Biology subjects

Iber, D.

Publications and source records attributed to Iber, D..

30 records · Page 2Linked to original sources

bioRxiv2021

Inference of Morphogen Gradient Precision from Molecular Noise Data

During development, morphogen gradients provide spatial information for tissue patterning. Gradients and readout mechanisms are inevitably variable, yet the resulting patterns are strikingly precise. Measurement limitations currently preclude precise detection of morphogen gradients over long distances. Here, we develop a new formalism to estimate gradient precision along the entire patterning axis from measurements close to the source. Using numerical simulations, we infer gradient variability from measured molecular noise levels in morphogen production, decay, and diffusion. The predicted precision is much higher than previously measured--precise enough to allow even single gradients to define the central progenitor boundaries during neural tube development. Finally, we show that the patterning mechanism is optimized for precise progenitor cell numbers, rather than precise boundary positions, as the progenitor domain size is particularly robust to gradient alterations. We conclude that single gradients can yield the observed developmental precision, which provides new prospects for tissue engineering.

developmental biology↗

bioRxiv2021

3D Cell Neighbour Dynamics in Growing Pseudostratified Epithelia

During morphogenesis, epithelial sheets remodel into complex geometries. How cells dynamically organize their contact with neighbouring cells in these tightly packed tissues is poorly understood. We have used light-sheet microscopy of growing mouse embryonic lung explants, three-dimensional cell segmentation, and physical theory to unravel the principles behind 3D cell organization in growing pseudostratified epithelia. We find that cells have highly irregular 3D shapes and exhibit numerous neighbour intercalations along the apical-basal axis as well as over time. Despite the fluidic nature, the cell packing configurations follow fundamental relationships previously described for apical epithelial layers, i.e., Eulers formula, Lewis law, and Aboav-Weaires law, at all times and across the entire tissue thickness. This arrangement minimizes the lateral cell-cell surface energy for a given cross-sectional area variability, generated primarily by the distribution and movement of nuclei. We conclude that the complex 3D cell organization in growing epithelia emerges from simple physical principles.

cell biology↗

bioRxiv2020

Morphological study of embryonic Chd8+/- mouse brains using light-sheet microscopy

ObjectiveAutism spectrum disorder (ASD) encompasses a group of neurodevelopmental conditions that remain poorly understood due to their genetic complexity. CHD8 is a risk allele strongly associated with ASD, and heterozygous Chd8 loss-of-function mice have been reported to exhibit macrocephaly in early postnatal stages. In this work, we sought to identify measurable brain alterations in early embryonic development. ResultsWe performed light-sheet fluorescence microscopy imaging of N-cadherin stained and optically cleared Chd8+/- and wild-type mouse brains at embryonic day 12.5 (E12.5). We report a detailed morphometric characterization of embryonic brain shapes and cortical neuroepithelial apical architecture. While Chd8+/- characteristic expansion of the forebrain and midbrain was not observed this early in embryogenesis, a tendency for a decreased lateral ventricular sphericity and an increased intraocular distance in Chd8+/- brains was found compared to controls. This study advocates the use of high-resolution microscopy technologies and multi-scale morphometric analyses of target brain regions to explore the etiology and cellular basis of Chd8 haploinsufficiency.

developmental biology↗

bioRxiv2020

The Biomechanical Basis of Biased Epithelial Tube Elongation

During lung development, epithelial branches expand preferentially in longitudinal direction. This bias in outgrowth has been linked to a bias in cell shape and in the cell division plane. How this bias arises is unknown. Here, we show that biased epithelial outgrowth occurs independent of the surrounding mesenchyme, of preferential turn-over of the extracellular matrix at the bud tips, and of FGF signalling. There is also no evidence for actin-rich filopodia at the bud tips. Rather, we find epithelial tubes to be collapsed during early lung and kidney development, and we observe fluid flow in the narrow tubes. By simulating the measured fluid flow inside segmented narrow epithelial tubes, we show that the shear stress levels on the apical surface are sufficient to explain the reported bias in cell shape and outgrowth. We use a cell-based vertex model to confirm that apical shear forces, unlike constricting forces, can give rise to both the observed bias in cell shapes and tube elongation. We conclude that shear stress may be a more general driver of biased tube elongation beyond its established role in angiogenesis. Summary StatementWe systematically analysed the requirements for biased elongating outgrowth of epithelial tubes during lung and kidney development, and provide evidence that fluid-flow induced shear stress drives their biased elongation.

