Alfredo Cruz

Scopus Publications

Multi-Omics Analyses on Maya-Land Tomatoes Shed Light on Plant Strategies to Thrive in High Temperatures
Luis F. Maceda‐López, Annie Espinal‐Centeno, Jose Juan Ordaz‐Ortiz, Alfredo Cruz‐Ramírez
Physiologia Plantarum, 2025
Heat stress limits tomato yield and quality. Deciphering the key genes and metabolites related to heat tolerance is essential for selecting tolerant varieties. In this study, we profiled the transcriptomes and metabolomes of roots and shoots in response to heat stress from a Maya‐land ecotype of heirloom tomato (Calkiní), which grows in lowlands and elevated temperatures. We compared them with those of another heirloom ecotype that grows in highlands and lower temperatures (Acaxochitlán). In our omics approach, several transcripts encode enzymes that participate in diverse biosynthetic pathways and produce differentially accumulated metabolites. Although both ecotypes display programs to deal with heat stress, the roots of the Calkiní ecotype showed an increased accumulation of diverse metabolites and the up‐regulation of key genes involved in molecular and physiological strategies to cope with heat stress. One of the key findings of this study is the elevated accumulation of transcripts and metabolites associated with phenylpropanoid and suberin biosynthesis in the heat‐resistant ecotype. Such increases correlate with substantial suberin deposition in the exodermis and endodermis of Calkiní roots, with enhanced gibberellin accumulation in the meristematic zone under heat stress. Additionally, we found differential expression and accumulation of metabolites and genes involved in the PA‐GAPC‐NFY heat stress tolerance pathway among both ecotypes. Our work strengthens the importance of studying Mexican native tomato varieties and ecotypes to identify traits that allow plants to cope with diverse biotic and abiotic stresses, specifically providing insights into the genetic and metabolic pathways linked to heat tolerance among ecotypes and tissues.
The MpANT-Auxin Loop Modulates Marchantia polymorpha Development
Dipp‐Álvarez Melissa, Lorenzo‐Manzanarez J. Luis, Flores‐Sandoval Eduardo, Espinal‐Centeno Annie, Méndez‐Álvarez Domingo, Fisher J. Tom, León‐Ruiz Jesús, Olvera‐Martínez Fernando, Bowman L. John, Arteaga‐Vázquez A. Mario, Alfredo Cruz‐Ramírez
Physiologia Plantarum, 2025
AINTEGUMENTA‐LIKE/PLETHORA/BABYBOOM (APB) genes are considered part of the ancestral developmental toolkit in land plants. In Arabidopsis thaliana, these transcription factors are induced by auxin and are primarily expressed in tissues with actively dividing cells, where they play essential roles in organ development. Marchantia polymorpha, a liverwort that diverged from A. thaliana early in embryophyte evolution, possesses a single APB ortholog, MpAINTEGUMENTA (MpANT), encoded in its genome. In this study, we aimed to characterize the function of MpANT. Analysis of a transcriptional fusion line indicates that MpANT is predominantly expressed in the meristematic region. We report that the MpANT promoter region contains several cis‐acting Auxin Responsive Elements (AREs) and demonstrate that its expression, which occurs predominantly in meristematic regions, is significantly altered by the addition of exogenous auxin and inhibition of auxin transport. These findings indicate that MpANT acts downstream of Auxin Response Factors (ARFs) and auxin signaling. Analyses of loss‐ and gain‐of‐function MpANT alleles highlight the importance of this transcription factor in meristem maintenance and cell proliferation. Additionally, we found that MpANT acts upstream of the auxin transporter MpPIN1 by influencing auxin distribution. Taken together, our findings reveal a feedforward regulatory loop involving auxin, MpANT, and MpPIN1 that is important for Marchantia development.
