Dinámica Genómica

Estamos interesados en combinar la biología de sistemas y sintética usando modelamiento a escala genómica para el diseño de fenotipos bacterianos de interés biotecnológico. Además, también estamos interesados en utilizar un enfoque teórico-experimental para estudiar los mecanismos genéticos y metabólicos que permiten a poblaciones de bacterias implementar estrategias colectivas para sobrevivir a medios ambientes hostiles e impredecibles, por ejemplo a sustancias antimicrobianas. En este sentido, también estamos interesados en estudiar el efecto de la estructura espacial en la dinámica temporal de la evolución de la resistencia a distintas combinaciones de antibióticos. Asimismo, construimos modelos evolutivos para analizar regiones específicas de los genomas de los organismos, como por ejemplo los cromosomas sexuales, que son uno de los elementos más dinámicos de los genomas de los vertebrados. Por otro lado, utilizando como modelo de experimentación la fijación biológica de nitrógeno, estudiamos la regulación de la expresión de genes en respuesta a diferentes estímulos del medio ambiente y los mecanismos que gobiernan esta respuesta.

Semblanza completa

Académicos del grupo

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Publicaciones del Grupo

AñoPublicaciónEnlace
2017Beardmore, Robert Eric, Pena-Miller, Rafael, Gori, Fabio, Iredell, Jonathan (2017) Antibiotic Cycling and Antibiotic Mixing: Which One Best Mitigates Antibiotic Resistance? MOLECULAR BIOLOGY AND EVOLUTION 34(4):802-817PMID:28096304
2017Vicens, Alberto, Andrade-Lopez, Karla, Cortez, Diego, Maria Gutierrez, Rosa, Trevino, Claudia L. (2017) Premammalian origin of the sperm-specific Slo3 channel FEBS OPEN BIO 7(3):382-390PMID:28286733
2017Utrilla, Jose (2017) Evolutionary Engineering of Microorganisms to Overcome Toxicity During Lignocellulose Hydrolysates Utilization Engineering of Microorganisms for the Production of Chemicals and Biofuels from Renewable Resources ():181-200
2016Utrilla, Jose, Vargas-Tah, Alejandra, Trujillo-Martinez, Berenice, Gosset, Guillermo, Martinez, Alfredo (2016) Production of D-lactate from sugarcane bagasse and corn stover hydrolysates using metabolic engineered Escherichia coli strains BIORESOURCE TECHNOLOGY 220():208-214PMID:27573474
2016Reyes-Gonzalez, Alma, Talbi, Chouhra, Rodriguez, Susana, Rivera, Patricia, Zamorano-Sanchez, David, Girard, Lourdes (2016) Expanding the regulatory network that controls nitrogen fixation in Sinorhizobium meliloti: elucidating the role of the two-component system hFixL-FxkR MICROBIOLOGY-SGM 162(6):979-988PMID:27010660
2016Trujillo-Paredes, Niurka, Valencia, Concepcion, Guerrero-Flores, Gilda, Arzate, Dulce-Maria, Baizabal, Jose-Manuel, Guerra-Crespo, Magdalena, Fuentes-Hernandez, Ayari, Zea-Armenta, Ivan, Covarrubias, Luis (2016) Regulation of differentiation flux by Notch signalling influences the number of dopaminergic neurons in the adult brain BIOLOGY OPEN 5(3):336-347PMID:26912775
2015Girard Cuesy, María de Lourdes, Zamorano Sánchez, David Salvador (2015) FNR - like proteins in rhizobia: past and future Biological Nitrogen Fixation 1():155-166
2015Fuentes-Hernandez, Ayari, Plucain, Jessica, Gori, Fabio, Pena-Miller, Rafael, Reding, Carlos, Jansen, Gunther, Schulenburg, Hinrich, Gudelj, Ivana, Beardmore, Robert (2015) Using a Sequential Regimen to Eliminate Bacteria at Sublethal Antibiotic Dosages Plos Biology 13(4):e1002104-PMID:25853342
2014San Millan, A., Pena-Miller, R., Toll-Riera, M., Halbert, Z. V., McLean, A. R., Cooper, B. S., MacLean, R. C. (2014) Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids Nature Communications 5():5208-5208PMID:25302567