developmental biology↗

bioRxiv2019

Cell-based simulations of Notch-dependent cell differentiation on growing domains

Notch signalling controls cell differentiation and proliferation in many tissues. The Notch signal is generated by the interaction between the Notch receptor of one cell with the Notch ligand (Delta or Jagged) of a neighbouring cell. Therefore, the pathway requires cell-cell contact in order to be active. During organ development, cell differentiation occurs concurrently with tissue growth and changes in cell morphology. How growth impacts on Notch signalling and cell differentiation remains poorly understood. Here, we developed a modelling environment to simulate Notch signalling in a growing tissue. We use our model to simulate the differentiation process of pancreatic progenitor cells. Our results suggest that Notch-mediated differentiation in the developing pancreas is first mediated by geometric effects that result in loss of Notch signalling on the tissue boundary, leading to the differentiation of tip versus trunk cells. A second wave of differentiation further happens in the trunk cells due to a reduction in the expression of the ligand Jagged, which has been shown to be controlled by signalling factors secreted from the surrounding mesenchyme. Our results bring new insights into how cells coordinate tissue growth with cell fate specification during organ development.

developmental biology↗

bioRxiv2019

A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells

How time is measured by neural stem cells during temporal neurogenesis has remained unresolved. By combining experiments and computational modelling, we here define a Shh/Gli-driven three-node timer underlying the sequential generation of motor neurons (MNs) and serotonergic neurons in the brainstem. The timer is founded on temporal decline of Gli-activator and Gli-repressor activities established through downregulation of Gli transcription. The circuitry conforms an incoherent feedforward loop, whereby Gli proteins promote expression of Phox2b and thereby MN-fate, but also account for a delayed activation of a self-promoting Tgf{beta}-node triggering a fate switch by repressing Phox2b. Hysteresis and spatial averaging by diffusion of Tgf{beta} counteracts noise and increases temporal accuracy at the population level. Our study defines how time is reliably encoded during the sequential specification of neurons.

developmental biology↗

bioRxiv2019

Cell-based Simulations of Biased Epithelial Lung Growth

During morphogenesis, epithelial tubes elongate. In case of the mammalian lung, biased elongation has been linked to a bias in cell shape and cell division, but it has remained unclear whether a bias in cell shape along the axis of outgrowth is sufficient for biased outgrowth and how it arises. Here, we use our 2D cell-based tissue simulation software LBIBCell to investigate the conditions for biased epithelial outgrowth. We show that the observed bias in cell shape and cell division can result in the observed bias in outgrowth only in case of strong cortical tension, and comparison to biological data suggests that the cortical tension in epithelia is likely sufficient. We explore mechanisms that may result in the observed bias in cell division and cell shapes. To this end, we test the possibility that the surrounding tissue or extracellular matrix acts as a mechanical constraint that biases growth in longitudinal direction. While external compressive forces can result in the observed bias in outgrowth, we find that they do not result in the observed bias in cell shapes. We conclude that other mechanisms must exist that generate the bias in lung epithelial outgrowth.

biophysics↗

bioRxiv2019

Minimisation of surface energy drives apical epithelial organisation and gives rise to Lewis’ law

The packing of cells in epithelia exhibits striking regularities, regardless of the organism and organ. One of these regularities is expressed in Lewis law, which states that the average apical cell area is linearly related to the number of neighbours, such that cells with larger apical area have on average more neighbours. The driving forces behind the almost 100-year old Lewis law have remained elusive. We now provide evidence that the observed apical epithelial packing minimizes surface energy at the intercellular apical adhesion belt. Lewis law emerges because the apical cell surfaces then assume the most regular polygonal shapes within a contiguous lattice, thus minimising the average perimeter per cell, and thereby surface energy. We predict that the linear Lewis law generalizes to a quadratic law if the variability in apical areas is increased beyond what is normally found in epithelia. We confirm this prediction experimentally by generating heterogeneity in cell growth in Drosophila epithelia. Our discovery provides a link between epithelial organisation, cell division and growth and has implications for the general understanding of epithelial dynamics.

biophysics↗

bioRxiv2019

Aboave-Weaire’s law in epithelia results from an angle constraint in contiguous polygonal lattices

