Diego Rasskin-Gutman

Notch activity acts as a sensor for extracellular calcium during vertebrate left-right determination

During vertebrate embryo development, the breaking of the initial bilateral symmetry is translated into asymmetric gene expression around the node and/or in the lateral plate mesoderm. The earliest conserved feature of this asymmetric gene expression cascade is the left-sided expression of Nodal, which depends on the activity of the Notch signalling pathway. Here we present a mathematical model describing the dynamics of the Notch signalling pathway during chick embryo gastrulation, which reveals a complex and highly robust genetic network that locally activates Notch on the left side of Hensens node. We identify the source of the asymmetric activation of Notch as a transient accumulation of extracellular calcium, which in turn depends on left–right differences in H+/K+-ATPase activity. Our results uncover a mechanism by which the Notch signalling pathway translates asymmetry in epigenetic factors into asymmetric gene expression around the node.

High-resolution episcopic microscopy: a rapid technique for high detailed 3D analysis of gene activity in the context of tissue architecture and morphology

We describe a new methodology for rapid 2D and 3D computer analysis and visualisation of gene expression and gene product pattern in the context of anatomy and tissue architecture. It is based on episcopic imaging of embryos and tissue samples, as they are physically sectioned, thereby producing inherently aligned digital image series and volume data sets, which immediately permit the generation of 3D computer representations. The technique uses resin as embedding medium, eosin for unspecific tissue staining, and colour reactions (β-galactosidase/Xgal or BCIP/NBT) for specific labelling of gene activity and mRNA pattern. We tested the potential of the method for producing high-resolution volume data sets of adult human and porcine tissue samples and of specifically and unspecifically stained mouse, chick, quail, frog, and zebrafish embryos. The quality of the episcopic images resembles the quality of digital images of true histological sections with respect to resolution and contrast. Specifically labelled structures can be extracted using simple thresholding algorithms. Thus, the method is capable of quickly and precisely detecting molecular signals simultaneously with anatomical details and tissue architecture. It has no tissue restrictions and can be applied for analysis of human tissue samples as well as for analysis of all developmental stages of embryos of a wide variety of biomedically relevant species.

Grist for Riedl's mill: a network model perspective on the integration and modularity of the human skull.

Riedls concept of burden neatly links development and evolution by ascertaining that structures that show a high degree of developmental co-dependencies with other structures are more constrained in evolution. The human skull can be precisely modeled as an articulated complex system of bones connected by sutures, forming a network of structural co-dependencies. We present a quantitative analysis of the morphological integration, modularity, and hierarchical organization of this human skull network model. Our overall results show that the human skull is a small-world network, with two well-delimited connectivity modules: one facial organized around the ethmoid bone, and one cranial organized around the sphenoid bone. Geometric morphometrics further support this two-module division, stressing the direct relationship between the developmental information enclosed in connectivity patterns and skull shape. Whereas the facial module shows a hierarchy of clustered blocks of bones, the bones of the cranial modules show a regular pattern of connections. We analyze the significance of these arrangements by hypothesizing specific structural roles for the most important bones involved in the formation of both modules, in the context of Riedls burden. We conclude that it is the morphological integration of each group of bones that defines the semi-hierarchical organization of the human skull, reflecting fundamental differences in the ontogenetic patterns of growth and the structural constraints that generate each module. Our study also demonstrates the adequacy of network analysis as an innovative tool to understand the morphological complexity of anatomical systems.

Structural Constraints in the Evolution of the Tetrapod Skull Complexity: Williston’s Law Revisited Using Network Models

Ever since the appearance of the first land vertebrates, the skull has undergone a simplification by loss and fusion of bones in all major groups. This well-documented evolutionary trend is known as “Williston’s Law”. Both loss and fusion of bones are developmental events that generate, at large evolutionary scales, a net reduction in the number of skull bones. We reassess this evolutionary trend by analyzing the patterns of skull organization captured in network models in which nodes represent bones and links represent suture joints. We also evaluate the compensatory process of anisomerism (bone specialization) suggested to occur as a result of this reduction by quantifying the heterogeneity and the ratio of unpaired bones in real skulls. Finally, we perform simulations to test the differential effect of bone losses in skull evolution. We show that the reduction in bone number during evolution is accompanied by a trend toward a more complex organization, rather than toward simplification. Our results indicate that the processes by which bones are lost or fused during development are central to explain the evolution of the morphology of the skull. Our simulations suggest that the evolutionary trend of increasing morphological complexity can be caused as a result of a structural constraint, the systematic loss of less connected bones during development.

Anatomical networks reveal the musculoskeletal modularity of the human head

Mosaic evolution is a key mechanism that promotes robustness and evolvability in living beings. For the human head, to have a modular organization would imply that each phenotypic module could grow and function semi-independently. Delimiting the boundaries of head modules, and even assessing their existence, is essential to understand human evolution. Here we provide the first study of the human head using anatomical network analysis (AnNA), offering the most complete overview of the modularity of the head to date. Our analysis integrates the many biological dependences that tie hard and soft tissues together, arising as a consequence of development, growth, stresses and loads, and motion. We created an anatomical network model of the human head, where nodes represent anatomical units and links represent their physical articulations. The analysis of the human head network uncovers the presence of 10 musculoskeletal modules, deep-rooted in these biological dependences, of developmental and evolutionary significance. In sum, this study uncovers new anatomical and functional modules of the human head using a novel quantitative method that enables a more comprehensive understanding of the evolutionary anatomy of our lineage, including the evolution of facial expression and facial asymmetry.

