128 research outputs found
Contractivity of a genetic circuit with internal feedback and cell-to-cell communication
No full text[EN] We consider a realistic model of the synthetic gene circuit combining cell-to-cell communication system via quorum sensing, and a synthetic repressible promoter implementing intracellular negative feedback control. The circuit has been shown to increase robustness with respect to both extrinsic and intrinsic noise elsewhere. As a first step towards an analytic analysis, in this paper we use contraction theory to perform a stability analysis. From it, we infer the components of the circuit most affecting the rate of contractivity, using biologically sensible values of the circuit parameters.This research was partially funded by grant FEDER-CICYT DPI2014-55276-C5-1-R. Yadira Boada thanks grant FPI/2013-3242 of the Universitat Politècnica de València.Picó-Marco, E.; Boada-Acosta, YF.; Picó, J.; Vignoni, A. (2016). Contractivity of a genetic circuit with internal feedback and cell-to-cell communication. IFAC-PapersOnLine. 49(26):213-218. https://doi.org/10.1016/j.ifacol.2016.12.128S213218492
Optimization Alternatives for Robust Model-based Design of Synthetic Biological Circuits
No full text[EN] Synthetic biology is reaching the situation where tuning devices by hand is no longer possible due to the complexity of the biological circuits being designed. Thus, mathematical models need to be used in order, not only to predict the behavior of the designed synthetic devices; but to help on the selection of the biological parts, i.e., guidelines for the experimental implementation. However, since uncertainties are inherent to biology, the desired dynamics for the circuit usually requires a trade-off among several goals. Hence, a multi-objective optimization design (MOOD) naturally arises to get a suitable parametrization (or range) of the required kinetic parameters to build a biological device with some desired properties. Biologists have classically addressed this problem by evaluating a set of random Monte Carlo simulations with parameters between an operation range. In this paper, We propose solving the MOOD by means of dynamic programming using both a global multi-objective evolutionary algorithm (MOLA) and a local gradient-based nonlinear programming (NLP) solver. The performance of both alternatives is then checked in the design of a well-known biological circuit: a genetic incoherent feed-forward loop showing adaptive behavior. (C) 2016, IFAC (International Federation of Antomatic Control) Hosting by Elsevier Ltd. All rights reserved.The research leading to these results has received funding from the European Union (FP7/2007-2013 under grant agreement no604068), the Spanish Government (FEDER-CICYT DPI2011-524 28112-C04-01, DPI2014-55276-C5-1-R, DPI2015-70975-P) and the National Council of Scientific and Technologic Development of Brazil (BJT-304804/2014-2). Yadira Boada thanks also grant FPI/2013-3242 of the Universitat Politecnica de ValenciaBoada-Acosta, YF.; Pitarch Pérez, JL.; Vignoni, A.; Reynoso Meza, G.; Picó, J. (2016). Optimization Alternatives for Robust Model-based Design of Synthetic Biological Circuits. IFAC-PapersOnLine. 49(7):821-826. https://doi.org/10.1016/j.ifacol.2016.07.291S82182649
Cantona: avances y resultados en el estudio de su patrón de asentamiento
No full textGarcía Cook, Ángel
2003a. “Cantona: La Ciudad” en William T.
Sanders; Alba Guadalupe Mastache; Robert H.
Cobean (coords.), El Urbanismo en Mesoamérica,
México, INAH-Penn State University,
pp. 312-343.2003b. “Proyecto Arqueológico Cantona. Informe
de los trabajos en campo llevados a cabo en la
Temporada 2002”, México, Archivo Técnico de la
Coordinación de Arqueología, INAH.García Cook, Ángel y Leonor B. Merino Carrión
1996a. “Proyecto Arqueológico Cantona. Informe
General: 1993-1996”, México, Archivo Técnico de
la Coordinación de Arqueología, INAH.1996b. “Investigación Arqueológica en Cantona,
Puebla”, Arqueología, Revista de la Coordinación
Nacional de Arqueología, núm. 15, enero-junio.1998a. “Cantona: Urbe Prehispánica en el Altiplano
Central de México”, Latin American Antiquity, vol. 9,
núm. 3, pp. 191-215.1998b. “Proyecto Arqueológico Cantona. Informe
de los trabajos en campo llevados a cabo en la
Temporada 1997”, México, Archivo Técnico de la
Coordinación de Arqueología, INAH.2000. “El Proyecto Arqueológico Cantona”, en L.