2014Mora, Yolanda, Diaz, Rafael, Vargas-Lagunas, Carmen, Peralta, Humberto, Guerrero, Gabriela, Aguilar, Alejandro, Encarnacion, Sergio, Girard, Lourdes, Mora, Jaime (2014) Nitrogen-Fixing Rhizobial Strains Isolated from Common Bean Seeds: Phylogeny, Physiology, and Genome Analysis Applied And Environmental Microbiology 80(18):5644-5654PMID:25002426
2014Arnoldini, Markus, Vizcarra, Ima Avalos, Pena-Miller, Rafael, Stocker, Nicolas, Diard, Mederic, Vogel, Viola, Beardmore, Robert E., Hardt, Wolf-Dietrich, Ackermann, Martin (2014) Bistable Expression of Virulence Genes in Salmonella Leads to the Formation of an Antibiotic-Tolerant Subpopulation Plos Biology 12(8):e1001928-PMID:25136970
2014Garcia-Garcia, J.D., Girard Cuesy, María de Lourdes, Hernández Delgado, Georgina, Saavedra, E., Pardo, J.P., Rodríguez-Zavala, J.S., Encalada, R., Reyes-Prieto, A., Mendoza-Cozatl, D.G., Moreno-Sánchez, R. (2014) Zn-bis-glutathionate is the best co-substrate of the monomeric phytochelatin synthase from the photosynthetic heavy metal-hyperaccumulator Euglena gracilis Metallomics 6(3):604-616PMID:24464102
2013Ramírez Yáñez, Mario, Guillén, G., Fuentes Membreño, Sara Isabel, Iñiguez Rabago, Luis Pedro, Aparicio Fabre, Rosaura, Zamorano Sánchez, David Salvador, Encarnación Guevara, Sergio Manuel, Panzeri, D., Castiglioni, B., Cremonesi, P., Strozzi, F., Stella, A., Girard Cuesy, María de Lourdes, Sparvoli, F., Hernández Delgado, Georgina (2013) Transcript profiling of common bean nodules subjected to oxidative stress Physiologia Plantarum 149(3):389-407PMID:23432573
2013Ramírez Yáñez, Mario, Flores-Pacheco, G., Reyes, J.L., Álvarez, A.L., Drevon, J.J., Girard Cuesy, María de Lourdes, Hernández Delgado, Georgina (2013) Two Common Bean Genotypes with Contrasting Response to Phosphorus Deficiency Show Variations in the microRNA 399-Mediated PvPHO2 Regulation within the PvPHR1 Signaling Pathway International Journal Of Molecular Sciences 14(4):8328-8344PMID:23591845
2013Aparicio Fabre, Rosaura, Guillén, G., Loredo, M., Arellano García, José de Jesús, Valdes López, Oswaldo, Ramírez Yáñez, Mario, Iñiguez Rabago, Luis Pedro, Panzeri, D., Castiglioni, B., Cremonesi, P., Strozzi, F., Stella, A., Girard Cuesy, María de Lourdes, Sparvoli, F., Hernández Delgado, Georgina (2013) Common bean (Phaseolus vulgaris L.) PvTIFY orchestrates global changes in transcript profile response to jasmonate and phosphorus deficiency Bmc Plant Biology 13():26-26PMID:23402340
2012Zamorano Sánchez, David Salvador, Reyes-González, A., Gómez Hernández, Nicolás, Rivera, P., Georgellis, D., Girard Cuesy, María de Lourdes (2012) FxkR Provides the Missing Link in the fixL-fixK Signal Transduction Cascade in Rhizobium etli CFN42 Molecular Plant-Microbe Interactions 25(11):1506-1517PMID:22809273
2012García-García, J.D., Olin-Sandoval, V., Saavedra, E., Girard Cuesy, María de Lourdes, Hernández Delgado, Georgina, Moreno-Sánchez, R. (2012) Sulfate uptake in photosynthetic Euglena gracilis. Mechanisms of regulation and contribution to cysteine homeostasis Biochimica Et Biophysica Acta-General Subjects 1820(10):1567-1575PMID:22609877
2012Talbi, C., Sánchez, C., Hidalgo-García, A., González, E.M., Arrese-Igor, C., Girard Cuesy, María de Lourdes, Bedmar, E.J., Delgado, M.J. (2012) Enhanced expression of Rhizobium etli cbb(3) oxidase improves drought tolerance of common bean symbiotic nitrogen fixation Journal Of Experimental Botany 63(14):5035-5043PMID:22511804
