Before programs: the physical origination of multicellular forms

By examining the formative role of physical processes in modern-day developmental systems, we infer that although such determinants are subject to constraints and rarely act in a "pure" fashion, they are identical to processes generic to all viscoelastic, chemically excitable media, non-living as well as living. The processes considered are free diffusion, immiscible liquid behavior, oscillation and multistability of chemical state, reaction-diffusion coupling and mechanochemical responsivity. We suggest that such processes had freer reign at early stages in the history of multicellular life, when less evolution had occurred of genetic mechanisms for stabilization and entrenchment of functionally successful morphologies. From this we devise a hypothetical scenario for pattern formation and morphogenesis in the earliest metazoa. We show that the expected morphologies that would arise during this relatively unconstrained "physical" stage of evolution correspond to the hollow, multilayered and segmented morphotypes seen in the gastrulation stage embryos of modern-day metazoa as well as in Ediacaran fossil deposits of approximately 600 Ma. We suggest several ways in which organisms that were originally formed by predominantly physical mechanisms could have evolved genetic mechanisms to perpetuate their morphologies.     

Generic physical mechanisms of morphogenesis and pattern formation as determinants in the evolution of multicellular organization

Early embryos of metazoan species are subject to the same set of physical forces and interactions as any small parcels of semi-solid material, living or nonliving. It is proposed that such “generic” properties of embryonic tissues have played a major role in the evolution of biological form and pattern by providing an array of morphological templates, during the early stages of metazoan phylogeny, upon which natural selection could act. The generic physical mechanisms considered include sedimentation, diffusion, and reaction-diffusion coupling, all of which can give rise to chemical nonuniformities (including periodic patterns) in eggs and small multicellular aggregates, and differential adhesion, which can lead to the formation of boundaries of non-mixing between adjacent cell populations. Generic mechanisms that produce chemical patterns, acting in concern with the capacity of cells to modulate their adhesivity (presumed to be a primitive, defining property of metazoa), could lead to multilayered gastrulae of various types, segmental organization, and many of the other distinguishing characteristics of extant and extinct metazoan body plans. Similar generic mechanisms, acting on small tissue primordia during and subsequent to the establishment of the major body plans, could have given rise to the forms of organs, such as the vertebrate limbs. Generic physical processes acting on a single system of cells and cell products can often produce a widely divergent set of morphological phenotypes, and these are proposed to be the raw material of the evolution of form. The establishment of any ecologically successful form by these mechanisms will be followed, under this hypothesis, by a period of genetic evolution, in which the recruitment of gene products to produce the “generically templated” morphologies by redundant pathways would be favoured by intense selection, leading to extensive genetic change with little impact on the fossil record. In this view, the stabilizing and reinforcing functions of natural selection are more important than its ability to effect incremental change in morphology. Aspects of evolution which are problematic from the standard neo-Darwinian viewpoint, or not considered within that framework, but which follow in a straightforward fashion from the view presented here, include the beginnings of an understanding of why organisms have the structure and appearance they’ do, why homoplasy (the recurrent evolution of certain forms) is so prevalent, why evolution has the tempo and mode it does (“punctuated equilibrium”), and why a “rapid” burst of morphological evolution occurred so soon after the origin of the metazoa.     

Variation and robustness of the mechanics of gastrulation: the role of tissue mechanical properties during morphogenesis

Diverse mechanisms of morphogenesis generate a wide variety of animal forms. In this work, we discuss two ways that the mechanical properties of embryonic tissues could guide one of the earliest morphogenetic movements in animals, gastrulation. First, morphogenetic movements are a function of both the forces generated by cells and the mechanical properties of the tissues. Second, cells could change their behavior in response to their mechanical environment. Theoretical studies of gastrulation indicate that different morphogenetic mechanisms differ in their inherent sensitivity to tissue mechanical properties. Those few empirical studies that have investigated the mechanical properties of amphibian and echinoderm gastrula-stage embryos indicate that there could be high embryo-to-embryo variability in tissue stiffness. Such high embryo-to-embryo variability would imply that gastrulation is fairly robust to variation in tissue stiffness. Cell culture studies demonstrate a wide variety of cellular responses to the mechanical properties of their microenvironment. These responses are likely to be developmentally regulated, and could either increase or decrease the robustness of gastrulation movements depending on which cells express which responses. Hence both passive physical and mechanoregulatory processes will determine how sensitive gastrulation is to tissue mechanics. Addressing these questions is important for understanding the significance of diverse programs of early development, and how genetic or environmental perturbations influence development. We discuss methods for measuring embryo-to-embryo variability in tissue mechanics, and for experimentally perturbing those mechanical properties to determine the sensitivity of gastrulation to tissue mechanics.     

Physical forces modulate cell differentiation and proliferation processes

Currently, the predominant hypothesis explains cellular differentiation and behaviour as an essentially genetically driven intracellular process, suggesting a gene‐centrism paradigm. However, although many living species genetic has now been described, there is still a large gap between the genetic information interpretation and cell behaviour prediction. Indeed, the physical mechanisms underlying the cell differentiation and proliferation, which are now known or suspected to guide such as the flow of energy through cells and tissues, have been often overlooked. We thus here propose a complementary conceptual framework towards the development of an energy‐oriented classification of cell properties, that is, a mitochondria‐centrism hypothesis based on physical forces‐driven principles. A literature review on the physical–biological interactions in a number of various biological processes is analysed from the point of view of the fluid and solid mechanics, electricity and thermodynamics. There is consistent evidence that physical forces control cell proliferation and differentiation. We propose that physical forces interfere with the cell metabolism mostly at the level of the mitochondria, which in turn control gene expression. The present perspective points towards a paradigm shift complement in biology.     