A Bacteriophage-Derived Primase-Helicase Orchestrates Plant Organellar DNA Replication
Carlos M. Morales‐Vázquez, Mayra A. Dagio‐Hernandez, Laura D. Camacho‐Manriquez, Antolin Peralta‐Castro, Claudia D. Raygoza, Diana Solano‐Argüello, Josue D. Mora‐Garduño, Rogelio Gonzalez‐Gonzalez, Humberto Herrera‐Ubaldo, Corina Díaz‐Quezada, Alfredo Cruz‐Ramírez, Stefan de Folter, José Antonio Pedroza‐García, Luis G. Brieba
Physiologia Plantarum, 2025
The mechanisms underlying the assembly and regulation of enzymatic complexes responsible for plant organellar DNA replication remain poorly characterized. Unlike the monophyletic origin of the gene products involved in animal mitochondrial replication, derived from T‐odd bacteriophages, plant organellar DNA replication relies on genes either unique to plants or with origins traceable to bacteria and bacteriophages. Here, we demonstrate that the bacteriophage‐related primase‐helicase from Arabidopsis thaliana (AtTwinkle) is essential for double‐stranded DNA unwinding. AtTwinkle functionally interacts with bacterial‐related organellar DNA polymerases (AtPolIs), which lack the ability to unwind large regions of dsDNA, coupling DNA unwinding to processive DNA synthesis at the leading strand of the replisome. Analysis of two T‐DNA insertion mutants of AtTwinkle reveals distinct phenotypic outcomes; these mutant lines are hereafter referred to as ph. The ph1 (−/−) mutant, which carries a T‐DNA insertion in the 5´ UTR region, is viable and exhibits no noticeable developmental differences compared to wild‐type plants. In contrast, the ph2 mutant, with a T‐DNA insertion in the 19th exon, displays embryo lethality. Despite these differences, both ph1 (−/−) and heterozygous ph2 (+/−) mutants show a reduction in organellar DNA copy numbers under non‐stress conditions and exhibit heightened sensitivity to DNA‐damaging agents. In summary, our findings demonstrate that AtTwinkle is essential for organellar DNA replication. The heightened sensitivity of insertion mutants to organelle‐specific genotoxic agents indicates that loss of AtTwinkle function reduces the availability of template DNA necessary for double‐strand break (DSB) repair. Collectively, our findings reveal that two proteins of distinct evolutionary origins—AtTwinkle and plant organellar DNA polymerases—coevolved to coordinate DNA replication in plant organelles.
A Strategy to Use Artificial MicroRNAs for Gene Silencing and Overcome (AmiGO)
Yujuan Du, Annie Espinal-Centeno, Ben Scheres, Mario A. Arteaga-Vázquez, Alfredo Cruz-Ramírez
Methods in Molecular Biology, 2025
Editorial: Molecular basis of stem cells underlying plant vitality
Chunli Chen, Alfredo Cruz-Ramirez, Yonghong Zhang, Masaki Ishikawa
Frontiers in Plant Science, 2024
Plant stem cells persisting in tissues throughout the plant's life are proliferative and undifferentiated cells and are crucial for growth and development. In embryogenesis, the fertilized egg cell, a totipotent stem cell, provides the cells that form the seedling. Postembryonically, pluripotent stem cells inhabit niches where they divide asymmetrically to selfrenew and to generate daughter cells, forming diverse plant tissues. Indeed, the adaptation capability of the plants towards environmental challenges relies on the preservation of plant stem cell niches. Moreover, physical damage often induces de novo formation of the stem cell niches in differentiated tissues, making it possible to regenerate organs from wounded parts or an entire plant body from a dissected tissue. Given their crucial roles in plant development and regeneration, it is imperative to elucidate the pivotal roles of stem cells on plant vitality at the molecular level. The research advancements, such as single-cell RNA sequencing, CRISPR-Case9 gene editing, live cell imaging, optical coherence tomography, bioinformatics and computational modeling, 3D printing and tissue engineering, and single-cell cloning techniques have contributed to study the roles of stem cells in plant development and stress response.A number of key factors crucial for the stem cell maintenance and homeostasis have been identified in plants, with ongoing efforts to clarify their regulatory systems. Notably, the homeodomain transcription factor WUSCHEL (WUS) and the class I KNOX transcription factor SHOOT MERSTEMLESS (STM) play essential roles in preserving pluripotent stem cells within the shoot apical meristem. WUS functions in the WUS-CLAVATA (WUS-CLV) pathway (Heidstra & Sabatini, 2014;Ma et al., 2019), a system crucial for maintaining the balance between self-renewal and differentiation of stem cells. STM, expressed throughout the shoot meristem, represses stem cell differentiation. These two transcription factors have been shown to interact, playing a significant role in the regulation of stem cell homeostasis. An AP2-family transcription factor PLETHORA (PLT), recognized as a master regulator in the root meristem, has been also shown to regulate de novo shoot regeneration (Kareem et al., 2015). Another transcriptional factor, a key regulator in regeneration rapidly induced upon wounding, is WOUND INDUCED DEDIFFERENATION 1(WIND1) (Iwase et al., 2011). Additionally, the plant hormones, including auxin, cytokinin, jasmonic acid, and gibberellins, environmental signals, light (in transmitting light signals to regulate plant growth), and temperature (affecting cell division and differentiation) are also marked as significant factors in stem cell homeostasis.Recent studies have shown that JA levels are elevated upon injury, and the expression of ERF109 and ERF115 was induced, but still, the role of JA is considered situation-dependent as JA has also been reported to inhibit callus formation after hypocotyl cutting (Ikeuchi et al., 2017;Zhang et al., 2019). Therefore, the underlying molecular events behind cell cycle activation and stem cell fate transition remain elusive.