2011Cervantes de la Luz, Laura, Bustos Arcos, Virginia Patricia, Girard Cuesy, María de Lourdes, Santamaria Gutiérrez, Rosa Isela, Dávila Ramos, José Guillermo, Vinuesa Fleischmann, Pablo, Romero Camarena, David René, Brom Klanner, Susana (2011) The conjugative plasmid of a bean-nodulating Sinorhizobium fredii strain is assembled from sequences of two Rhizobium plasmids and the chromosome of a Sinorhizobium strain Bmc Microbiology 11(1):1-11PMID:21702991
2011Gómez Hernández, Nicolás, Reyes González, Alma Ruth, Sanchez, C., Pérez-Tejada Domínguez, Yolanda, Delgado, M.J., Girard Cuesy, María de Lourdes (2011) Regulation and Symbiotic Role of nirK and norC Expression in Rhizobium etli Molecular Plant-Microbe Interactions 24(2):233-245PMID:21043576
2011Díaz Mendez, Rafael, Vargas Lagunas, María del Carmen, Villalobos López, Miguel Angel, Peralta Díaz, Humberto, Pérez-Tejada Domínguez, Yolanda, Encarnación Guevara, Sergio Manuel, Girard Cuesy, María de Lourdes, Mora Celis, Jaime (2011) argC Orthologs from Rhizobiales Show Diverse Profiles of Transcriptional Efficiency and Functionality in Sinorhizobium meliloti Journal Of Bacteriology 193(2):460-472PMID:21075924
2010Talbi, C., Delgado, M. J., Girard, L., Ramirez-Trujillo, A., Caballero-Mellado, J., Bedmar, E. J. (2010) Burkholderia phymatum Strains Capable of Nodulating Phaseolus vulgaris Are Present in Moroccan Soils Applied And Environmental Microbiology 76(13):4587-4591PMID:20472732
2010Sanchez, Cristina, Gates, Andrew J., Meakin, Georgina E., Uchiumi, Toshiki, Girard, Lourdes, Richardson, David J., Bedmar, Eulogio J., Delgado, Maria J. (2010) Production of Nitric Oxide and Nitrosylleghemoglobin Complexes in Soybean Nodules in Response to Flooding Molecular Plant-Microbe Interactions 23(5):702-711PMID:20367476
2010Talbi, C., Sánchez, C., Girard Cuesy, María de Lourdes, Bedmar, E., Delgado, M.J. (2010) La sobreexpresión de la oxidasa cbb3 de Rhizobium etli incrementa la tolerancia de Phaseolus vulgaris a la sequía Avances en el metabolismo del Nitrógeno ():223-228
2009Onofre-Lemus, Janette, Hernandez-Lucas, Ismael, Girard, Lourdes, Caballero-Mellado, Jesus (2009) ACC (1-Aminocyclopropane-1-Carboxylate) Deaminase Activity, a Widespread Trait in Burkholderia Species, and Its Growth-Promoting Effect on Tomato Plants Applied And Environmental Microbiology 75(20):6581-6590PMID:19700546
2008Valdes-Lopez, Oswaldo, Arenas-Huertero, Catalina, Ramirez, Mario, Girard, Lourdes, Sanchez, Federico, Vance, Carroll P., Reyes, Jose Luis, Hernandez, Georgina (2008) Essential role of MYB transcription factor: PvPHR1 and microRNA: PvmiR399 in phosphorus-deficiency signalling in common bean roots Plant Cell And Environment 31(12):1834-1843PMID:18771575
2008Vargas Lagunas, María del Carmen, Villalobos, M.A., Díaz Mendez, Rafael, Flores, M.A., Contreras Martínez, Sandra, Encarnación Guevara, Sergio Manuel, Pérez-Tejada Domínguez, Yolanda, Dunn, Michael Frederick, Girard Cuesy, María de Lourdes, Mora Celis, Jaime (2008) Comparative Analysis of ArgC protein expression in Rhizobium species Current Plant Science and Biotechnology. Agriculture Biological Nitrogen Fixation, Sustainable Agriculture and the Environment 42(0):239-240
2007Granados Baeza, Manuel Jesús, Gómez Hernández, Nicolás, Mora, Yolanda, Delgado, M.J., Romero Camarena, David René, Girard Cuesy, María de Lourdes (2007) Novel reiterated Fnr-type proteins control the production of the symbiotic terminal oxidase cbb(3) in Rhizobium etli CFN42 Molecular Plant-Microbe Interactions 20(10):1241-1249PMID:17918626