Miranbell y J. Litvak (coords.), Arqueología, Historia
y Antropología. In Memoriam José Luis Lorenzo
Bautista, México, INAH (Científica, 415) pp. 161-203.2001. “Proyecto Arqueológico Cantona. Informe de
los trabajos en campo llevados a cabo en la
Temporada 2000”, México, Archivo Técnico de la
Coordinación de Arqueología, INAH.Lara Galicia, Aline P.
2003. “El yacimiento de Obsidiana en Oyameles-
Zaragoza, Puebla: Evidencias de explotación
prehispánica”, tesis de licenciatura, México, ENAH,
INAH.Martínez Calleja, Yadira
2002. “Proyecto Arqueológico Cantona. Informe de
Actividades 2002”, México, Archivo técnico del
PAC, INAH.2004. “Proyecto Arqueológico Cantona. Informe de
las actividades realizadas durante la temporada2003”, México, Archivo PAC, SCIPA, INAH.Mastache, A. Guadalupe y Robert H. Cobean
2003. “Urbanismo en Tula” en William T. Sanders,
Alba Guadalupe Mastache y Robert Cobean
(coords.), El Urbanismo en Mesoamérica, INAH-Penn
State University, pp. 218-255.Morales Vigil, Erika
2003. “Informe Técnico, del Proyecto Norte de la
Cuenca de Oriental y Proyecto Arqueológico
Cantona”, México, Archivo del Proyecto
Arqueológico Cantona, DEA.Zamora Rivera, Mónica
2004. “Proyecto Arqueológico Cantona. Informe de
las actividades realizadas en el detallado del plano
de la Ciudad”, México, Archivo PAC, SCIPA, INAH
Integrating mathematical modeling into synthetic biology education: a comprehensive approach through webinars and syllabus development
No full text[EN] Mathematical modeling is a fundamental aspect of synthetic biology, enabling precise design and analysis of biological systems. To enhance students' understanding of this critical topic, we developed a series of webinars aimed at teaching mathematical modeling to iGEM teams. These webinars were initially created to maintain student engagement during a period of restricted lab access but quickly demonstrated their value as an effective educational tool. The success of these webinars highlighted the suitability of mathematical modeling as a topic well-suited to both onsite and online learning environments. Recognizing this, we expanded the content into a comprehensive syllabus for undergraduate courses in synthetic biology at the Universitat Polit & egrave;cnica de Valencia in Spain and Universidad de las Fuerzas Armadas-ESPE in Ecuador. The course now serves as a core component of synthetic biology education, offering students a robust framework for understanding and applying mathematical models. It includes a series of lectures, practical exercises, and case studies, all designed to deepen students' knowledge and skills in this essential area. To support educators and students, we have also developed a deck of slides and example scripts that provide practical examples and reinforce the concepts taught in the course. This manuscript presents the development, implementation, and impact of these educational initiatives, demonstrating how mathematical modeling can be effectively integrated into synthetic biology curricula to prepare students for real-world challenges in the field.The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This research was funded by MCIN/AEI/10.13039/501100011033 grant
numbers PID2020-117271RB-C21 and PID2023-151077OB-I00. YB gives thanks to Universitat Politecnica de Valencia (Grant PAID-10-21 Acceso al Sistema Espanol de Ciencia e Innovacion), and Secretaria de Educacion Superior, Ciencia, Tecnologia e Innovacion-Ecuador (Scholarship Convocatoria Abierta 2011).Boada-Acosta, YF.; Beluzán-Flores, FJ.; Vignoni, A. (2024). Integrating mathematical modeling into synthetic biology education: a comprehensive approach through webinars and syllabus development. Frontiers in Education. 9. https://doi.org/10.3389/feduc.2024.1486293S
Advancements in synthetic biology-based bacterial cancer therapy: A modular design approach.
