Alfredo Cruz-Ramírez

Alfredo Cruz-Ramírez
Center for Research and Advanced Studies of the National Polytechnic Institute | Cinvestav · LANGEBIO - Laboratorio Nacional de Genómica para la Biodiversidad-U.G.A.

PhD

About

98
Publications
23,666
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3,859
Citations
Additional affiliations
June 2013 - present
May 2013 - May 2016
Center for Research and Advanced Studies of the National Polytechnic Institute
Position
  • Profesor Cinvestav 2C
January 2012 - present
Utrecht University

Publications

Publications (98)
Article
Fermentation is a biochemical process used by humans since thousands of years ago. Currently this process is crucial for the production of diverse foods and beverages worldwide. Bacteria, yeasts and other fungi are reported as pivotal for different fermentation processes and pulque fermentation is not the exception. Historically most of the papers...
Article
Full-text available
Background: Limb regeneration in the axolotl is achieved by epimorphosis, thus depending on the blastema formation, a mass of progenitor cells capable of proliferating and differentiating to recover all lost structures functionally. During regeneration, the blastema cells accelerate the cell cycle and duplicate its genome, which is inherently diff...
Preprint
Transposable elements and other repetitive elements are silenced by the RNA-directed DNA methylation pathway (RdDM). In RdDM, POLIV-derived transcripts are converted into double stranded RNA (dsRNA) by the activity of RDR2 and subsequently processed into 24 nucleotide short interfering RNAs (24-nt siRNAs) by DCL3. 24-nt siRNAs are recruited by AGO4...
Article
Full-text available
PrimPol is a novel Primase–Polymerase that synthesizes RNA and DNA primers de novo a nd extents from these primers as a DNA polymerase. Animal PrimPol is involved in nuclear and mitochondrial DNA replication by virtue of its translesion DNA synthesis (TLS) and repriming activities. Here we report that the plant model Arabidopsis thaliana encodes a...
Article
Full-text available
Lateral root (LR) formation is an example of a plant post-embryonic organogenesis event. LRs are issued from non-dividing cells entering consecutive steps of formative divisions, proliferation and elongation. The chromatin remodeling protein PICKLE (PKL) negatively regulates auxin-mediated LR formation through a mechanism that is not yet known. Her...
Article
Full-text available
The remarkable regenerative capabilities of the salamander Ambystoma mexicanum have turned it into one of the principal models to study limb regeneration. During this process, a mass of low differentiated and highly proliferative cells, called blastema, propagates to reestablish the lost tissue in an accelerated way. Such a process implies the repl...
Article
Full-text available
Ferns are a representative clade in plant evolution although underestimated in the genomic era. Ceratopteris richardii is an emergent model for developmental processes in ferns, yet a complete scheme of the different growth stages is necessary. Here, we present a developmental analysis, at the tissue and cellular levels, of the first shoot-borne ro...
Article
The biggest non-tree perennial plant species endemic to Mexico were called metl in the Nahua culture; during colonial times, renamed with the Antillean word maguey. Carl von Linné finally renamed them as Agave, a Greek-Latin root word meaning admirable. Since pre-Columbian times, one of the major products obtained from some Agave species is the fer...
Article
Full-text available
Ambystoma mexicanum (axolotl) has been one of the major experimental models for the study of regeneration during the past 100 years. Axolotl limb regeneration takes place through a multi-stage and complex developmental process called epimorphosis that involves diverse events of cell reprogramming. Such events start with dedifferentiation of somatic...
Conference Paper
Full-text available
Plant hormones are master regulators of developmental and genetic mechanisms to deal with diverse environmental cues. Upon phosphate (Pi) limitation, vascular plants modify phytohormone metabolism to coordinate diverse mechanisms to overcome such stress. However, the transcriptional program underlying the hormonal signaling in response to Pi scarci...
Article
Full-text available
The axolotl (Ambystoma mexicanum) is a caudate amphibian, which has an extraordinary ability to restore a wide variety of damaged structures by a process denominated epimorphosis. While the origin and potentiality of progenitor cells that take part during epimorphic regeneration are known to some extent, the metabolic changes experienced and their...
Article
Full-text available
Phosphate (Pi) is a pivotal nutrient that constraints plant development and productivity in natural ecosystems. Land colonization by plants, more than 470 million years ago, evolved adaptive mechanisms to conquer Pi-scarce environments. However, little is known about the molecular basis underlying such adaptations at early branches of plant phyloge...
Preprint
Full-text available
Phosphate (Pi) is a pivotal nutrient that constraints plant development and productivity in natural ecosystems. Land colonization by plants, more than 470 million years ago, evolved adaptive mechanisms to conquer Pi-scarce environments. However, little is known about the molecular basis underlying such adaptations at early branches of plant phyloge...
Preprint
Full-text available