RETINOBLASTOMA-RELATED interactions with key factors of the RNA-directed DNA methylation (RdDM) pathway and its influence on root development
Jesús León-Ruiz, Annie Espinal-Centeno, Ikram Blilou, Ben Scheres, Mario Arteaga-Vázquez, Alfredo Cruz-Ramírez
Planta, 2023
Predicted landscape of RETINOBLASTOMA-RELATED LxCxE-mediated interactions across the Chloroplastida
Jesús A. León‐Ruiz, Alfredo Cruz Ramírez
Plant Journal, 2022
The colonization of land by a single streptophyte algae lineage some 450 million years ago has been linked to multiple key innovations such as 3D growth, alternation of generations, the presence of stomata, as well as innovations inherent to the birth of major plant lineages, such as the origins of vascular tissues, roots, seeds, and flowers. Multicellularity, which evolved multiple times in the Chloroplastida coupled with precise spatiotemporal control of proliferation and differentiation were instrumental for the evolution of these traits. RETINOBLASTOMA-RELATED (RBR), the plant homolog of the metazoan Retinoblastoma protein (pRB), is a highly conserved and multifunctional core cell cycle regulator that has been implicated in the evolution of multicellularity in the green lineage as well as in plant multicellularity-related processes such as proliferation, differentiation, stem cell regulation and asymmetric cell division. RBR fulfills these roles through context-specific protein-protein interactions (PPI) with proteins containing the Leu-x-Cys-x-Glu (LxCxE) short-linear motif (SLiM), however, how RBR-LxCxE interactions have changed throughout major innovations in the Viridiplantae kingdom is a question that remains unexplored. Here, we employ an in silico evo-devo approach to predict and analyze potential RBR-LxCxE interactions in different representative species of key Chloroplastida lineages, providing a valuable resource for deciphering RBR-LxCxE multiple functions. Furthermore, our analyses suggest that RBR-LxCxE interactions are an important component of RBR functions and that interactions with chromatin modifiers/remodelers, DNA replication and repair machinery are highly conserved throughout the Viridiplantae, while LxCxE interactions with transcriptional regulators likely diversified throughout the water-to-land transition.
Cancer in Amphibia, a rare phenomenon?
Esteban Torres‐Dimas, Alfredo Cruz‐Ramírez, Rosa María Bermúdez‐Cruz
Cell Biology International, 2022
Compared to other animals, the spontaneous occurrence of tumors in wild amphibians is relatively rare, generally limited to specific populations or species. The number of reports of spontaneous tumors in amphibians known up to 1986 was 491 cases in anurans and about 253 cases in urodeles. Similarly, there have been many, unsuccessful attempts to chemically or biologically induce tumors in amphibians. With these considerations, it is inevitable to wonder: do urodeles and anurans have an inherent resistance to cancer? Here, we review the spontaneous and induced occurrence of tumors in amphibians in a timeline, as well as failed attempts to induce tumors in these amphibians. Indeed, recent studies seem to indicate that there is a relationship between regeneration and cancer because regenerating tissues seem to resist tumorigenesis, as opposed to nonregenerative tissues of the same amphibian models. Although the mechanisms that allow regenerating tissues to resist tumorigenesis have not been elucidated, it is worth to note that, in addition to the apparent relationship between regeneration and cancer, amphibians possess characteristics that could contribute to their ability to resist the development of neoplastic events. The implications of these features in cancer susceptibility are discussed.
