BIOLOGY OF RIBORREGUATION SYNTHETIC SYSTEMS: THERMODYNAMICS, NOISE AND OPERABILITY (Q3169794): Difference between revisions
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BIOLOGY OF RIBORREGUATION SYNTHETIC SYSTEMS: THERMODYNAMICS, NOISE AND OPERABILITY | |||
Revision as of 03:31, 9 October 2021
Project Q3169794 in Spain
| Language | Label | Description | Also known as |
|---|---|---|---|
| English | BIOLOGY OF RIBORREGUATION SYNTHETIC SYSTEMS: THERMODYNAMICS, NOISE AND OPERABILITY |
Project Q3169794 in Spain |
Statements
105,875.0 Euro
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211,750.0 Euro
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50.0 percent
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1 January 2019
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31 December 2021
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AGENCIA CONSEJO SUPERIOR DE INVESTIGACIONES CIENTIFICAS
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46190
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EL MATERIAL GENETICO PUEDE SER PROGRAMADO PARA EXPRESAR SISTEMAS QUE DETECTEN, PROCESEN (SIGUIENDO CALCULOS LOGICOS) Y RESPONDAN A (EN FORMA DE EXPRESION GENICA) DIFERENTES SEÑALES MOLECULARES. LA BIOLOGIA SINTETICA ENCARA ESTO SIGUIENDO PRINCIPIOS FUNDAMENTALES DE INGENIERIA DE SISTEMAS; ES DECIR, MEDIANTE LA COMBINACION DE MODELOS MATEMATICOS PARA CAPTURAR LA DINAMICA DE EXPRESION GENICA, EXPERIMENTOS PARA MONITORIZAR DE MANERA CUANTITATIVA LAS CARACTERISTICAS DEL SISTEMA (RETROALIMENTANDO EL PROCESO DE DISEÑO) Y LA ESTANDARIZACION DE PARTES GENETICAS PARA COMPOSICION MODULAR. CIERTAMENTE, EL DISEÑO INICIAL DE CIRCUITOS SE BASA EN MODELOS DE REGULACION INCOMPLETOS/SIMPLISTAS ESTABLECIDOS POR DESARROLLOS PREVIOS DE BIOLOGIA MOLECULAR Y DE SISTEMAS. UNA VEZ DISEÑADO Y CARACTERIZADO PARA SU FUNCIONALIDAD PRINCIPAL, UN CIRCUITO SINTETICO AUN PRESENTA MULTIPLES INTERROGANTES, GENERALMENTE IGNORADOS. POR EJEMPLO, ¿LOS MODELOS UTILIZADOS PARA GUIAR EL DISEÑO SON LO SUFICIENTEMENTE PREDICTIVOS?, ¿EL COMPORTAMIENTO ES CONSISTENTE A NIVEL DE POBLACION Y DE UNA UNICA CELULA?, O ¿CUAL ES LA ESTABILIDAD EVOLUTIVA DE UNA CONSTRUCCION SINTETICA EN UN ORGANISMO? CREEMOS QUE LA RESOLUCION DE ESTAS PREGUNTAS CONDUCIRA A UNA RESINTESIS EN LA COMPRENSION DE LA FUNCION DEL CIRCUITO. TRABAJO PIONERO EN BIOLOGIA SINTETICA SE CENTRO EN LA REGULACION TRANSCRIPCIONAL, LO QUE LLEVO A IMPLEMENTACIONES GENETICAS DE PUERTAS LOGICAS, BIESTABLES Y OSCILADORES. EN LOS ULTIMOS AÑOS, SIN EMBARGO, EL ARN SE HA EXPLOTADO PARA DISEÑAR PROGRAMAS DE EXPRESION GENICA QUE SE EJECUTAN DE FORMA ROBUSTA IN VIVO, GRACIAS A SU VERSATILIDAD FUNCIONAL Y DISEÑABILIDAD A NIVEL DE NUCLEOTIDO. PRUEBA DE ESTA IDONEIDAD SON NUEVOS MECANISMOS DE