Stuart A. Newman

Epigenetic Mechanisms of Character Origination

The close mapping between genotype and morphological phenotype in many contemporary metazoans has led to the general notion that the evolution of organismal form is a direct consequence of evolving genetic programs. In contrast to this view, we propose that the present relationship between genes and form is a highly derived condition, a product of evolution rather than its precondition. Prior to the biochemical canalization of developmental pathways, and the stabilization of phenotypes, interaction of multicellular organisms with their physicochemical environments dictated a many-to-many mapping between genomes and forms. These forms would have been generated by epigenetic mechanisms: initially physical processes characteristic of condensed, chemically active materials, and later conditional, inductive interactions among the organisms constituent tissues. This concept, that epigenetic mechanisms are the generative agents of morphological character origination, helps to explain findings that are difficult to reconcile with the standard neo-Darwinian model, e.g., the burst of body plans in the early Cambrian, the origins of morphological innovation, homology, and rapid change of form. Our concept entails a new interpretation of the relationship between genes and biological form.

Role of transforming growth factor-β in chondrogenic pattern formation in the embryonic limb: Stimulation of mesenchymal condensation and fibronectin gene expression by exogenenous TGF-β and evidence for endogenous TGF-β-like activity☆

The possible role of TGF-β-like molecules in skeletal pattern formation in the embryonic vertebrate limb was studied by analyzing the mechanism of enhancement of chondrogenesis in chick wing bud mesenchyme in vitro and testing for the presence and distribution of endogenous TGF-β-like activity in this tissue. Transient exposure (3–6 hr) to TGF-β1 (1–2 ng/ml) on the day after plating resulted in a 1.5- to 2-fold enhancement of accumulation of Alcian blue (pH 1.0)-stainable extracellular matrix 5 days later. The enhancement of differentiation was preceded by an acceleration and an increase in the extent of precartilage condensation formation, visualized by Hoffman Modulation Contrast microscopy a day after TGF-β treatment. In contrast, neither condensation nor subsequent chondrogenesis was stimulated by transient treatment with TGF-β1 on the day of plating. The effectiveness of a TGF-β treatment regimen in enhancing chondrogenesis was correlated with its effectiveness in stimulating condensation formation. Exposures to the factor for 3–6 hr on the day after plating, which most consistently stimulated both condensation formation and chondrogenesis, also corresponded to a peak in the enhancement of the steady-state level of fibronectin mRNA (fourfold to eightfold over control levels) measured at the end of the treatment period. The elevation in fibronectin mRNA levels brought about by this treatment persisted throughout the period of condensation. Endogenous TGF-β-like activity was detected in limb mesenchyme: extracts of freshly isolated and cultured limb tissues contained 6–25 pg TGF-β-like activity per 1 × 106 cells by the Mv1Lu cell proliferation inhibition assay, and indirect immunofluorescence using a polyclonal antibody directed against a TGF-β-related peptide indicated a patchy distribution of endogenous TGF-β-like reactivity within a day after culture. These findings are discussed in relation to the “fibronectin prepattern” hypothesis for limb pattern formation.

CompuCell, a multi-model framework for simulation of morphogenesis

MOTIVATION CompuCell is a multi-model software framework for simulation of the development of multicellular organisms known as morphogenesis. It models the interaction of the gene regulatory network with generic cellular mechanisms, such as cell adhesion, division, haptotaxis and chemotaxis. A combination of a state automaton with stochastic local rules and a set of differential equations, including subcellular ordinary differential equations and extracellular reaction-diffusion partial differential equations, model gene regulation. This automaton in turn controls the differentiation of the cells, and cell-cell and cell-extracellular matrix interactions that give rise to cell rearrangements and pattern formation, e.g. mesenchymal condensation. The cellular Potts model, a stochastic model that accurately reproduces cell movement and rearrangement, models cell dynamics. All these models couple in a controllable way, resulting in a powerful and flexible computational environment for morphogenesis, which allows for simultaneous incorporation of growth and spatial patterning. RESULTS We use CompuCell to simulate the formation of the skeletal architecture in the avian limb bud. AVAILABILITY Binaries and source code for Microsoft Windows, Linux and Solaris are available for download from http://sourceforge.net/projects/compucell/

The mechanism of precartilage mesenchymal condensation: A major role for interaction of the cell surface with the amino-terminal heparin-binding domain of fibronectin☆

Using low magnification Hoffman Modulation Contrast microscopy to rapidly identify precartilage mesenchymal condensations in chick limb bud cultures, we have determined the effect on condensation number of treatments disruptive of the interaction of cell surface components with endogenously produced fibronectin. A monoclonal antibody directed against the amino-terminal heparin-binding domain of fibronectin reduced the number of condensations by more than 50%, as did the oligopeptide gly-arg-gly, which is a repeated motif in that fibronectin domain. In contrast, monoclonal antibodies directed against the collagen- and integrin-binding domains of fibronectin, or oligopeptides containing the fibronectin integrin-recognition sequence arg-gly-asp-ser, had no significant effect on condensation number. Addition of Flavobacterium heparinase to cultures also reduced condensation number by more than 50%. Alcian blue staining of sulfated proteoglycan was greatly reduced in differentiated cultures that had been exposed to treatments that reduced condensation number. Taken together with the accompanying study, which directly demonstrates an adhesive interaction between the amino-terminal domain of extracellular fibronectin and heparin-like molecules on the surfaces of latex bead probes, the data presented here strongly indicate a major role for the corresponding cell-matrix interaction in mediating precartilage condensation in limb mesenchyme.

