation strategies. Which evolutionary conditions (population size, mutation effect, environmental fluctuation rate, and selection pressure) favor bistability (i.e. epigenetic switchi...