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1.  Root Architecture Diversity and Meristem Dynamics in Different Populations of Arabidopsis thaliana 
Arabidopsis thaliana has been an excellent model system for molecular genetic approaches to development and physiology. More recently, the potential of studying various accessions collected from diverse habitats has been started to exploit. Col-0 has been the best-studied accession but we now know that several traits show significant divergences among them. In this work, we focused in the root that has become a key system for development. We studied root architecture and growth dynamics of 12 Arabidopsis accessions. Our data reveal a wide variability in root architecture and root length among accessions. We also found variability in the root apical meristem (RAM), explained mainly by cell size at the RAM transition domain and possibly by peculiar forms of organization at the stem cell niche in some accessions. Contrary to Col-0 reports, in some accessions the RAM size not always explains the variations in the root length; indicating that elongated cell size could be more relevant in the determination of root length than the RAM size itself. This study contributes to investigations dealing with understanding the molecular and cellular basis of phenotypic variation, the role of plasticity on adaptation, and the developmental mechanisms that may restrict phenotypic variation in response to contrasting environmental conditions.
doi:10.3389/fpls.2016.00858
PMCID: PMC4910468  PMID: 27379140
natural variation; root morphology; RAM; stem cell niche; Arabidopsis accessions
2.  A Dynamic Gene Regulatory Network Model That Recovers the Cyclic Behavior of Arabidopsis thaliana Cell Cycle 
PLoS Computational Biology  2015;11(9):e1004486.
Cell cycle control is fundamental in eukaryotic development. Several modeling efforts have been used to integrate the complex network of interacting molecular components involved in cell cycle dynamics. In this paper, we aimed at recovering the regulatory logic upstream of previously known components of cell cycle control, with the aim of understanding the mechanisms underlying the emergence of the cyclic behavior of such components. We focus on Arabidopsis thaliana, but given that many components of cell cycle regulation are conserved among eukaryotes, when experimental data for this system was not available, we considered experimental results from yeast and animal systems. We are proposing a Boolean gene regulatory network (GRN) that converges into only one robust limit cycle attractor that closely resembles the cyclic behavior of the key cell-cycle molecular components and other regulators considered here. We validate the model by comparing our in silico configurations with data from loss- and gain-of-function mutants, where the endocyclic behavior also was recovered. Additionally, we approximate a continuous model and recovered the temporal periodic expression profiles of the cell-cycle molecular components involved, thus suggesting that the single limit cycle attractor recovered with the Boolean model is not an artifact of its discrete and synchronous nature, but rather an emergent consequence of the inherent characteristics of the regulatory logic proposed here. This dynamical model, hence provides a novel theoretical framework to address cell cycle regulation in plants, and it can also be used to propose novel predictions regarding cell cycle regulation in other eukaryotes.
Author Summary
In multicellular organisms, cells undergo a cyclic behavior of DNA duplication and delivery of a copy to daughter cells during cell division. In each of the main cell-cycle (CC) stages different sets of proteins are active and genes are expressed. Understanding how such cycling cellular behavior emerges and is robustly maintained in the face of changing developmental and environmental conditions, remains a fundamental challenge of biology. The molecular components that cycle through DNA duplication and citokinesis are interconnected in a complex regulatory network. Several models of such network have been proposed, although the regulatory network that robustly recovers a limit-cycle steady state that resembles the behavior of CC molecular components has been recovered only in a few cases, and no comprehensive model exists for plants. In this paper we used the plant Arabidopsis thaliana, as a study system to propose a core regulatory network to recover a cyclic attractor that mimics the oscillatory behavior of the key CC components. Our analyses show that the proposed GRN model is robust to transient alterations, and is validated with the loss- and gain-of-function mutants of the CC components. The interactions proposed for Arabidopsis thaliana CC can inspire predictions for further uncovering regulatory motifs in the CC of other organisms including human.
doi:10.1371/journal.pcbi.1004486
PMCID: PMC4560428  PMID: 26340681
3.  A model of the regulatory network involved in the control of the cell cycle and cell differentiation in the Caenorhabditis elegans vulva 
BMC Bioinformatics  2015;16(1):81.
Background
There are recent experimental reports on the cross-regulation between molecules involved in the control of the cell cycle and the differentiation of the vulval precursor cells (VPCs) of Caenorhabditis elegans. Such discoveries provide novel clues on how the molecular mechanisms involved in the cell cycle and cell differentiation processes are coordinated during vulval development. Dynamic computational models are helpful to understand the integrated regulatory mechanisms affecting these cellular processes.
Results
Here we propose a simplified model of the regulatory network that includes sufficient molecules involved in the control of both the cell cycle and cell differentiation in the C. elegans vulva to recover their dynamic behavior. We first infer both the topology and the update rules of the cell cycle module from an expected time series. Next, we use a symbolic algorithmic approach to find which interactions must be included in the regulatory network. Finally, we use a continuous-time version of the update rules for the cell cycle module to validate the cyclic behavior of the network, as well as to rule out the presence of potential artifacts due to the synchronous updating of the discrete model. We analyze the dynamical behavior of the model for the wild type and several mutants, finding that most of the results are consistent with published experimental results.
Conclusions
Our model shows that the regulation of Notch signaling by the cell cycle preserves the potential of the VPCs and the three vulval fates to differentiate and de-differentiate, allowing them to remain completely responsive to the concentration of LIN-3 and lateral signal in the extracellular microenvironment.