No full textSynthetic biology aims to program living bacteria cells with artificial genetic circuits for user-defined functions, transforming them into powerful tools with numerous applications in various fields, including oncology. Cancer treatments have serious side effects on patients due to the systemic action of the drugs involved. To address this, new systems that provide localized antitumoral action while minimizing damage to healthy tissues are required. Bacteria, often considered pathogenic agents, have been used as cancer treatments since the early 20th century. Advances in genetic engineering, synthetic biology, microbiology, and oncology have improved bacterial therapies, making them safer and more effective. Here we propose six modules for a successful synthetic biology-based bacterial cancer therapy, the modules include Payload, Release, Tumor-targeting, Biocontainment, Memory, and Genetic Circuit Stability Module. These will ensure antitumor activity, safety for the environment and patient, prevent bacterial colonization, maintain cell stability, and prevent loss or defunctionalization of the genetic circuit.This research was funded by MCIN/AEI/10.13039/501100011033
Grant numbers PID2020-117271RB-C21 and TED2021-131049B-I00,
Generalitat Valenciana GVA Grant CIAICO/2021/159, Centro de
Investigacion ´ Biom´edica en Red de Cancer ´ (CIBERONC) Grant CB16-12-
00350, Instituto de Salud Carlos III (Grant PI22/01221), and GVA Grant
AICO/2021/333.
A Arboleda-García thanks the Grant PAID-01–21 Programa de Ayudas de Investigacion ´ y Desarrollo from Universitat Polit`ecnica de
Val`encia, Spain. I Alarcon-Ruiz thanks the FPU grant (FPU20/04814)
from the Spanish Government. L Boada-Acosta thanks the Grant Santiago Grisolía GRISOLIAP/2021/030 from Conselleria de Innovacion, ´
Universidades, Ciencia y Sociedad Digital and Generalitat Valenciana,
Spain. Y Boada is thankful for the Grant PAID-10-21 Acceso al Sistema
Espanol ˜ de Ciencia e Innovacion ´ from Universitat Polit`ecnica de
Val`encia, Spain; and the Scholarship Convocatoria Abierta 2011 from
Secretaría de Educacion ´ Superior, Ciencia, Tecnología e Innovacion, ´
Ecuador. The authors are grateful to Prof. Jesús Pico ´ for his guidance
during the preparation of this manuscript. BioRender was used to
illustrate the figures under a paid license for publication authorization.S
Multiobjective Identification of a Feedback Synthetic Gene Circuit
No full text© 2020 IEEE. Personal use of this material is permitted. Permissíon from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertisíng or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.[EN] Kinetic (i.e., dynamic) semimechanistic models based on the first principles are particularly important in systems and synthetic biology since they can explain and predict the functional behavior that emerges from the time-varying concentrations in cellular components. However, gene circuit models are nonlinear higher order ones and have a large number of parameters. In addition, experimental measurements are often scarce, and enough signal excitability for identification cannot always be achieved. These characteristics render the identification problem ill-posed, so most gene circuit models present incomplete parameter identifiability. Thus, parameter identification of typical biological models still appears as an open problem, where ensemble modeling approaches and multiobjective optimization arise as natural options. We address the problem of identifying the stochastic model of a closed-loop synthetic genetic circuit designed to minimize the gene expression noise. The model results from the feedback interaction between two subsystems. Besides incomplete parameter identifiability, the closed-loop dynamics cannot be directly identified due to the lack of enough input signal excitability. We apply a two-stage approach. First, the open-loop averaged time-course experimental data are used to identify a reduced-order stochastic model of the system direct chain. Then, closed-loop steady-state stochastic distributions are used to identify the remaining parameters in the feedback configuration. In both cases, multiobjective optimization is used to address the parameter identifiability, providing sets of parameters valid for different state-space regions. The methodology gives good identification results, provides clear guidelines on the effect of the parameters under different scenarios, and it is particularly useful for easily combining time-course population averaged and steady-state single-cell distribution experimental data.This work was supported by the European Union and Spanish Government, MINECO/AEI/FEDER under Grant DPI2017-82896-C2-1-R. The work of Y. Boada was supported by the Universitat Politecnica de Valencia under Grant FPI/2013-3242.Boada-Acosta, YF.; Vignoni, A.; Picó, J. (2020). Multiobjective Identification of a Feedback Synthetic Gene Circuit. IEEE Transactions on Control Systems Technology. 28(1):208-223. https://doi.org/10.1109/TCST.2018.2885694S20822328