It has long been noted that the cell arrangements in epithelia, regardless of their origin, exhibit some striking regularities: first, the average number of cell neighbours at the apical side is (close to) six. Second, the average apical cell area is linearly related to the number of neighbours, such that cells with larger apical area have on average more neighbours, a relation termed Lewis law. Third, Aboav-Weaires (AW) law relates the number of neighbours that a cell has to that of its direct neighbours. While the first rule can be explained with topological constraints in contiguous polygonal lattices, and the second rule (Lewis law) with the minimisation of the lateral contact surface energy, the driving forces behind the AW law have remained elusive. We now show that also the AW law emerges to minimise the lateral contact surface energy in polygonal lattices by driving cells to the most regular polygonal shape, but while Lewis law regulates the side lengths, the AW law controls the angles. We conclude that global apical epithelial organization is the result of energy minimisation under topological constraints.

biophysics↗

bioRxiv2018

Notch2 signaling regulates Id4 and cell cycle genes to maintain neural stem cell quiescence in the adult hippocampus

Neural stem cells (NSCs) in the adult hippocampal dentate gyrus (DG) can be quiescent or proliferative, but how they are maintained is largely unknown. With age DG NSCs become increasingly dormant, which impinges on neuron generation. We addressed how NSC activity is controlled and found that Notch2 promotes quiescence by regulating their transition to the activated state. Notch2-ablation induces cell cycle genes and markers of active NSCs. Conversely, quiescent NSC-associated genes, including Id4, are down regulated after Notch2 deletion. We found that Notch2 binds the Id4 promoter and positively regulates transcription. Similar to Notch2, Id4 overexpression promotes DG NSC quiescence and Id4 knockdown rescues proliferation, even when Notch2 signaling is activated. We show that Notch2 regulates age-dependent DG NSC dormancy and Notch2 inhibition rejuvenates neurogenesis in the DG of aged mice. Our data indicate that a Notch2-Id4 axis promotes adult DG NSC quiescence and dormancy.

neuroscience↗

bioRxiv2018

Travelling waves in somitogenesis: collective cellular properties emerge from time-delayed juxtacrine oscillation coupling

The sculpturing of the vertebrate body plan into segments begins with the sequential formation of somites in the presomitic mesoderm (PSM). The rhythmicity of this process is controlled by travelling waves of gene expression. These kinetic waves emerge from coupled cellular oscillators and sweep across the PSM. In zebrafish, the oscillations are driven by autorepression of her genes and are synchronized via Notch signalling. Mathematical modelling has played an important role in explaining how collective properties emerge from the molecular interactions. Increasingly more quantitative experimental data permits the validation of those mathematical models, yet leads to increasingly more complex model formulations that hamper an intuitive understanding of the underlying mechanisms. Here, we review previous efforts, and design a mechanistic model of the her1 oscillator, which represents the experimentally viable her7;hes6 double mutant. This genetically simplified system is ideally suited to conceptually recapitulate oscillatory entrainment and travelling wave formation, and to highlight open questions. It shows that three key parameters, the autorepression delay, the juxtacrine coupling delay, and the coupling strength, are sufficient to understand the emergence of the collective period, the collective amplitude, and the synchronization of neighbouring Her1 oscillators. Moreover, two spatiotemporal time delay gradients, in the autorepression and in the juxtacrine signalling, are required to explain the collective oscillatory dynamics and synchrony of PSM cells. The highlighted developmental principles likely apply more generally to other developmental processes, including neurogenesis and angiogenesis.

developmental biology↗

bioRxiv2018

Positional information encoded in the dynamic differences between neighbouring oscillators during vertebrate segmentation.

How cells track their position during the segmentation of the vertebrate body remains elusive. For decades, this process has been interpreted according to the clock-and-wavefront model, where molecular oscillators set the frequency of somite formation while the positional information is encoded in signaling gradients. Recent experiments using ex vivo explants challenge this interpretation, suggesting that positional information is encoded in the properties of the oscillators. Here, we propose that positional information is encoded in the differential levels of neighboring oscillators. The differences gradually increase because both the oscillator amplitude and the period increase with time. When this difference exceeds a certain threshold, the segmentation program starts. Using this framework, we quantitatively fit experimental data from in vivo and ex vivo mouse segmentation, and propose mechanisms of somite scaling. Our results suggest a novel mechanism of spatial pattern formation based on the local interactions between dynamic molecular oscillators.

developmental biology↗