Electronic supplementary material
The online version of this article (doi:10.1186/s12859-015-0498-z) contains supplementary material, which is available to authorized users.
doi:10.1186/s12859-015-0498-z
PMCID: PMC4367908  PMID: 25884811
C. elegans; Vulva; Fate determination; Cell cycle
4.  Chronic Exercise Increases Plasma Brain-Derived Neurotrophic Factor Levels, Pancreatic Islet Size, and Insulin Tolerance in a TrkB-Dependent Manner 
PLoS ONE  2014;9(12):e115177.
Background
Physical exercise improves glucose metabolism and insulin sensitivity. Brain-derived neurotrophic factor (BDNF) enhances insulin activity in diabetic rodents. Because physical exercise modifies BDNF production, this study aimed to investigate the effects of chronic exercise on plasma BDNF levels and the possible effects on insulin tolerance modification in healthy rats.
Methods
Wistar rats were divided into five groups: control (sedentary, C); moderate- intensity training (MIT); MIT plus K252A TrkB blocker (MITK); high-intensity training (HIT); and HIT plus K252a (HITK). Training comprised 8 weeks of treadmill running. Plasma BDNF levels (ELISA assay), glucose tolerance, insulin tolerance, and immunohistochemistry for insulin and the pancreatic islet area were evaluated in all groups. In addition, Bdnf mRNA expression in the skeletal muscle was measured.
Principal Findings
Chronic treadmill exercise significantly increased plasma BDNF levels and insulin tolerance, and both effects were attenuated by TrkB blocking. In the MIT and HIT groups, a significant TrkB-dependent pancreatic islet enlargement was observed. MIT rats exhibited increased liver glycogen levels following insulin administration in a TrkB-independent manner.
Conclusions/Significance
Chronic physical exercise exerted remarkable effects on insulin regulation by inducing significant increases in the pancreatic islet size and insulin sensitivity in a TrkB-dependent manner. A threshold for the induction of BNDF in response to physical exercise exists in certain muscle groups. To the best of our knowledge, these are the first results to reveal a role for TrkB in the chronic exercise-mediated insulin regulation in healthy rats.
doi:10.1371/journal.pone.0115177
PMCID: PMC4274083  PMID: 25531651
5.  Flower Development as an Interplay between Dynamical Physical Fields and Genetic Networks 
PLoS ONE  2010;5(10):e13523.
In this paper we propose a model to describe the mechanisms by which undifferentiated cells attain gene configurations underlying cell fate determination during morphogenesis. Despite the complicated mechanisms that surely intervene in this process, it is clear that the fundamental fact is that cells obtain spatial and temporal information that bias their destiny. Our main hypothesis assumes that there is at least one macroscopic field that breaks the symmetry of space at a given time. This field provides the information required for the process of cell differentiation to occur by being dynamically coupled to a signal transduction mechanism that, in turn, acts directly upon the gene regulatory network (GRN) underlying cell-fate decisions within cells. We illustrate and test our proposal with a GRN model grounded on experimental data for cell fate specification during organ formation in early Arabidopsis thaliana flower development. We show that our model is able to recover the multigene configurations characteristic of sepal, petal, stamen and carpel primordial cells arranged in concentric rings, in a similar pattern to that observed during actual floral organ determination. Such pattern is robust to alterations of the model parameters and simulated failures predict altered spatio-temporal patterns that mimic those described for several mutants. Furthermore, simulated alterations in the physical fields predict a pattern equivalent to that found in Lacandonia schismatica, the only flowering species with central stamens surrounded by carpels.
doi:10.1371/journal.pone.0013523
PMCID: PMC2965087  PMID: 21048956
6.  Floral Morphogenesis: Stochastic Explorations of a Gene Network Epigenetic Landscape 
PLoS ONE  2008;3(11):e3626.
In contrast to the classical view of development as a preprogrammed and deterministic process, recent studies have demonstrated that stochastic perturbations of highly non-linear systems may underlie the emergence and stability of biological patterns. Herein, we address the question of whether noise contributes to the generation of the stereotypical temporal pattern in gene expression during flower development. We modeled the regulatory network of organ identity genes in the Arabidopsis thaliana flower as a stochastic system. This network has previously been shown to converge to ten fixed-point attractors, each with gene expression arrays that characterize inflorescence cells and primordial cells of sepals, petals, stamens, and carpels. The network used is binary, and the logical rules that govern its dynamics are grounded in experimental evidence. We introduced different levels of uncertainty in the updating rules of the network. Interestingly, for a level of noise of around 0.5–10%, the system exhibited a sequence of transitions among attractors that mimics the sequence of gene activation configurations observed in real flowers. We also implemented the gene regulatory network as a continuous system using the Glass model of differential equations, that can be considered as a first approximation of kinetic-reaction equations, but which are not necessarily equivalent to the Boolean model. Interestingly, the Glass dynamics recover a temporal sequence of attractors, that is qualitatively similar, although not identical, to that obtained using the Boolean model. Thus, time ordering in the emergence of cell-fate patterns is not an artifact of synchronous updating in the Boolean model. Therefore, our model provides a novel explanation for the emergence and robustness of the ubiquitous temporal pattern of floral organ specification. It also constitutes a new approach to understanding morphogenesis, providing predictions on the population dynamics of cells with different genetic configurations during development.
doi:10.1371/journal.pone.0003626
PMCID: PMC2572848  PMID: 18978941

Results 1-6 (6)