Ferns are a representative clade in plant evolution although underestimated in the genomic era. Ceratopteris richardii is an emergent model for developmental processes in ferns, yet a complete scheme of the different growth stages is necessary. Here, we present a developmental analysis, at the tissue and cellular levels, of the first shoot-borne ro...
Preprint
Full-text available
The axolotl (Ambystoma mexicanum) is a caudate amphibian, which has an extraordinary ability to restore a wide variety of damaged structures by a process denominated epimorphosis. While the origin and potentiality of progenitor cells that take part during epimorphic regeneration are known to some extent, the metabolic changes experienced and their...
Preprint
Full-text available
Metamorphosis is a postembryonic developmental process that involves morphophysiological and behavioral changes, allowing organisms to adapt into a novel environment. In some amphibians, aquatic organisms undergo metamorphosis to adapt in a terrestrial environment. These organisms experience major changes in their circulatory, respiratory, digestiv...
Preprint
Some of the biggest non-three plants endemic to Mexico were called metl in the Nahua culture. During colonial times they were renamed with the antillan word maguey . This was changed again by Carl von Linné who called them Agave (a greco-latin voice for admirable). For several Mexican prehispanic cultures, Agave species were not only considered as...
Article
Full-text available
Desert plants have developed mechanisms for adapting to hostile desert conditions, yet these mechanisms remain poorly understood. Here, we describe two unique modes used by desert date palms (Phoenix dactylifera L.) to protect their meristematic tissues during early organogenesis. We used X-ray micro-computed tomography combined with high-resolutio...
Preprint
Full-text available
Lateral root (LR) formation is an example of plant post-embryonic organogenesis event. LRs are issued from non-dividing cells entering consecutive steps of formative divisions, proliferation and elongation. The chromatin remodeling protein PICKLE negatively regulates auxin-mediated LR formation through a mechanism that is not yet known. Here we sho...
Article
Full-text available
Comparative genomics has revealed that members of early divergent lineages of land plants share a set of highly conserved transcription factors (TFs) with flowering plants. While gene copy numbers have expanded through time, it has been predicted that diversification, co-option, and reassembly of gene regulatory networks implicated in development a...
Article
The plant hormone ethylene induces auxin biosynthesis and transport and modulates root growth and branching. However, its function on root stem cells and the identity of interacting factors for the control of meristem activity remains unclear. Genetic analysis for primary root growth in wild-type (WT) Arabidopsis thaliana seedlings and ethylene-rel...
Article
Full-text available
In the originally published version of this Article, the sequenced axolotl strain (the homozygous white mutant) was denoted as ‘D/D’ rather than ‘d/d’ in Fig. 1a and the accompanying legend, the main text and the Methods section. The original Article has been corrected online.
Article
Full-text available
Salamanders serve as important tetrapod models for developmental, regeneration and evolutionary studies. An extensive molecular toolkit makes the Mexican axolotl (Ambystoma mexicanum) a key representative salamander for molecular investigations. Here we report the sequencing and assembly of the 32-gigabase-pair axolotl genome using an approach that...
Article
The axolotl (Ambystoma mexicanum) is the vertebrate model system with the highest regeneration capacity. Experimental tools established over the past 100 years have been fundamental to start unraveling the cellular and molecular basis of tissue and limb regeneration. In the absence of a reference genome for the Axolotl, transcriptomic analysis beco...
Article
The Arabidopsis thaliana gene XYLEM NAC DOMAIN1 (XND1) is upregulated in xylem tracheary elements. Yet overexpression of XND1 blocks differentiation of tracheary elements. The molecular mechanism of XND1 action was investigated. Phylogenetic and motif analyses indicated that XND1 and its homologs are present only in angiosperms and possess a highly...
Article
Low inorganic phosphate (Pi) availability causes terminal differentiation of the root apical meristem (RAM), a phenomenon known as root meristem exhaustion or determined growth. Here, we report that the CLE14 peptide acts as a key player in this process. Low Pi stress induces iron mobilization in the RAM through the action of LPR1/LPR2, causing exp...
Data
Figure S1. Sequence and arrangement of the 3XM‐EZ2 bidirectional enhancer element. In Italics is represented minimum prom NOS at 5′ in opposite direction, and at the 3′ extreme the minimum promoter −46 S. In box, restriction sites EcoR1, Spe I and Bgl II. In bold enhancer 3XM‐EZ2. Underlined P1BS sites. Lowercase, attB1 and attB2 recombination site...
Article
Full-text available
Since the development of agriculture, humans have relied on the cultivation of plants to satisfy our increasing demand for food, natural products, and other raw materials. As we understand more about plant development, we can better manipulate plants to fulfill our particular needs. Auxins are a class of simple metabolites that coordinate many deve...
Article
Full-text available