Standard Calibration and On-Line Estimation of Cell-Specific Growth and Protein Synthesis Rates in Chi.Bio Mini-Bioreactors
No full text[EN] Low-cost mini-bioreactor platforms are becoming increasingly important in synthetic biology and biotechnology for the characterization of genetic constructs and their initial scaling-up to large-scale cultures. Key process variables are the specific growth rate of cells and the synthesis rate of reporter proteins associated with transcriptional units of interest. These variables are of paramount importance for the characterization of gene synthetic circuits. In addition, their on-line estimation can be used for real-time monitoring of cells' metabolic state and gene circuit dynamic performance, thus allowing for on-line decision taking. In this work, we first describe a procedure for the calibration of absorbance and fluorescence measurements, ensuring standardized and comparable units across different experimental setups and measurement devices. Then, we implement an observer-based software sensor that uses the calibrated on-line measurements to simultaneously estimate the specific growth and protein synthesis rates. We implemented the calibration procedure and software sensor in a Chi.Bio mini-bioreactor platform. The experimental results show very good performance and pave the way for the use of mini-bioreactor platforms in the real-time characterization of gene synthetic circuits under dynamically regulated time-varying complex scenarios.This research was funded by MCIN/AEI/10.13039/501100011033 Grants Number PID2020-117271RB-C21 and PID2023-151077OB-I00. H.D.I. holds a "Contrato predoctoral para la formacion de doctores, convocatoria 2021" (PRE2021-098767) from Agencia Estatal de Investigacion. A.A. thanks the Universitat Politecnica de Valencia for their support through Grant PAID-01-21 (Subprogram 1). Y.B. was funded by Grant PAID-10-21 Acceso al Sistema Espanol de Ciencia e Innovacion and Grant AYUDA PAID-06-24 (20250092) from Universitat Politecnica de Valencia. Y.B. also thanks to Secretaria de Educacion Superior, Ciencia, Tecnologia e Innovacion of Ecuador (Scholarship Convocatoria Abierta 2011).Harold José;Arboleda-García, Mario Andrés;Boada-Acosta, Yadira Fernanda;Vignoni, Alejandro;Picó, Jesús (2025). Standard Calibration and On-Line Estimation of Cell-Specific Growth and Protein Synthesis Rates in Chi.Bio Mini-Bioreactors. Applied Sciences. 15(13). https://doi.org/10.3390/app15137442S151
Modelling and experimental validation of signalling pathways with relevance to homologous mammalian systems
No full textHaploidní buňky pivních kvasinek Saccharomyces cervisiae používají ke vzájemné komunikaci speciální proteiny, feromony. Receptor, který rozponává feromony v kvasinkách, patří do dobře známé a popsané skupiny receptorů spřažených s G proteinem, které se vyskytují v savčích buňkách, kde umožňují např. čich, reakci imunitního sytému apod. V této práci je představen mechanismus ladění aktivace takového receptoru a uveden jednoduchý model jeho funkce v kvasinkách. Je ukázano, že aktivaci receptoru je možné dynamicky ladit změnou síly zpětné vazby, která odpovídá míře exprese Sst2 proteinu, který je přirozeným negativním regulátorem G proteinu.ObhájenoHaploid cells of budding yeast Saccharomyces cervisiae use special proteins, called pheromones, for communication. The receptor that recognizes pheromones in yeast belongs to a well-described family of so called GPCRs (G protein-coupled receptors) that are present in mammalian cells enabling the sense of smell, the immune system response, etc. In this work, a mechanism for tuning of the receptor activation is presented and a simple model of the corresponding system inside the yeast is introduced. It is shown that it is possible to dynamically tune the receptor activation by varying the feedback strength corresponding to expression levels of the Sst2 protein which is a native feedback regulator of the G protein
Funcionalidad familiar y autoestima en los/as niños/as de 7 a 11 años atendidos en el Hospital Básico 11 B.C.B. “Galápagos” de Riobamba.