Construction of the axolotl cell landscape using combinatorial hybridization sequencing at single-cell resolution
Fang Ye, Guodong Zhang, Weigao E., Haide Chen, Chengxuan Yu, Lei Yang, Yuting Fu, Jiaqi Li, Sulei Fu, Zhongyi Sun, Lijiang Fei, Qile Guo, Jingjing Wang, Yanyu Xiao, Xinru Wang, Peijing Zhang, Lifeng Ma, Dapeng Ge, Suhong Xu, Juan Caballero-Pérez, Alfredo Cruz-Ramírez, Yincong Zhou, Ming Chen, Ji-Feng Fei, Xiaoping Han, Guoji Guo
Nature Communications, 2022
The Mexican axolotl (Ambystoma mexicanum) is a well-established tetrapod model for regeneration and developmental studies. Remarkably, neotenic axolotls may undergo metamorphosis, a process that triggers many dramatic changes in diverse organs, accompanied by gradually decline of their regeneration capacity and lifespan. However, the molecular regulation and cellular changes in neotenic and metamorphosed axolotls are still poorly investigated. Here, we develop a single-cell sequencing method based on combinatorial hybridization to generate a tissue-based transcriptomic landscape of the neotenic and metamorphosed axolotls. We perform gene expression profiling of over 1 million single cells across 19 tissues to construct the first adult axolotl cell landscape. Comparison of single-cell transcriptomes between the tissues of neotenic and metamorphosed axolotls reveal the heterogeneity of non-immune parenchymal cells in different tissues and established their regulatory network. Furthermore, we describe dynamic gene expression patterns during limb development in neotenic axolotls. This system-level single-cell analysis of molecular characteristics in neotenic and metamorphosed axolotls, serves as a resource to explore the molecular identity of the axolotl and facilitates better understanding of metamorphosis.
Yeast and nonyeast fungi: the hidden allies in pulque fermentation
Carolina Rocha-Arriaga, Alfredo Cruz-Ramirez
Current Opinion in Food Science, 2022
Transcriptional analysis of Ceratopteris richardii young sporophyte reveals conservation of stem cell factors in the root apical meristem
Alejandro Aragón-Raygoza, Luis Herrera-Estrella, Alfredo Cruz-Ramírez
Frontiers in Plant Science, 2022
Evidence of requirement for homologous-mediated DNA repair during Ambystoma mexicanum limb regeneration
Ulises Omar García‐Lepe, Esteban Torres‐Dimas, Annie Espinal‐Centeno, Alfredo Cruz‐Ramírez, Rosa María Bermúdez‐Cruz
Developmental Dynamics, 2022
Arabidopsis thaliana PrimPol is a primase and lesion bypass DNA polymerase with the biochemical characteristics to cope with DNA damage in the nucleus, mitochondria, and chloroplast
Paola L. García-Medel, Antolín Peralta-Castro, Noe Baruch-Torres, Alma Fuentes-Pascacio, José A. Pedroza-García, Alfredo Cruz-Ramirez, Luis G. Brieba
Scientific Reports, 2021
DNA repair during regeneration in Ambystoma mexicanum
Ulises Omar García‐Lepe, Alfredo Cruz‐Ramírez, Rosa María Bermúdez‐Cruz
Developmental Dynamics, 2021
Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis
Krisztina Ötvös, Pál Miskolczi, Peter Marhavý, Alfredo Cruz-Ramírez, Eva Benková, Stéphanie Robert, László Bakó
International Journal of Molecular Sciences, 2021
Vision, challenges and opportunities for a plant cell atlas