2007Flores López, Margarita, Morales Reyes, Lucía Guadalupe, Gonzaga Jáuregui, Claudia Gabriela, Domínguez Vidaña, Rocío, Zepeda Mendoza, Cinthya Jeanette, Yáñez Cuna, Jorge Omar, Gutiérrez Arcelus, María, Lemus Vergara, Tzitziki Janik, Valle García, David, Ávila Arcos, María del Carmen, Blanco Melo, Daniel, Medina Ruiz, Sofía, Meza Sosa, Karla Fabiola, Ayala Ortega, Erandi, García Alonso, Delfino, Bustos Arcos, Virginia Patricia, González Zúñiga, Víctor Manuel, Girard Cuesy, María de Lourdes, Tusie-Luna, T., Dávila Ramos, José Guillermo, Palacios de la Lama, Rafael (2007) Recurrent DNA inversion rearrangements in the human genome Proceedings Of The National Academy Of Sciences Of The United States Of America 104(15):6099-6106PMID:17389356
2005Bueno, E., Gomez-Hernandez, Nicolas, Girard, L, Bedmar, E.J., Delgado, M.J. (2005) Function of the Rhizobium etli CFN42 nirK gene in nitrite metabolism BIOCHEMICAL SOCIETY TRANSACTIONS 33(1):162-163PMID:15667294
2005Vargas Lagunas, María del Carmen, Encarnación Guevara, Sergio Manuel, Girard Cuesy, María de Lourdes, Reyes Pérez, Agustín, Pérez-Tejada Domínguez, Yolanda, Mora Celis, Jaime (2005) Characterization of the alternative protection programs against oxidative-stress in free life and simbiosis from Rhizobium etli Current Plant Science and Biotechnology. Agriculture Biological Nitrogen Fixation, Sustainable Agriculture and the Environment 41():331-
2004Brom Klanner, Susana, Girard Cuesy, María de Lourdes, Tun Garrido, Cristina Soleda, García de los Santos, Alejandro, Bustos Arcos, Virginia Patricia, González Zúñiga, Víctor Manuel, Romero Camarena, David René (2004) Transfer of the symbiotic plasmid of Rhizobium etli CFN42 requires cointegration with p42a, which may be mediated by site-specific recombination Journal Of Bacteriology 186(22):7538-7548PMID:15516565
2004Vargas, M. del C., Encarnacin, S., Girard, M. de L., Reyes, A., Mora, Y., Mora, J. (2004) Physiological and proteome characterizations of oxidative-stress response in Rhizobium etli during free life and symbiosis with Phaseolus vulgaris. MOLECULAR & CELLULAR PROTEOMICS 3(10, S):160-160
2003González Zúñiga, Víctor Manuel, Bustos Arcos, Virginia Patricia, Ramírez Romero, Miguel Ángel, Medrano Soto, Luis Arturo, Salgado Osorio, Heladia, Hernández González, Ismael Luis, Hernández Celis, Juan Carlos, Quintero Hernández, Verónica, Moreno Hagelsieb, Gabriel, Girard Cuesy, María de Lourdes, Rodríguez Sánchez, Oscar, Flores López, Margarita, Cevallos Gaos, Miguel Ángel Carlos, Collado Vides, Pedro Julio, Romero Camarena, David René, Dávila Ramos, José Guillermo (2003) The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments. Genome Biology 4(6):R36-PMID:12801410
2002Brom Klanner, Susana, Girard Cuesy, María de Lourdes, García de los Santos, Alejandro, Sanjuan-Pinilla, J.M., Olivares, J., Sanjuan, J. (2002) Conservation of plasmid-encoded traits among bean-nodulating Rhizobium species Applied And Environmental Microbiology 68(5):2555-2561PMID:11976134
2001López, O., Morera, C., Miranda-Ríos, J., Girard Cuesy, María de Lourdes, Romero Camarena, David René, Soberón Chávez, Mario (2001) Regulation of gene expression in response to oxygen in Rhizobium etli: Role of FnrN in fixNOQP expression and in symbiotic nitrogen fixation Journal Of Bacteriology 183(24):6999-7006PMID:11717256
2000Girard Cuesy, María de Lourdes, Brom Klanner, Susana, Dávalos Rodríguez, Araceli Elvira, López, O., Soberón Chávez, Mario, Romero Camarena, David René (2000) Differential regulation of fixN-reiterated genes in Rhizobium etli by a novel fixL-fixK-cascade Molecular Plant-Microbe Interactions 13(12):1283-1292PMID:11106020