Nonuniform distribution of fibronectin during avian limb development

Abstract Using indirect immunofluorescence we have examined the distribution of the cell surface and extracellular matrix glycoprotein fibronectin at the epithelial-mesenchymal interface and in the mesenchyme of developing chick and duck wing buds. At all stages examined, in both species, staining for fibronectin is greatly enhanced in the basement membrane subjacent to the apical ectodermal ridge (AER), a site of inductive tissue interaction, relative to the epithelial basement membranes in the noninductive dorsal and ventral limb epithelial-mesenchymal interfaces. In stage 23, 25, and 28 chick limb buds, staining for fibronectin is uniform in the least mature distal mesenchyme, retained between more proximal cells undergoing precartilage condensation and lost in those regions undergoing myogenesis, and persistent in all but the most mature cartilage present at the latest stage examined. These results are consistent with a role for fibronectin in AER-induced limb outgrowth, and with a transient role for the glycoprotein in the formation of the skeletal pattern of the limb.

Dynamical mechanisms for skeletal pattern formation in the vertebrate limb

We describe a ‘reactor–diffusion’ mechanism for precartilage condensation based on recent experiments on chondrogenesis in the early vertebrate limb and additional hypotheses. Cellular differentiation of mesenchymal cells into subtypes with different fibroblast growth factor (FGF) receptors occurs in the presence of spatio–temporal variations of FGFs and transforming growth factor–betas (TGF–βs). One class of differentiated cells produces elevated quantities of the extracellular matrix protein fibronectin, which initiates adhesion–mediated preskeletal mesenchymal condensation. The same class of cells also produces an FGF–dependent laterally acting inhibitor that keeps condensations from expanding beyond a critical size. We show that this ‘reactor–diffusion’ mechanism leads naturally to patterning consistent with skeletal form, and describe simulations of spatio–temporal distribution of these differentiated cell types and the TGF–β and inhibitor concentrations in the developing limb bud.

A Framework for Three-Dimensional Simulation of Morphogenesis

We present COMPUCELL3D, a software framework for three-dimensional simulation of morphogenesis in different organisms. COMPUCELL3D employs biologically relevant models for cell clustering, growth, and interaction with chemical fields. COMPUCELL3D uses design patterns for speed, efficient memory management, extensibility, and flexibility to allow an almost unlimited variety of simulations. We have verified COMPUCELL3D by building a model of growth and skeletal pattern formation in the avian (chicken) limb bud. Binaries and source code are available, along with documentation and input files for sample simulations, at http:// compucell.sourceforge.net.

Phenotypic and dynamical transitions in model genetic networks I. Emergence of patterns and genotype-phenotype relationships

SUMMARY Genotype–phenotype interactions during the evolution of form in multicellular organisms is a complex problem but one that can be aided by computational approaches. We present here a framework within which developmental patterns and their underlying genetic networks can be simulated. Gene networks were chosen to reflect realistic regulatory circuits, including positive and negative feedback control, and the exchange of a subset of gene products between cells, or within a syncytium. Some of these networks generate stable spatial patterns of a subset of their molecular constituents, and can be assigned to categories (e.g., “emergent” or “hierarchic”) based on the topology of molecular circuitry. These categories roughly correspond to what has been discussed in the literature as “self‐organizing” and “programmed” processes of development. The capability of such networks to form patterns of repeating stripes was studied in network ensembles in which parameters of gene‐gene interaction were caused to vary in a manner analogous to genetic mutation. The evolution under mutational change of individual representative networks of each category was also simulated. We have found that patterns with few stripes (≤3) are most likely to originate in the form of a hierarchic network, whereas those with greater numbers of stripes (≥4) originate most readily as emergent networks. However, regardless of how many stripes it contains, once a pattern is established, there appears to be an evolutionary tendency for emergent mechanisms to be replaced by hierarchic mechanisms. These results have potential significance for the understanding of genotype‐phenotype relationships in the evolution of metazoan form.

On multiscale approaches to three-dimensional modelling of morphogenesis

In this paper we present the foundation of a unified, object-oriented, three-dimensional biomodelling environment, which allows us to integrate multiple submodels at scales from subcellular to those of tissues and organs. Our current implementation combines a modified discrete model from statistical mechanics, the Cellular Potts Model, with a continuum reaction–diffusion model and a state automaton with well-defined conditions for cell differentiation transitions to model genetic regulation. This environment allows us to rapidly and compactly create computational models of a class of complex-developmental phenomena. To illustrate model development, we simulate a simplified version of the formation of the skeletal pattern in a growing embryonic vertebrate limb.

The distal boundary of myogenic primordia in chimeric avian limb buds and its relation to an accessible population of cartilage progenitor cells.

Using chimeras consisting of chick embryos that had received substitution grafts of quail somites, we have determined the distalmost extension of the myogenic primordia in the outgrowing wing bud at 5 days of incubation. At Hamburger-Hamilton stage 25 the most distal premuscle cell is consistently 300 mum or more from the apex of the wing mesoblast. The stage 25 wing tip resembles very early whole limb buds in not having proceeded beyond the mesenchymal state or having expressed markers of terminal differentiation. However, unlike early whole limb buds it is free of a myogenic subpopulation. We therefore propose that the stage 25 wing tip is the appropriate system for in vitro and molecular studies of cartilage differentiation.