Summary Phosphate (Pi)-deficient soils are a major limitant factor for crop production in many regions of the world. Despite that plants have innovated several developmental and biochemical strategies to deal with this stress, there are still massive extensions of land which combine several abiotic stresses, including phosphate starvation, that lim...
Chapter
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MicroRNAs (miRNAs) are endogenous non-coding RNAs that play important regulatory roles in animals and plants by targeting mRNAs for cleavage or transla‐ tional repression. Small RNAs are classified into different types by their biogenesis and mode of action, such as miRNAs, siRNAs, piRNAs, and snoRNAs. In the case of miRNAs, this specific type regu...
Article
Full-text available
Our concept of cell reprogramming and cell plasticity has evolved since John Gurdon transferred the nucleus of a completely differentiated cell into an enucleated Xenopus laevis egg thereby generating embryos which developed into tadpoles. More recently, induced expression of transcription factors, oct4, sox2, klf4 and c-myc has evidenced the plast...
Article
miRNAs are a class of small non-coding RNAs that regulate gene expression in eukaryotes. They are involved in the control of many plant developmental processes, including fruit development. The information available on miRNAs, related to expression, abundance, and conservation in several species, provides a new opportunity to study the role of miRN...
Article
Full-text available
The Anthurium is a plant genus belonging to the Araceae that comprises up to 800 species, which are native of an extensive tropical and subtropical area including several countries in America. Various species of Anthurium are grown and commercialized as potted plants, for landscaping or to produce flowers due to its great popularity as ornamental p...
Article
Full-text available
Phosphate (Pi) availability is a significant limiting factor for plant growth and productivity in both natural and agricultural systems. To cope with such limiting conditions, plants have evolved a myriad of developmental and biochemical strategies to enhance the efficiency of Pi acquisition and assimilation to avoid nutrient starvation. In the pas...
Article
Full-text available
Plant cells cannot rearrange their positions; therefore, sharp tissue boundaries must be accurately programmed. Movement of the cell fate regulator SHORT-ROOT from the stele to the ground tissue has been associated with transferring positional information across tissue boundaries. The zinc finger BIRD protein JACKDAW has been shown to constrain SHO...
Data
Primers used in FAMA-RBR study. DOI: http://dx.doi.org/10.7554/eLife.03271.017
Chapter
Full-text available
One of the biggest challenges in the coming years is to reduce the impact of chronic diseases. Unhealthy eating is an increasing problem and underlies much of the increase in mortality from chronic diseases that are occurring worldwide. Diets based on plant foods are strongly associated with reduced risks in major chronic diseases, but the constitu...
Article
Full-text available
Maintenance of mitotic cell clusters such as meristematic cells depends on their capacity to maintain the balance between cell division and cell differentiation necessary to control organ growth. In the Arabidopsis thaliana root meristem, the antagonistic interaction of two hormones, auxin and cytokinin, regulates this balance by positioning the tr...
Article
Full-text available
Author Summary In the plant Arabidposis thaliana, root meristems (in the growing tip of the root) contain slowly dividing cells that act as an organizing center for the root stem cells that surround them. This centre is called the quiescent centre (QC). In this study, we show that the slow rate of division in the QC is regulated by the interaction...
Article
Full-text available
Nuclear Factor Y (NF-Y) is a heterotrimeric complex formed by NF-YA/NF-YB/NF-YC subunits that binds to the CCAAT-box in eukaryotic promoters. In contrast to other organisms, in which a single gene encodes each subunit, in plants gene families of over 10 members encode each of the subunits. Here we report that five members of the Arabidopsis thalian...
Data
Full-text available
NF-YA expression level in transgenic Arabidopsis lines overexpressing NF-YAs . (PDF)
Data
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NF-YA overexpression delays dark-induced senescence. (PDF)
Data
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Motifs enrichment in deregulated genes in estradiol treated PXVE transgenic lines. (PDF)
Data
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Z-score for TATA-box and CCAAT-box motifs in the promoters of differentially expressed genes in PXVE transgenic lines. (PDF)
Data
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Motifs enrichment in the promoters of repressed genes in PXVE:NF-YA2SRDX lines that change in its PXVE:NF-YA2 counterpart, putative indirect targets. (PDF)
Data
Functional classification of differentially expressed transcripts in estradiol-inducible lines according to MAPMAN categories using the web-based tool Classification Superviewer. (XLS)
Data
Temporal and Spatial expression pattern of NF-YAs and miR169s in response to Pi availability. (PDF)
Data
Full-text available
qRT-PCR analysis of miR169nm overexpressing lines. (PDF)
Data
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Ectopic expression of NF-YAs and miR169nm affects seed weight and silique size. (PDF)
Data
Chlorophyll content of wild-type, P35S:NF-YA and P35S:miR169nm lines. (PDF)
Data
Full-text available
Dark-induced cell elongation is affected in NF-YA overexpressing plants. (PDF)