CONTROL Y CIRCUITOS FUNCIONALES CON MOLECULAS DE ARN QUIMERICAS. EN ESTE PROYECTO, NOS CENTRAREMOS EN RIBORREGULADORES DE INICIACION DE LA TRADUCCION, ES DECIR, PEQUEÑAS MOLECULAS DE ARN CAPACES DE INTERACTUAR DE FORMA MUY ESPECIFICA CON LA REGION 5' NO TRADUCIDA DE UN ARN MENSAJERO PARA REGULAR LA UNION DE RIBOSOMAS. EN PRIMER LUGAR, DESARROLLAREMOS UN NUEVO MODELO TERMODINAMICO DE LAS INTERACCIONES ARN-ARN IN VIVO SIGUIENDO UNA DESCRIPCION ENERGETICA DETALLADA. ADOPTAREMOS UN ESQUEMA FUERA DEL EQUILIBRIO Y COMBINAREMOS CALCULOS ESTRUCTURALES CON ECUACIONES DIFERENCIALES. ESTO SERA INSTRUMENTAL PARA RECONOCER PROCESOS DINAMICOS DE REPLEGAMIENTO INTERMOLECULAR CON IMPACTO EN EXPRESION. ADEMAS, ANALIZAREMOS EL COMPORTAMIENTO ESTOCASTICO DE LA RIBORREGULACION MEDIANTE LA MONITORIZACION DE LA EXPRESION A NIVEL DE CELULA UNICA. VINCULAREMOS LAS CARACTERISTICAS ESTRUCTURALES DEL ARN CON EL GRADO DE VARIABILIDAD ENTRE CELULAS, DESARROLLANDO MODELOS MATEMATICOS CAPACES DE PREDECIR DICHOS PATRONES. FINALMENTE, ESTUDIAREMOS EL RANGO DE OPERABILIDAD DE UN CIRCUITO BASADO EN ARN PREVIAMENTE DISEÑADO. UTILIZAREMOS UN CIRCUITO CAPAZ DE REALIZAR OPERACIONES LOGICAS. PARA ESO, ESTUDIAREMOS EL COMPORTAMIENTO DINAMICO EN DIFERENTES CONDICIONES AMBIENTALES, ESTUDIAREMOS EL IMPACTO SOBRE EL CRECIMIENTO DE LA EXPRESION HETEROLOGA DE ARN Y ANALIZAREMOS LA ESTABILIDAD EVOLUTIVA DEL CIRCUITO REALIZANDO EVOLUCION EXPERIMENTAL. LA COMPRENSION DEL COMPORTAMIENTO DINAMICO EXTENDIDO DE SISTEMAS GENETICOS SINTETICOS FACILITA EN ULTIMA INSTANCIA EL DESARROLLO DE PRINCIPIOS DE DISEÑO EN BIOLOGIA. EN SUMA, EL IMPACTO EN CIENCIA BASICA DE ARN Y BIOLOGIA SINTETICA, ASI COMO LAS APLICACIONES ACTUALES Y EN PERSPECTIVA, HACEN ESTA INVESTIGACION MULTIDISCIPLINAR OPORTUNA Y PERTINENTE. (Spanish)
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GENETIC MATERIAL CAN BE PROGRAMMED TO EXPRESS SYSTEMS THAT SENSE, PROCESS (FOLLOWING LOGIC CALCULATIONS) AND RESPOND TO (IN THE FORM OF GENE EXPRESSION) DIFFERENT MOLECULAR SIGNALS. SYNTHETIC BIOLOGY AIMS AT APPROACHING THIS BY FOLLOWING FUNDAMENTAL SYSTEMS ENGINEERING PRINCIPLES, THAT IS, THROUGH THE COMBINATION OF MATHEMATICAL MODELING TO CAPTURE GENE EXPRESSION DYNAMICS, EXPERIMENTS TO MONITOR IN A QUANTITATIVE WAY THE FEATURES OF THE SYSTEM TO FEEDBACK THE DESIGN PROCESS, AND GENETIC PART STANDARDIZATION FOR MODULAR COMPOSABILITY. CERTAINLY, INITIAL CIRCUIT DESIGN RELIES ON INCOMPLETE OR SIMPLISTIC MODELS OF REGULATION ESTABLISHED BY PREVIOUS MOLECULAR AND SYSTEMS BIOLOGY DEVELOPMENTS. ONCE DESIGNED AND CHARACTERIZED FOR ITS MAIN FUNCTIONALITY, A SYNTHETIC CIRCUIT STILL PRESENTS MULTIPLE QUERIES, USUALLY OVERLOOKED. FOR EXAMPLE, ARE THE MODELS USED TO GUIDE THE DESIGN PREDICTIVE ENOUGH?, IS THE BEHAVIOR