Competition in notch signaling with cis enriches cell fate decisions

Notch signaling is involved in cell fate choices during the embryonic development of Metazoa. Commonly, Notch signaling arises from the binding of the Notch receptor to its ligands in adjacent cells driving cell-to-cell communication. Yet, cell-autonomous control of Notch signaling through both ligand-dependent and ligand-independent mechanisms is known to occur as well. Examples include Notch signaling arising in the absence of ligand binding, and cis-inhibition of Notch signaling by titration of the Notch receptor upon binding to its ligands within a single cell. Increasing experimental evidences support that the binding of the Notch receptor with its ligands within a cell (cis-interactions) can also trigger a cell-autonomous Notch signal (cis-signaling), whose potential effects on cell fate decisions and patterning remain poorly understood. To address this question, herein we mathematically and computationally investigate the cell states arising from the combination of cis-signaling with additional Notch signaling sources, which are either cell-autonomous or involve cell-to-cell communication. Our study shows that cis-signaling can switch from driving cis-activation to effectively perform cis-inhibition and identifies under which conditions this switch occurs. This switch relies on the competition between Notch signaling sources, which share the same receptor but differ in their signaling efficiency. We propose that the role of cis-interactions and their signaling on fine-grained patterning and cell fate decisions is dependent on whether they drive cis-inhibition or cis-activation, which could be controlled during development. Specifically, cis-inhibition and not cis-activation facilitates patterning and enriches it by modulating the ratio of cells in the high-ligand expression state, by enabling additional periodic patterns like stripes and by allowing localized patterning highly sensitive to the precursor state and cell-autonomous bistability. Our study exemplifies the complexity of regulations when multiple signalng sources share the same receptor and provides the tools for their characterization

Single-cell approaches for understanding morphogenesis using Computational Morphodynamics

In multicellular organisms cells grow, divide and adopt different fates, resulting in tissues and organs with specific functions. In recent years, a number of studies have brought quantitative knowledge about how these processes are orchestrated, shed-ding new light on cells as active and central players in morphogenesis. We explore recent advances in understanding plant morphogenesis from a quantitative perspective, defining the re-search field of Computational Morphodynamics. The focus is on studies combining theoretical and experimental approaches integrating hypotheses of how molecular and mechanical regulation at the cellular level lead to tissue behaviour. Finally, we dis-cuss some of the main challenges for future work

Editorial: pattern formation in biology

Over the past two decades, the study of pattern formation in biology has attracted the attention of many scientists from diverse fields, ranging from developmental biology, cell biology and synthetic biology, to physics, mathematics and computer science. Quantitative and interdisciplinary approaches have become essential for understanding these challenging phenomena. This Research Topic contains a collection of articles and reviews that use quantitative and interdisciplinary perspectives to understand the underlying mechanisms driving biological pattern formation. Modeling morphogenetic processes, gene regulatory network dynamics and morphogen gradients link the articles of this Research Topic, with a focus on three research areas: 1) underlying mechanisms of patterning processes; 2) cross-talk of morphogenetic and pattern formation processes, and 3) mathematical methods for modeling and quantifying biological patterning and morphogenesis. Below, each of the present Research Topic papers is briefly discussed.Centro Regional de Estudios Genómico

Nitrate modulates stem cell dynamics in Arabidopsis shoot meristems through cytokinins

The shoot apical meristem (SAM) is responsible for the generation of all the aerial parts of plants. Given its critical role, dynamical changes in SAM activity should play a central role in the adaptation of plant architecture to the environment. Using quantitative microscopy, grafting experiments, and genetic perturbations, we connect the plant environment to the SAM by describing the molecular mechanism by which cytokinins signal the level of nutrient availability to the SAM. We show that a systemic signal of cytokinin precursors mediates the adaptation of SAM size and organogenesis rate to the availability of mineral nutrients by modulating the expression of WUSCHEL, a key regulator of stem cell homeostasis. In time-lapse experiments, we further show that this mechanism allows meristems to adapt to rapid changes in nitrate concentration, and thereby modulate their rate of organ production to the availability of mineral nutrients within a few days. Our work sheds light on the role of the stem cell regulatory network by showing that it not only maintains meristem homeostasis but also allows plants to adapt to rapid changes in the environment

Auxin Influx Carriers Control Vascular Patterning and Xylem Differentiation in Arabidopsis thaliana