2000Reyes, J.D., Tabche, M.L., Morera, C., Girard Cuesy, María de Lourdes, Romero Camarena, David René, Krol, E., Miranda, J., Soberón Chávez, Mario (2000) Expression pattern of Rhizobium etli ccmIEFH genes involved in c-type cytochrome maturation Gene 250(1-2):149-157PMID:10854788
1999Soberon, M, Lopez, O, Morera, C, Girard, MD, Tabche, ML, Miranda, J (1999) Enhanced nitrogen fixation in a Rhizobium etli ntrC mutant that overproduces the Bradyrhizobium japonicum symbiotic terminal oxidase cbb(3) Applied And Environmental Microbiology 65(5):2015-2019PMID:10223993
1998Flores, M, Mavingui, P, Girard, L, Perret, X, Broughton, WJ, Martinez-Romero, E, Davila, G, Palacios, R (1998) Three replicons of Rhizobium sp. strain NGR234 harbor symbiotic gene sequences Journal Of Bacteriology 180(22):6052-6053PMID:9811668
1997RamirezRomero, MA, Bustos, P, Girard, L, Rodriguez, O, Cevallos, MA, Davila, G (1997) Sequence, localization and characteristics of the replicator region of the symbiotic plasmid of Rhizobium etli MICROBIOLOGY-SGM 143(8):2825-2831PMID:9274036
1996Girard, L, Valderrama, B, Palacios, R, Romero, D, Davila, G (1996) Transcriptional activity of the symbiotic plasmid of Rhizobium etli is affected by different environmental conditions MICROBIOLOGY-SGM 142(10):2847-2856
1996Valderrama, B, Davalos, A, Girard, L, Morett, E, Mora, J (1996) Regulatory proteins and cis-acting elements involved in the transcriptional control of Rhizobium etli reiterated nifH genes Journal Of Bacteriology 178(11):3119-3126PMID:8655489
1995ROMERO, D, MARTINEZSALAZAR, J, GIRARD, L, BROM, S, DAVILA, G, PALACIOS, R, FLORES, M, RODRIGUEZ, C (1995) DISCRETE AMPLIFIABLE REGIONS (AMPLICONS) IN THE SYMBIOTIC PLASMID OF RHIZOBIUM-ETLI CFN42 Journal Of Bacteriology 177(4):973-980PMID:7860608
1993Flores López, Margarita, Brom Klanner, Susana, Stepkowsky, Tomász, Girard Cuesy, María de Lourdes, Dávila Ramos, José Guillermo, Romero Camarena, David René, Palacios de la Lama, Rafael (1993) GENE AMPLIFICATION IN RHIZOBIUM - IDENTIFICATION AND INVIVO CLONING OF DISCRETE AMPLIFIABLE DNA REGIONS (AMPLICONS) FROM RHIZOBIUM-LEGUMINOSARUM BIOVAR PHASEOLI Proceedings Of The National Academy Of Sciences Of The United States Of America 90(11):4932-4936PMID:8506337
1991MARTINEZSALAZAR, JM, ROMERO, D, GIRARD, MD, DAVILA, G (1991) MOLECULAR-CLONING AND CHARACTERIZATION OF THE RECA GENE OF RHIZOBIUM-PHASEOLI AND CONSTRUCTION OF RECA MUTANTS Journal Of Bacteriology 173(10):3035-3040PMID:2022610
1991GIRARD, MD, FLORES, M, BROM, S, ROMERO, D, PALACIOS, R, DAVILA, G (1991) STRUCTURAL COMPLEXITY OF THE SYMBIOTIC PLASMID OF RHIZOBIUM-LEGUMINOSARUM BV PHASEOLI Journal Of Bacteriology 173(8):2411-2419PMID:2013564
1991ROMERO, D, BROM, S, MARTINEZSALAZAR, J, GIRARD, MD, PALACIOS, R, DAVILA, G (1991) AMPLIFICATION AND DELETION OF A NOD-NIF REGION IN THE SYMBIOTIC PLASMID OF RHIZOBIUM-PHASEOLI Journal Of Bacteriology 173(8):2435-2441PMID:2013567
1991BROM, S, DELOSSANTOS, AG, DELOURDESGIRARD, M, DAVILA, G, PALACIOS, R, ROMERO, D (1991) HIGH-FREQUENCY REARRANGEMENTS IN RHIZOBIUM-LEGUMINOSARUM BV. PHASEOLI PLASMIDS Journal Of Bacteriology 173(3):1344-1346PMID:1991727
1985Quinto, Carmen, de la Vega, Humberto, Flores López, Margarita, Leemans, J., Cevallos Gaos, Miguel Ángel Carlos, Pardo Galván, Marco Aurelio, Azpiroz, Ricardo, Girard Cuesy, María de Lourdes, Calva Mercado, Edmundo, Palacios de la Lama, Rafael (1985) NITROGENASE REDUCTASE - A FUNCTIONAL MULTIGENE FAMILY IN RHIZOBIUM-PHASEOLI Proceedings Of The National Academy Of Sciences Of The United States Of America 82(4):1170-1174PMID:16593543