, Jahed Ahmed, Oluwafemi Alaba, Gazala Ameen, Vaishali Arora, Mario A Arteaga-Vazquez, Alok Arun, Julia Bailey-Serres, Laura E Bartley, George W Bassel, Dominique C Bergmann, Edoardo Bertolini, Kaushal Kumar Bhati, Noel Blanco-Touriñán, Steven P Briggs, Javier Brumos, Benjamin Buer, Adrien Burlaocot, Sergio Alan Cervantes-Pérez, Sixue Chen, Bruno Contreras-Moreira, Francisco J CORPAS, Alfredo Cruz-Ramirez, Cesar L Cuevas-Velazquez, Josh T Cuperus, Lisa I David, Stefan de Folter, Peter H Denolf, Pingtao Ding, William P Dwyer, Matthew MS Evans, Nancy George, Pubudu P Handakumbura, Maria J Harrison, Elizabeth S Haswell, Venura Herath, Yuling Jiao, Robert E Jinkerson, Uwe John, Sanjay Joshi, Abhishek Joshi, Lydia-Marie Joubert, Ramesh Katam, Harmanpreet Kaur, Yana Kazachkova, Sunil K Kenchanmane Raju, Mather A Khan, Rajdeep Khangura, Ajay Kumar, Arun Kumar, Pankaj Kumar, Pradeep Kumar, Dhruv Lavania, Tedrick Thomas Salim Lew, Mathew G Lewsey, Chien-Yuan Lin, Dianyi Liu, Le Liu, Tie Liu, Ansul Lokdarshi, Ai My Luong, Iain C Macaulay, Sakil Mahmud, Ari Pekka Mähönen, Kamal Kumar Malukani, Alexandre P Marand, Carly A Martin, Claire D McWhite, Devang Mehta, Miguel Miñambres Martín, Jenny C Mortimer, Lachezar A Nikolov, Tatsuya Nobori, Trevor M Nolan, Aaron J Ogden, Marisa S Otegui, Mark-Christoph Ott, José M Palma, Puneet Paul, Atique U Rehman, Maida Romera-Branchat, Luis C Romero, Ronelle Roth, Saroj K Sah, Rachel Shahan, Shyam Solanki, Bao-Hua Song, Rosangela Sozzani, Gary Stacey, Anna N Stepanova, Nicolas L Taylor, Marcela K Tello-Ruiz, Tuan M Tran, Rajiv Kumar Tripathi, Batthula Vijaya Lakshmi Vadde Vadde, Tamas Varga, Marija Vidovic, Justin W Walley, Zhiyong Wang, Renate A Weizbauer, James Whelan, Asela J Wijeratne, Tingting Xiang, Shouling Xu, Ramin Yadegari, Houlin Yu, Hai Ying Yuan, Fabio Zanini, Feng Zhao, Jie Zhu, Xiaohong Zhuang, Suryatapa Ghosh Jha, Alexander T Borowsky, Benjamin J Cole, Noah Fahlgren, Andrew Farmer, Shao-shan Carol Huang, Purva Karia, Marc Libault, Nicholas J Provart, Selena L Rice, Maite Saura-Sanchez, Pinky Agarwal, Amir H Ahkami, Christopher R Anderton, Steven P Briggs, Jennifer AN Brophy, Peter Denolf, Luigi F Di Costanzo, Moises Exposito-Alonso, Stefania Giacomello, Fabio Gomez-Cano, Kerstin Kaufmann, Dae Kwan Ko, Sagar Kumar, Andrey V Malkovskiy, Naomi Nakayama, Toshihiro Obata, Marisa S Otegui, Gergo Palfalvi, Elsa H Quezada-Rodríguez, Rajveer Singh, R Glen Uhrig, Jamie Waese, Klaas Van Wijk, R Clay Wright, David W Ehrhardt, Kenneth D Birnbaum, Seung Y Rhee
Elife, 2021
Conservation analysis of core cell cycle regulators and their transcriptional behavior during limb regeneration in Ambystoma mexicanum
Annie Espinal-Centeno, Melissa Dipp-Álvarez, Carlos Saldaña, Laszlo Bako, Alfredo Cruz-Ramírez
Mechanisms of Development, 2020
Development and cell cycle activity of the root apical meristem in the fern ceratopteris richardii
Alejandro Aragón-Raygoza, Alejandra Vasco, Ikram Blilou, Luis Herrera-Estrella, Alfredo Cruz-Ramírez
Genes, 2020
Deep microbial community profiling along the fermentation process of pulque, a biocultural resource of Mexico
Carolina Rocha-Arriaga, Annie Espinal-Centeno, Shamayim Martinez-Sánchez, Juan Caballero-Pérez, Luis D. Alcaraz, Alfredo Cruz-Ramírez
Microbiological Research, 2020