CONSISTENT AT THE POPULATION AND SINGLE CELL LEVELS?, OR WHAT IS THE EVOLUTIONARY STABILITY OF A SYNTHETIC CONSTRUCT IN A LIVING ORGANISM? WE BELIEVE THAT THE PROPER RESOLUTION OF THESE QUESTIONS WILL LEAD TO A RESYNTHESIS IN THE UNDERSTANDING OF CIRCUIT FUNCTION. PIONEER WORK IN SYNTHETIC BIOLOGY RESTED ON THE MANIPULATION OF THE LAYER OF TRANSCRIPTIONAL REGULATION, LEADING TO GENETIC IMPLEMENTATIONS OF LOGIC GATES, TOGGLE SWITCHES, AND OSCILLATORS. IN RECENT YEARS, HOWEVER, RNA HAS BEEN EXPLOITED AS AN IDEAL SUBSTRATE TO ENGINEER GENE EXPRESSION PROGRAMS THAT ROBUSTLY RUN IN VIVO, THANKS TO ITS FUNCTIONAL VERSATILITY AND MODEL-BASED DESIGNABILITY AT THE NUCLEOTIDE LEVEL. PROOF OF THIS SUITABILITY ARE NOVEL MECHANISMS OF GENE EXPRESSION CONTROL WITH CHIMERIC RNA MOLECULES AND INCREASINGLY COMPLEX FUNCTIONAL CIRCUITS ENGINEERED WITH REGULATORY RNAS. IN THIS PROJECT, WE WILL FOCUS ON RIBOREGULATORS OF TRANSLATION INITIATION, THAT IS, SMALL RNA MOLECULES ABLE TO INTERACT IN A VERY SPECIFIC MANNER WITH THE 5' UNTRANSLATED REGION OF A MESSENGER RNA TO REGULATE RIBOSOME BINDING. IN FIRST PLACE, WE WILL DEVELOP A NOVEL THERMODYNAMIC MODEL OF RNA-RNA INTERACTIONS IN VIVO BY FOLLOWING A DETAILED DESCRIPTION OF THE CORRESPONDING ENGERGY LANDSCAPE. WE WILL ADOPT A NON-EQUILIBRIUM SCHEME AND WE WILL COMBINE STRUCTURAL CALCULATIONS WITH DIFFERENTIAL EQUATIONS. THIS WILL BE INSTRUMENTAL TO RECOGNIZE DYNAMIC PROCESSES OF INTERMOLECULAR REFOLDING WITH IMPACT ON GENE EXPRESSION. IN ADDITION, WE WILL ANALYZE THE STOCHASTIC BEHAVIOR OF RIBOREGULATION BY MONITORING GENE EXPRESSION AT SINGLE CELL RESOLUTION. WE WILL LINK RNA STRUCTURAL FEATURES WITH THE EXTENT OF CELL-TO-CELL VARIABILITY, DEVELOPING MATHEMATICAL MODELS ABLE TO PREDICT SUCH PATTERNS. FINALLY, WE WILL STUDY THE OPERABILITY RANGE OF A PREVIOUSLY ENGINEERED RNA-BASED CIRCUIT. WE WILL USE A CIRCUIT ABLE TO PERFORM LOGIC OPERATIONS. FOR THAT, WE WILL STUDY THE DYNAMIC BEHAVIOR IN DIFFERENT ENVIRONMENTAL CONDITIONS, STUDY THE IMPACT ON GROWTH RATE OF HETEROLOGOUS RNA EXPRESSION, AND ANALYZE THE EVOLUTIONARY STABILITY OF THE CIRCUIT BY PERFORMING EXPERIMENTAL EVOLUTION THROUGH PARALLEL SERIAL DILUTIONS. THE FULL UNDERSTANDING OF THE EXTENDED DYNAMIC BEHAVIOR OF ENGINEERED GENETIC SYSTEMS ULTIMATELY FACILITATES THE DEVELOPMENT OF DESIGN PRINCIPLES TO MAKE BIOLOGY MORE PREDICTABLE AND DESIGNABLE. IN SUM, THE IMPACT ON BASIC RNA SCIENCE AND SYNTHETIC BIOLOGY, AS WELL AS THE CURRENT AND PERSPECTIVE APPLICATIONS, MAKE THIS MULTIDISCIPLINARY INVESTIGATION TIMELY AND RELEVANT. (English)
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Paterna
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Identifiers
PGC2018-101410-B-I00
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