No full textPdfLa investigación parte del enfoque cualitativo en el marco del paradigma fenomenológico, cuyo propósito fue demostrar la funcionalidad familiar y la autoestima en los/as niños/as de 7 a 11 años atendidos en el Hospital Básico 11 B.C.B. “Galápagos” de Riobamba. Para la recolección de datos se empleó el método clínico a través de la entrevista y observación; además el cuestionario de funcionalidad familiar FF-SILL, la escala de Rosembergautoestima (niños) y el test proyectivo H.T.P. Se tomó en cuenta criterios diagnósticos de la clasificación CIE10: Problemas en relación entre esposos o pareja y Soporte familiar inadecuado para determinar los casos de estudio registrados en las correspondientes historias clínicas. Los resultados obtenidos reflejaron cuatro familias moderadamente funcionales y cuatro familias disfuncionales, siendo común la disfuncionalidad en todos los sistemas familiares analizados; en lo concerniente a la autoestima, se observó dos niños con Autoestima media y seis niños/as con Autoestima baja, en concordancia con los resultados de
las pruebas psicológicas. Determinadas características como la mala comunicación, la rigidez, los problemas de carácter y la marcada tendencia a la emocionalidad por los bajos grados de diferenciación presentes en los miembros que conforman los sistemas familiares predisponen
a la disfuncionalidad familiar, observándose además (sistémicamente) que determinados patrones comportamentales se repiten por influencia transgeneracional. El resultado lleva a inferir que la funcionalidad familiar incide en la autoestima de los/as niños/as.The research arises from the qualitative approach in the framework of the phenomenological paradigm, whose purpose was to demonstrate the familiar functionality and self-esteem in children from 7 to 11 years assisted in the B.C.B. 11 "Galapagos" Basic Hospital of Riobamba. The clinical method was used to collect the data through the interview and observation and Questionnaire FF-SILL family functionality, Rosemberg-Esteem Scale (children) and the projective test H.T.P. It was
used ICD10 diagnostic criteria for the classification: Relationship problems between spouses or a mate and Inadequate family support to determine the study cases registered in the clinical histories. The results were gotten reflected four moderately functional families and four dysfunctional families, resulting common the dysfunctionality in all family systems analyzed; related to self-esteem, it was observed to two children with medium self-esteem and six children with low self-esteem, consistent to psychological tests. Certain features such as poor communication, rigidity, problems of character and marked tendency to emotionality by low grades of differentiation present in the members that make family systems predispose to family dysfunction, also observed (systemically) that certain behavioral patterns are repeated by trans generational influence. The result infers that family functionality affects the self-esteem of the children
A systems engineering approach to model, tune and test synthetic gene circuits
No full textLa biología sintética se define como la ingeniería de la biología: el (re)diseño y construcción de nuevas partes, dispositivos y sistemas biológicos para realizar nuevas funciones con fines útiles, que se basan en principios elucidados de la biología y la ingeniería. Para facilitar la construcción rápida, reproducible y predecible de estos sistemas biológicos a partir de conjuntos de componentes es necesario desarrollar nuevos métodos y herramientas. La tesis plantea la optimización multiobjetivo como el marco adecuado para tratar los problemas comunes que surgen en el diseño racional y el ajuste óptimo de los circuitos genéticos sintéticos. Utilizando un enfoque clásico de ingeniería de sistemas, la tesis se centra principalmente en: i) el modelado de circuitos genéticos sintéticos basado en los primeros principios, ii) la estimación de parámetros de modelos a partir de datos experimentales y iii) el ajuste basado en modelos para lograr el desempeño deseado de los circuitos.
Se han utilizado dos circuitos genéticos sintéticos de diferente naturaleza y con diferentes objetivos y problemas: un circuito de realimentación de tipo 1 incoherente (I1-FFL) que exhibe la importante propiedad biológica de adaptación, y un circuito de detección de quorum sensing y realimentación (QS/Fb) que comprende dos bucles de realimentación entrelazados -uno intracelular y uno basado en la comunicación de célula a célula- diseñado para regular el nivel medio de expresión de una proteína de interés mientras se minimiza su varianza a través de la población de células. Ambos circuitos han sido analizados in silico e implementados in vivo.
En ambos casos, se han desarrollado modelos de estos circuitos basado en primeros principios. Se presta especial atención a ilustrar cómo obtener modelos de orden reducido susceptibles de estimación de parámetros, pero manteniendo el significado biológico.
La estimación de los parámetros del modelo a partir de los datos experimentales se considera en diferentes escenarios, tanto utilizando modelos determinísticos como estocásticos. Para el circuito I1-FFL se consideran modelos determinísticos. Aquí, la tesis plantea la utilización de modelos locales utilizando la optimización multiobjetivo para realizar la estimación de parámetros del modelo bajo escenarios con estructura de modelo incompleta. Para el circuito QS/Fb, una estructura controlada por realimentación, el problema tratado es la falta de excitabilidad de las señales. La tesis propone una metodología de estimación en dos etapas utilizando modelos estocásticos. La metodología permite utilizar datos de curso temporal promediados de la población y mediciones de distribución en estado estacionario para una sola célula.