Functional Characterization of the Lin28/let-7 Circuit During Forelimb Regeneration in Ambystoma mexicanum and Its Influence on Metabolic Reprogramming
Hugo Varela-Rodríguez, Diana G. Abella-Quintana, Annie Espinal-Centeno, Luis Varela-Rodríguez, David Gomez-Zepeda, Juan Caballero-Pérez, Paola L. García-Medel, Luis G. Brieba, José J. Ordaz-Ortiz, Alfredo Cruz-Ramirez
Frontiers in Cell and Developmental Biology, 2020
Transcriptional and morpho-physiological responses of Marchantia polymorpha upon phosphate starvation
Félix Rico-Reséndiz, Sergio Alan Cervantes-Pérez, Annie Espinal-Centeno, Melissa Dipp-Álvarez, Araceli Oropeza-Aburto, Enrique Hurtado-Bautista, Andrés Cruz-Hernández, John L. Bowman, Kimitsune Ishizaki, Mario A. Arteaga-Vázquez, Luis Herrera-Estrella, Alfredo Cruz-Ramírez
International Journal of Molecular Sciences, 2020
Multi-organ transcriptomic landscape of Ambystoma velasci metamorphosis
Janet Palacios-Martinez, Juan Caballero-Perez, Annie Espinal-Centeno, Gilberto Marquez-Chavoya, Hilda Lomeli, Enrique Salas-Vidal, Denhi Schnabel, Jesus Chimal-Monroy, Alfredo Cruz-Ramirez
Developmental Biology, 2020
CONSTITUTIVE TRIPLE RESPONSE1 and PIN2 act in a coordinate manner to support the indeterminate root growth and meristem cell proliferating activity in Arabidopsis seedlings
Alejandro Méndez-Bravo, León Francisco Ruiz-Herrera, Alfredo Cruz-Ramírez, Plinio Guzman, Miguel Martínez-Trujillo, Randy Ortiz-Castro, José López-Bucio
Plant Science, 2019
A phylogenetic study of the ANT family points to a preANT gene as the ancestor of basal and euANT transcription factors in land plants
Melissa Dipp-Álvarez, Alfredo Cruz-Ramírez
Frontiers in Plant Science, 2019
Transcriptional profiling of the CAM plant Agave salmiana reveals conservation of a genetic program for regeneration
Sergio Alan Cervantes-Pérez, Annie Espinal-Centeno, Araceli Oropeza-Aburto, Juan Caballero-Pérez, Francisco Falcon, Alejandro Aragón-Raygoza, Lino Sánchez-Segura, Luis Herrera-Estrella, Andrés Cruz-Hernández, Alfredo Cruz-Ramírez
Developmental Biology, 2018
The axolotl genome and the evolution of key tissue formation regulators
Sergej Nowoshilow, Siegfried Schloissnig, Ji-Feng Fei, Andreas Dahl, Andy W. C. Pang, Martin Pippel, Sylke Winkler, Alex R. Hastie, George Young, Juliana G. Roscito, Francisco Falcon, Dunja Knapp, Sean Powell, Alfredo Cruz, Han Cao, Bianca Habermann, Michael Hiller, Elly M. Tanaka, Eugene W. Myers
Nature, 2018
Transcriptional landscapes of Axolotl (Ambystoma mexicanum)
Juan Caballero-Pérez, Annie Espinal-Centeno, Francisco Falcon, Luis F. García-Ortega, Everardo Curiel-Quesada, Andrés Cruz-Hernández, Laszlo Bako, Xuemei Chen, Octavio Martínez, Mario Alberto Arteaga-Vázquez, Luis Herrera-Estrella, Alfredo Cruz-Ramírez
Developmental Biology, 2018
XYLEM NAC DOMAIN1, an angiosperm NAC transcription factor, inhibits xylem differentiation through conserved motifs that interact with RETINOBLASTOMA-RELATED
Chengsong Zhao, Theres Lasses, Laszlo Bako, Danyu Kong, Bingyu Zhao, Bidisha Chanda, Aureliano Bombarely, Alfredo Cruz-Ramírez, Ben Scheres, Amy M. Brunner, Eric P. Beers
New Phytologist, 2017
Phosphate Starvation-Dependent Iron Mobilization Induces CLE14 Expression to Trigger Root Meristem Differentiation through CLV2/PEPR2 Signaling