Auxin is an essential hormone for plant growth and development. Auxin influx carriers AUX1/LAX transport auxin into the cell, while auxin efflux carriers PIN pump it out of the cell. It is well established that efflux carriers play an important role in the shoot vascular patterning, yet the contribution of influx carriers to the shoot vasculature remains unknown. Here, we combined theoretical and experimental approaches to decipher the role of auxin influx carriers in the patterning and differentiation of vascular tissues in the Arabidopsis inflorescence stem. Our theoretical analysis predicts that influx carriers facilitate periodic patterning and modulate the periodicity of auxin maxima. In agreement, we observed fewer and more spaced vascular bundles in quadruple mutants plants of the auxin influx carriers aux1lax1lax2lax3. Furthermore, we show AUX1/LAX carriers promote xylem differentiation in both the shoot and the root tissues. Influx carriers increase cytoplasmic auxin signaling, and thereby differentiation. In addition to this cytoplasmic role of auxin, our computational simulations propose a role for extracellular auxin as an inhibitor of xylem differentiation. Altogether, our study shows that auxin influx carriers AUX1/LAX regulate vascular patterning and differentiation in plants.Peer reviewe

Pattern formation through lateral inhibition mediated by Notch signaling

[cat] Els organismes multicel·lulars estan constituïts per diferents tipus cel·lulars ordenats d’una certa manera, formant teixits amb funcions específiques. L’organització de cèl·lules de tipus diferents pot donar lloc a patrons espacio-temporals Aquesta Tesi es basa en l’estudi de com a partir d’un teixit de cèl·lules equivalents — estat homogeni precursor — s’estableixen patrons ordenats de tipus cel·lulars diferents. En particular, ens hem centrat en l’estudi d’un tipus de patrons que sorgeixen en teixits animals que tenen dos tipus cel·lulars i que presenten un ordre fi en el teixit, i.e. de longitud d’ona de poques cèl·lules. Aquest tipus de patrons són formats degut al efecte de la inhibició lateral. La inhibició lateral és un fenomen en el qual cèl·lules precursores equivalents intenten adoptar un cert estat o destí cel·lular per a diferenciar-se en un tipus cel·lular en particular, i al mateix temps inhibeixen a les seves cèl·lules veïnes que adquireixin aquest mateix estat. Aquest procés dinàmic dóna lloc a un patró fi, on les cèl·lules que han finalment adoptat l’estat desitjat vénen rodejades per cèl·lules que són inhibides, i que acabaran diferenciant-se en un tipus cel·lular diferent. Aquest tipus de patró es troba en una àmplia varietat de teixits animals, com ara en la retina ,i en l’oïda interna de vertebrats, i en l’ull de la mosca Drosophila[eng] Multicellular organisms are constituted by different kinds of cells which are arranged in a particular way, forming tissues with specific functions. The organization of these different cells can give rise to regular spatiotemporal patterns. In this Thesis we evaluate from a theoretical perspective the effects of different regulatory elements of the Notch signaling pathway in lateral inhibition patterning. These new elements under study are motivated by recent experimental observations. For studying them, we reformulate a phenomenological model proposed by Collier and colleagues (1996). Our modeling approach is based on coupled ordinary differential equations in hexagonal and irregular bidimensional lattices. We use both deterministic and stochastic approaches. We analyze the pattern formation capabilities of our proposed models by using different analytical tools and integrate numerically our dynamical equations. We focus on four main topics. In the first topic we study how a neurogenic differentiation wavefront in the embryonic vertebrate retina depends on the state of the invaded tissue. Our results show that the properties (pattern formed, shape and velocity) of progressing fronts of lateral inhibition depend crucially on the presence of ligand ahead of the differentiation front. We find similar results in a planar growing wavefront that would mimic morphogenetic furrow progression in embryonic Drosophila eye. Hence, our results point to a mechanism for neurogenic front regulation, and to a potential new design principle. In the second topic, we study the effects of a diffusible ligand in the context of lateral inhibition. We show that the diffusible ligand per se combined with its inhibition by Notch is not able to generate a pattern. Our results indicate that diffusible ligand with the classical lateral inhibition circuit softens and destroys the lateral inhibition pattern. At intermediate diffusion rates, diffusion can help to create perfect patterns. The third topic focuses on the study of receptor-ligand interactions within the same cell, what is called cis-interactions. We study the effect of Notch signal-productive cis-interactions in combination with another signaling source in two different situations: (i) in a multicellular scenario, where the other signaling source would be provided by the trans-interactions, and (ii) in a single-cell scenario in which a basal ligand-independent signaling source would be provided. In both situations, we predict that cis-interactions can drive cis-inhibition - i.e. an effective depletion of the signal production rate - at weak cis-signaling rates when acting together with a stronger signaling source, e.g. trans-interactions or with a ligand-independent signaling source. Our work also shows that cis-inhibition in the single-cell system together with a basal signal production can drive bistability. In the multicellular case, we observe that by increasing the amount of cis-interactions in the cis-inhibition scenario the proportion of high-Delta fated cells in a tissue gradually increases. In the fourth topic we study the case of hair cell differentiation in the embryonic chick inner ear. In this context, Notch pathway operates in two opposite modes with two different ligands: first, lateral induction through Jag1 ligand and afterwards, lateral inhibition through Dl1 ligand. We predict that relative signaling rates (or strengths) by Jag1 and Dl1 when bound to Notch are critical for the transit of operating modes. Also, we predict that in the lateral inhibition stage, competition between Dl1 and Jag1 ligands arise. This competition introduces an extra intercellular mutual inhibitory feedback loop, contributing to lateral inhibition. Overall, this Thesis presents new theoretical results and predictions on pattern formation in the context of lateral inhibition mediated by Notch signaling