El ajuste de circuitos basado en modelos para lograr un desempeño deseado también se aborda mediante la optimización multiobjetivo. Para el circuito QS/Fb se realiza un análisis estocástico completo. La tesis aborda cómo tener en cuenta correctamente tanto el ruido intrínseco como el extrínseco, las dos principales fuentes de ruido en los circuitos genéticos. Se analiza el equilibrio entre ambas fuentes de ruido y el papel que desempeñan en el bucle de realimentación intracelular, y en la realimentación extracelular de toda la población. La principal conclusión es que la compleja interacción entre ambos canales de realimentación obliga al uso de la optimización multiobjetivo para el adecuado ajuste del circuito. En esta tesis además del uso adecuado de herramientas de optimización multiobjetivo, la principal preocupación es cómo derivar directrices para el ajuste in silico de parámetros de circuitos que puedan aplicarse de forma realista in vivo en un laboratorio estándar. Como alternativa al análisis de sensibilidad de parámetros clásico, la tesis propone el uso de técnicas de clustering a lo largo de los frentes de Pareto, relacionando el comprLa biologia sintètica es defineix com l'enginyeria de la biologia: el (re) disseny i construcció de noves parts, dispositius i sistemes biològics per a realitzar noves funcions útils que es basen a principis elucidats de la biologia i l'enginyeria. Per facilitar la construcció ràpida, reproduïble i predictible de aquests sistemes biològics a partir de conjunts de components és necessari desenvolupar nous mètodes i eines.
La tesi planteja la optimització multiobjectiu com el marc adequat per a tractar els problemes comuns que apareixen en el disseny racional i l' ajust òptim dels circuits genètics sintètics. Utilitzant un enfocament clàssic d'enginyeria de sistemes, la tesi es centra principalment en: i) el modelatge de circuits genètics sintètics basat en primers principis, ii) l' estimació de paràmetres de models a partir de dades experimentals i iii) l' ajust basat en models per aconseguir el rendiment desitjat dels circuits.
S'han utilitzat dos circuits genètics sintètics de diferent naturalesa i amb diferents objectius i problemes: un circuit de prealimentació de tipus 1 incoherent (I1-FFL) que exhibeix la important propietat biològica d'adaptació, i un circuit de quorum sensing i realimentació (QS/Fb) que comprèn dos bucles de realimentació entrellaçats -un intracel·lular i un basat en la comunicació de cèl·lula a cèl·lula- dis-senyat per regular el nivell mitjà d'expressió normal d'una proteïna d'interès mentre es minimitza la seua variació al llarg de la població de cèl·lules. Els dos circuits han estat analitzats in silico i implementats in vivo.
En tots dos casos, s'han desenvolupat models basats en primers principis d'aquests circuits. Després es presta especial atenció a delinear com obtenir models d'ordre reduït susceptibles de estimació de paràmetres, però mantenint el significat biològic. L' estimació dels paràmetres del model a partir de les dades experimentals es considera en diferents escenaris, tant utilitzant models determinístics com estocàstics. Per al circuit I1-FFL es consideren models determinístics. La tesi planteja la utilització de models locals utilitzant la optimització multiobjectiu per realitzar l'estimació de parametres del model sota escenaris amb estructura de model incompleta (dinàmica no modelada). Per al circuit de QS/Fb, una estructura controlada per realimentació, el problema tractat és la manca d'excitabilitat dels senyals. La tesi proposa una metodologia de estimació en dues etapes utilitzant models estocàstics. La metodologia permet utilitzar dades de curs temporal promediats de la població i mesures de distribució en estat estacionari d'una sola una cèl·lula.