Dolores Gutiérrez-Alanís, Lenin Yong-Villalobos, Pedro Jiménez-Sandoval, Fulgencio Alatorre-Cobos, Araceli Oropeza-Aburto, Javier Mora-Macías, Federico Sánchez-Rodríguez, Alfredo Cruz-Ramírez, Luis Herrera-Estrella
Developmental Cell, 2017
The Role of microRNAs in Animal Cell Reprogramming
María Concepción Cruz-Santos, Alejandro Aragón-Raygoza, Annie Espinal-Centeno, Mario Arteaga-Vázquez, Andrés Cruz-Hernández, Laszlo Bako, Alfredo Cruz-Ramírez
Stem Cells and Development, 2016
MiRNAs analysis during prickly pear development
A. Cruz-Hernández, T. Escobar-Feregrino, R.G. Guevara-González, I. Torres-Pacheco, J. Caballero-Pérez, A. Cruz-Ramírez, L. Herrera-Estrella, M. Arteaga-Vázquez
Acta Horticulturae, 2016
Methylome analysis reveals an important role for epigenetic changes in the regulation of the Arabidopsis response to phosphate starvation
Lenin Yong-Villalobos, Sandra Isabel González-Morales, Kazimierz Wrobel, Dolores Gutiérrez-Alanis, Sergio Alan Cervantes-Peréz, Corina Hayano-Kanashiro, Araceli Oropeza-Aburto, Alfredo Cruz-Ramírez, Octavio Martínez, Luis Herrera-Estrella
Proceedings of the National Academy of Sciences of the United States of America, 2015
Arabidopsis BIRD zinc finger proteins jointly stabilize tissue boundaries by confining the cell fate regulator SHORT-ROOT and contributing to fate specification
Yuchen Long, Wouter Smet, Alfredo Cruz-Ramírez, Bas Castelijns, Wim de Jonge, Ari Pekka Mähönen, Benjamin P. Bouchet, Gabino Sanchez Perez, Anna Akhmanova, Ben Scheres, Ikram Blilou
Plant Cell, 2015
Irreversible fate commitment in the Arabidopsis stomatal lineage requires a FAMA and RETINOBLASTOMA-RELATED module
Juliana L Matos, On Sun Lau, Charles Hachez, Alfredo Cruz-Ramírez, Ben Scheres, Dominique C Bergmann
Elife, 2014
XErratum: A PLETHORA-auxin transcription module controls cell division plane rotation through MAP65 and CLASP (Cell (2013) 149 (383-396))
Pankaj Dhonukshe, Daan A. Weits, Alfredo Cruz-Ramirez, Eva E. Deinum, Simon H. Tindemans, Klementina Kakar, Kalika Prasad, Ari Pekka Mähönen, Chris Ambrose, Michiko Sasabe, Guy Wachsmann, Marijn Luijten, Tom Bennett, Yasunori Machida, Renze Heidstra, Geoffrey Wasteneys, Bela M. Mulder, Ben Scheres
Cell, 2013
A SCARECROW-RETINOBLASTOMA Protein Network Controls Protective Quiescence in the Arabidopsis Root Stem Cell Organizer
Alfredo Cruz-Ramírez, Sara Díaz-Triviño, Guy Wachsman, Yujuan Du, Mario Arteága-Vázquez, Hongtao Zhang, Rene Benjamins, Ikram Blilou, Anne B. Neef, Vicki Chandler, Ben Scheres
Plos Biology, 2013
RETINOBLASTOMA-RELATED protein stimulates cell differentiation in the Arabidopsis root meristem by interacting with cytokinin signaling
S. Perilli, J. M. Perez-Perez, R. Di Mambro, C. L. Peris, S. Diaz-Trivino, M. Del Bianco, E. Pierdonati, L. Moubayidin, A. Cruz-Ramirez, P. Costantino, B. Scheres, S. Sabatini
Plant Cell, 2013
Functional and Transcriptome Analysis Reveals an Acclimatization Strategy for Abiotic Stress Tolerance Mediated by Arabidopsis NF-YA Family Members
Marco Antonio Leyva-González, Enrique Ibarra-Laclette, Alfredo Cruz-Ramírez, Luis Herrera-Estrella
Plos One, 2012
Translational regulation of Arabidopsis XIPOTL1 is modulated by phosphocholine levels via the phylogenetically conserved upstream open reading frame 30