Cell lineage transport: a mechanism for molecular gradient formation.

Gradient formation is a fundamental patterning mechanism during embryo development, commonly related to secreted proteins that move along an existing field of cells. Here, we mathematically address the feasibility of gradients of mRNAs and non‐secreted proteins. We show that these gradients can arise in growing tissues whereby cells dilute and transport their molecular content as they divide and grow, a mechanism we termed ‘cell lineage transport.’ We provide an experimental test by unveiling a distal‐to‐proximal gradient of Hoxd13 in the vertebrate developing limb bud driven by cell lineage transport, corroborating our model. Our study indicates that gradients of non‐secreted molecules exhibit a power‐law profile and can arise for a wide range of biologically relevant parameter values. Dilution and nonlinear growth confer robustness to the spatial gradient under changes in the cell cycle period, but at the expense of sensitivity in the timing of gradient formation. We expect that gradient formation driven by cell lineage transport will provide future insights into understanding the coordination between growth and patterning during embryonic development.

Anatomical Network Analysis Shows Decoupling of Modular Lability and Complexity in the Evolution of the Primate Skull

Modularity and complexity go hand in hand in the evolution of the skull of primates. Because analyses of these two parameters often use different approaches, we do not know yet how modularity evolves within, or as a consequence of, an also-evolving complex organization. Here we use a novel network theory-based approach (Anatomical Network Analysis) to assess how the organization of skull bones constrains the co-evolution of modularity and complexity among primates. We used the pattern of bone contacts modeled as networks to identify connectivity modules and quantify morphological complexity. We analyzed whether modularity and complexity evolved coordinately in the skull of primates. Specifically, we tested Herbert Simon’s general theory of near-decomposability, which states that modularity promotes the evolution of complexity. We found that the skulls of extant primates divide into one conserved cranial module and up to three labile facial modules, whose composition varies among primates. Despite changes in modularity, statistical analyses reject a positive feedback between modularity and complexity. Our results suggest a decoupling of complexity and modularity that translates to varying levels of constraint on the morphological evolvability of the primate skull. This study has methodological and conceptual implications for grasping the constraints that underlie the developmental and functional integration of the skull of humans and other primates.

Beyond the functional matrix hypothesis: a network null model of human skull growth for the formation of bone articulations

Craniofacial sutures and synchondroses form the boundaries among bones in the human skull, providing functional, developmental and evolutionary information. Bone articulations in the skull arise due to interactions between genetic regulatory mechanisms and epigenetic factors such as functional matrices (soft tissues and cranial cavities), which mediate bone growth. These matrices are largely acknowledged for their influence on shaping the bones of the skull; however, it is not fully understood to what extent functional matrices mediate the formation of bone articulations. Aiming to identify whether or not functional matrices are key developmental factors guiding the formation of bone articulations, we have built a network null model of the skull that simulates unconstrained bone growth. This null model predicts bone articulations that arise due to a process of bone growth that is uniform in rate, direction and timing. By comparing predicted articulations with the actual bone articulations of the human skull, we have identified which boundaries specifically need the presence of functional matrices for their formation. We show that functional matrices are necessary to connect facial bones, whereas an unconstrained bone growth is sufficient to connect non‐facial bones. This finding challenges the role of the brain in the formation of boundaries between bones in the braincase without neglecting its effect on skull shape. Ultimately, our null model suggests where to look for modified developmental mechanisms promoting changes in bone growth patterns that could affect the development and evolution of the head skeleton.

Random Loss and Selective Fusion of Bones Originate Morphological Complexity Trends in Tetrapod Skull Networks

The tetrapod skull has undergone a reduction in number of bones in all major lineages since the origin of vertebrates, an evolutionary trend known as Williston’s Law. Using connectivity relations between bones as a proxy for morphological complexity we showed that this reduction in number of bones generated an evolutionary trend toward more complex skulls. This would imply that connectivity patterns among bones impose structural constraints on bone loss and fusion that increase bone burden due to the formation of new functional and developmental dependencies; thus, the higher the number of connections, the higher the burden. Here, we test this hypothesis by exploring plausible evolutionary scenarios based on selective versus random processes of bone loss and fusion. To do this, we have built a computational model that reduces iteratively the number of bones by loss and fusion, starting from hypothetical ancestral skulls represented as Gabriel networks in which bones are nodes and suture connections are links. Simulation results indicate that losses and fusions of bones affect skull structure differently whether they target bones at random or selectively depending on the number of bone connections. Our findings support a mixed scenario for Williston’s Law: the random loss of poorly connected bones and the selective fusion of the most connected ones. This evolutionary scenario offers a new explanation for the increase of morphological complexity in the tetrapod skull by reduction of bones during development.

The multiple directions of evolutionary change.

The theory of Punctuated Equilibria challenges the neo-Darwinian tenet that evolution is a uniform process. Recently, an article by Hunt has found that directional change during the evolution of a lineage is relatively small (occurring only in 5% of 250 analyzed traits). Of those traits that were shown to follow a trend, size was more likely to show gradual changes, whereas shape changes were more random. Here, we provide a short view of the nature of evolutionary trends, showing that directional change within lineages and among clades provides valuable evolutionary information about the processes involved in their generation.