L' ajust de circuits basat en models per aconseguir el rendiment desitjat dels circuits també s' aborda mitjançant la optimització multiobjectiu. Per al circuit QS/Fb, es fa un anàlisi estocàstic complet. La tesi aborda com tenir en compte correctament tant el soroll intrínsec com l' extrínsec, les dues principals fonts de soroll en els circuits genètics sintètics. S' analitza l'equilibri entre dues fonts de soroll i el paper que exerceixen en el bucle de realimentació intracel·lular, les i en la realimentació extracel·lular de tota la població. La principal conclusió es que la complexa interacció entre els dos canals de realimentació fa necessari l' ús de la optimització multiobjectiu per al adequat ajust del circuit. En aquesta tesi, a més de l'ús adequat d'eines d'optimització multiobjectiu, la principal preocupació és com derivar directives per al ajust in silico de paràmetres de circuits que puguin aplicar-se de forma realista en viu en un laboratori estàndard. Així, com a alternativa a l'anàlisi de sensibilitat de paràmetres clàssic, la tesi proposa l'ús de l' tècniques de l'agrupació al llarg dels fronts de Pareto, relacionant el compromís de dessempeny amb les regions en l'espai d'paràmetres.Synthetic biology is defined as the engineering of biology: the deliberate (re)design and construction of novel biological and biologically based parts, devices and systems to perform new functions for useful purposes, that draws on principles elucidated from biology and engineering. Methods and tools are needed to facilitate fast, reproducible and predictable construction of biological systems from sets of biological components.
This thesis raises multi-objective optimization as the proper framework to deal with common problems arising in rational design and optimal tuning of synthetic gene circuits. Using a classical systems engineering approach, the thesis mainly addresses: i) synthetic gene circuit modeling based on first principles, ii) model parameters estimation from experimental data and iii) model-based tuning to achieve desired circuit performance.
Two gene synthetic circuits of different nature and with different goals and inherent problems have been used throughout the thesis: an Incoherent type 1 feedforward circuit (I1-FFL) that exhibits the important biological property of adaptation, and a Quorum sensing/Feedback circuit (QS/Fb) comprising two intertwined feedback loops -an intracellular one and a cell-to-cell communication-based one-- designed to regulate the mean expression level of a protein of interest while minimizing its variance across the population of cells. Both circuits have been analyzed in silico and implemented in vivo.
In both cases, circuit modeling based on first principles has been carried out. Then, special attention is paid to illustrate how to obtain reduced order models amenable for parameters estimation yet keeping biological significance.
Model parameters estimation from experimental data is considered in different scenarios, both using deterministic and stochastic models. For the I1-FFL circuit, deterministic models are considered. In this case, the thesis raises ensemble modeling using multi-objective optimization to perform model parameters estimation under scenarios with incomplete model structure (unmodeled dynamics). For the QS/Fb gene circuit, a feedback controlled structure, the lack of excitability of the signals is the problem addressed. The thesis proposes a two-stage estimation methodology using stochastic models. The methodology allows using population averaged time-course data and steady state distribution measurements at the single-cell level.
Model-based circuit tuning to achieve desired circuit performance is also addressed using multi-objective optimization. First, for the QS/Fb feedback control circuit, a complete stochastic analysis is performed. Here, the thesis addresses how to correctly take into account both intrinsic and extrinsic noise, the two main sources of noise in gene synthetic circuits. The trade-off between both sources of noise, and the role played by in the intracellular single-cell feedback loop and the extracellular population-wide feedback is analyzed. The main conclusion being that the complex interplay between both feedback channels compel the use of multi-objective optimization for proper tuning of the circuit to achieve desired performance. Thus, the thesis wraps up all the previous results and uses them to address circuit tuning for desired performance. Here, besides the proper use of multi-objective optimization tools, the main concern is how to derive guidelines for circuit parameters tuning in silico that can realistically be applied in vivo in a standard laboratory. Thus, as an alternative to classical parameters sensitivity analysis, the thesis proposes the use of clustering techniques along the optimal Pareto fronts relating the performance trade-offs with regions in the circuits parameters space.This work has been partially supported by the Spanish Government (CICYT DPI2014-
55276-C5-1) and the European Union (FEDER). The author was recipient of the grant
Formación de Personal Investigador by the Universitat Politècnica de València, subprogram 1 (FPI/2013-3242).
She was also recipient of the competitive grants for pre-doctoral stays Erasmus Student Placement-European Programme 2015, and FPI Mobility program 2016 of the
Universitat Politècnica de València.
She also received the competitive grant for a pre-doctoral stay Becas de movilidad
para Jóvenes Profesores e Investigadores 2016, Programa de Becas Iberoamérica of
the Santander Bank.Boada Acosta, YF. (2018). A systems engineering approach to model, tune and test synthetic gene circuits [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/112725TESI
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