Fulgencio Alatorre-Cobos, Alfredo Cruz-Ramírez, Celine A. Hayden, Claudia-Anahí Pérez-Torres, Anne-Laure Chauvin, Enrique Ibarra-Laclette, Erika Alva-Cortés, Richard A. Jorgensen, Luis Herrera-Estrella
Journal of Experimental Botany, 2012
A bistable circuit involving SCARECROW-RETINOBLASTOMA integrates cues to inform asymmetric stem cell division
Alfredo Cruz-Ramírez, Sara Díaz-Triviño, Ikram Blilou, Verônica A. Grieneisen, Rosangela Sozzani, Christos Zamioudis, Pál Miskolczi, Jeroen Nieuwland, René Benjamins, Pankaj Dhonukshe, Juan Caballero-Pérez, Beatrix Horvath, Yuchen Long, Ari Pekka Mähönen, Hongtao Zhang, Jian Xu, James A.H. Murray, Philip N. Benfey, Laszlo Bako, Athanasius F.M. Marée, Ben Scheres
Cell, 2012
A PLETHORA-auxin transcription module controls cell division plane rotation through MAP65 and CLASP
Pankaj Dhonukshe, Daan A. Weits, Alfredo Cruz-Ramirez, Eva E. Deinum, Simon H. Tindemans, Klementina Kakar, Kalika Prasad, Ari Pekka Mähönen, Chris Ambrose, Michiko Sasabe, Guy Wachsmann, Marijn Luijten, Tom Bennett, Yasunori Machida, Renze Heidstra, Geoffrey Wasteneys, Bela M. Mulder, Ben Scheres
Cell, 2012
Molecular analysis of marigold (Tagetes erecta) APETALA2 in flower development
H. Alegría-Mundo, L. Yong, A. Cruz-Ramírez, L. Herrera-Estrella, A. Cruz-Hernández
Acta Horticulturae, 2012
Functional analysis of the Arabidopsis PLDZ2 promoter reveals an evolutionarily conserved low-Pi-responsive transcriptional enhancer element
Araceli Oropeza-Aburto, Alfredo Cruz-Ramírez, Gustavo J. Acevedo-Hernández, Claudia-Anahí Pérez-Torres, Juan Caballero-Pérez, Luis Herrera-Estrella
Journal of Experimental Botany, 2012
Effect of Nutrient Availability on Root System Development
Alfredo Cruz-Ramrez, Carlos Caldern-Vzquez, Luis Herrera-Estrella
Root Development, 2009
The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine environment
Luis David Alcaraz, Gabriela Olmedo, Germán Bonilla, René Cerritos, Gustavo Hernández, et al.
Proceedings of the National Academy of Sciences of the United States of America, 2008
Phosphate availability alters lateral root development in Arabidopsis by modulating auxin sensitivity via a mechanism involving the TIR1 auxin receptor
Claudia-Anahí Pérez-Torres, José López-Bucio, Alfredo Cruz-Ramírez, Enrique Ibarra-Laclette, Sunethra Dharmasiri, et al.
Plant Cell, 2008
Phospholipase DZ2 plays an important role in extraplastidic galactolipid biosynthesis and phosphate recycling in Arabidopsis roots
Alfredo Cruz-Ramírez, Araceli Oropeza-Aburto, Francisco Razo-Hernández, Enrique Ramírez-Chávez, Luis Herrera-Estrella
Proceedings of the National Academy of Sciences of the United States of America, 2006
Phosphate starvation induces a determinate developmental program in the roots of Arabidopsis thaliana
Lenin Sánchez-Calderón, José López-Bucio, Alejandra Chacón-López, Alfredo Cruz-Ramírez, Fernanda Nieto-Jacobo, et al.
Plant and Cell Physiology, 2005
The xipotl mutant of arabidopsis reveals a critical role for phospholipid metabolism in root system development and epidermal cell integrity
Alfredo Cruz-Ramírez, José López-Bucio, Gabriel Ramírez-Pimentel, Andrés Zurita-Silva, Lenin Sánchez-Calderon, et al.
Plant Cell, 2004
The role of nutrient availability in regulating root architecture
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