Quantifying gene expression domains in plant shoot apical meristems

Accepted version of the manuscript for publication in the Book "Flower Development: Methods and Protocols, Second Edition. Jose Luis Riechmann and Cristina Ferrandiz, eds. Methods in Molecular Biology. Springer. "The shoot apical meristem is the plant tissue that produces the plant aerial organs such as flowers and leaves. To better understand how does the shoot apical meristem develop and adapt to the environment, imaging developing shoot meristems expressing fluorescence reporters through laser confocal microscopy is becoming increasingly important. Yet, there are not many computational pipelines enabling a systematic and high-throughput characterisation of the produced microscopy images. This chapter provides a simple method to analyse 3D images obtained through laser scanning microscopy and quantitatively characterise radially or axially symmetric 3D fluorescence domains expressed in a tissue or organ by a reporter. Then, it presents different computational pipelines aiming at performing high-throughput quantitative image analysis of gene expression in plant inflorescence and floral meristems. This methodology has notably enabled to characterise quantitatively how stem cells responded to environmental perturbations in the Arabidopsis inflorescence meristem and will open new avenues in the use of quantitative analysis of gene expression in shoot apical meristems. Overall, the presented methodology provides a simple framework to analyse quantitatively gene expression domains from 3D confocal images at the tissue and organ level, which can be applied to shoot meristems and other organs and tissues

Competition in notch signaling with cis enriches cell fate decisions

Notch signaling is involved in cell fate choices during the embryonic development of Metazoa. Commonly, Notch signaling arises from the binding of the Notch receptor to its ligands in adjacent cells driving cell-to-cell communication. Yet, cell-autonomous control of Notch signaling through both ligand-dependent and ligand-independent mechanisms is known to occur as well. Examples include Notch signaling arising in the absence of ligand binding, and cis-inhibition of Notch signaling by titration of the Notch receptor upon binding to its ligands within a single cell. Increasing experimental evidences support that the binding of the Notch receptor with its ligands within a cell (cis-interactions) can also trigger a cell-autonomous Notch signal (cis-signaling), whose potential effects on cell fate decisions and patterning remain poorly understood. To address this question, herein we mathematically and computationally investigate the cell states arising from the combination of cis-signaling with additional Notch signaling sources, which are either cell-autonomous or involve cell-to-cell communication. Our study shows that cis-signaling can switch from driving cis-activation to effectively perform cis-inhibition and identifies under which conditions this switch occurs. This switch relies on the competition between Notch signaling sources, which share the same receptor but differ in their signaling efficiency. We propose that the role of cis-interactions and their signaling on fine-grained patterning and cell fate decisions is dependent on whether they drive cis-inhibition or cis-activation, which could be controlled during development. Specifically, cis-inhibition and not cis-activation facilitates patterning and enriches it by modulating the ratio of cells in the high-ligand expression state, by enabling additional periodic patterns like stripes and by allowing localized patterning highly sensitive to the precursor state and cell-autonomous bistability. Our study exemplifies the complexity of regulations when multiple signalng sources share the same receptor and provides the tools for their characterization

Single-Cell Approaches for Understanding Morphogenesis Using Computational Morphodynamics

In multicellular organisms cells grow, divide and adopt different fates, resulting in tissues and organs with specific functions. In recent years, a number of studies have brought quantitative knowledge about how these processes are orchestrated, shedding new light on cells as active and central players in morphogenesis. We explore recent advances in understanding plant morphogenesis from a quantitative perspective, defining the research field of Computational Morphodynamics. The focus is on studies combining theoretical and experimental approaches integrating hypotheses of how molecular and mechanical regulation at the cellular level lead to tissue behaviour. Finally, we discuss some of the main challenges for future work

A switch between cis-activation and cis-inhibition.

<p>(A–C) Stationary Notch signal in a cell () <i>versus</i> the amount of ligand in that cell () and the amount of primary signaling source () for (A) , (B) and (C) . Red lines show the Notch signal dependence on in the absence of the primary signaling source () and for a primary signaling source with . Decreasing curves indicate cis-inhibition and increasing curves show cis-activation. In B, cis-interactions drive cis-activation at low values, whereas they drive cis-inhibition at higher . (D) Parameter space showing where cis-activation (gray region) and cis-inhibition (white region) occurs, according to inequality 5. (E–F) Effective circuit architectures of the model when cis-interactions drive cis-activation (top) and cis-inhibition (bottom) for (E) isolated cells with a primary signaling source (straight arrow) and for (F) two adjacent cells that interact through trans-binding. Black arrows stand for activation, while red blunt arrows for inhibition. Parameter values: in panels A–C, and in panel D.</p