Mechanisms of pattern formation in development and evolution

We present a classification of developmental mechanisms that have been shown experimentally to generate pattern and form in metazoan organisms. We propose that all such mechanisms can be organized into three basic categories and that two of these may act as composite mechanisms in two different ways. The simple categories are cell autonomous mechanisms in which cells enter into specific arrangements ('patterns') without interacting, inductive mechanisms in which cell communication leads to changes in pattern by reciprocal or hierarchical alteration of cell phenotypes ('states') and morphogenetic mechanisms in which pattern changes by means of cell interactions that do not change cell states. The latter two types of mechanism can be combined either morphostatically, in which case inductive mechanisms act first, followed by the morphogenetic mechanism, or morphodynamically, in which case both types of mechanisms interact continuously to modify each other's dynamics. We propose that this previously unexplored distinction in the operation of composite developmental mechanisms provides insight into the dynamics of many developmental processes. In particular, morphostatic and morphodynamic mechanisms respond to small changes in their genetic and microenvironmental components in dramatically different ways. We suggest that these differences in 'variational properties' lead to morphostatic and morphodynamic mechanisms being represented to different extents in early and late stages of development and to their contributing in distinct ways to morphological transitions in evolution.     

Epithelial morphogenesis: filopodia at work

Spreading and fusion of epithelial sheets are conserved morphogenetic mechanisms that help shape embryos and tissues. Recent findings suggest that the formation of dynamic filopodia at the leading front of the epithelia plays a critical role in regulating cell movement and recognition during these processes.     

Copying nodes versus editing links: the source of the difference between genetic regulatory networks and the WWW

We study two kinds of networks: genetic regulatory networks and the World Wide Web. We systematically test microscopic mechanisms to find the set of such mechanisms that optimally explain each networks' specific properties. In the first case we formulate a model including mainly random unbiased gene duplications and mutations. In the second case, the basic moves are website generation and rapid surf-induced link creation (/destruction). The different types of mechanisms reproduce the appropriate observed network properties. We use those to show that different kinds of networks have strongly system-dependent macroscopic experimental features. The diverging properties result from dissimilar node and link basic dynamics. The main non-uniform properties include the clustering coefficient, small-scale motifs frequency, time correlations, centrality and the connectivity of outgoing links. Some other features are generic such as the large-scale connectivity distribution of incoming links (scale-free) and the network diameter (small-worlds). The common properties are just the general hallmark of autocatalysis (self-enhancing processes), while the specific properties hinge on the specific elementary mechanisms. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Online.     

Pinching and pushing: fold formation in the Drosophila dorsal epidermis

Epithelial folding is a fundamental morphogenetic process that shapes planar epithelial sheets into complex three-dimensional structures. Multiple mechanisms can generate epithelial folds, including apical constriction, which acts locally at the cellular level, differential growth on the tissue scale, or buckling because of compression from neighboring tissues. Here, we investigate the formation of dorsally located epithelial folds at segment boundaries during the late stages of Drosophila embryogenesis. We found that the fold formation at the segment boundaries occurs through the juxtaposition of two key morphogenetic processes: local apical constriction and tissue-level compressive forces from posterior segments. Further, we found that epidermal spreading and fold formation are accompanied by spatiotemporal pulses of Hedgehog (Hh) signaling. A computational model that incorporates the local forces generated from the differential tensions of the apical, basal, and lateral sides of the cell and active forces generated within the whole tissue recapitulates the overall fold formation process in wild-type and Hh overexpression conditions. In sum, this work demonstrates how epithelial folding depends on multiple, separable physical mechanisms to generate the final morphology of the dorsal epidermis. This work illustrates the modularity of morphogenetic unit operations that occur during epithelial morphogenesis.     

Number of whorls and umbel rays in Acetabularia]

It was found in the proposed model of morphogenesis of Acetabularia that the number of whorls N (as well as the number of umbel rays) depends on the degree of mechanical instability of the deforming cell wall (the greater is instability, the higher is the value N). The genetic control of final morphogenetic processes can be realized by setting definite physical conditions and properties. The theoretical estimates of N carried out for different cases agree fairly well with the experimental data obtained.     

Water deficit and growth. Co-ordinating processes without an orchestrator?

Water deficit affects plant growth via reduced carbon accumulation, cell number and tissue expansion. We review the ways in which these processes are co-ordinated. Tissue expansion and its sensitivity to water deficit may be the most crucial process, involving tight co-ordination between the mechanisms which govern cell wall mechanical properties and plant hydraulics. The analyses of sensitivities, time constants and genetic correlations suggest that tissue expansion is loosely co-ordinated with cell division and carbon accumulation which may have limited direct effects on growth under water deficit. We therefore argue for essentially uncoupled mechanisms with feedbacks between them, rather than for a co-ordinated re-programming of all processes. Consequences on plant modelling and plant breeding in dry environment are discussed.     

The bhopalator: a molecular model of the living cell based on the concepts of conformons and dissipative structures

A molecular model of the living cell has been formulated based on a new theory of enzymic catalysis which takes into account the complementary roles of free energy and genetic information. The elementary units of free energy and genetic information that are necessary and sufficient for effectuating molecular mechanisms responsible for the life of the cell are called conformons. Conformons are visualized as a collection of a small number of catalytic residues of enzymes or segments of nucleic acids that are arranged in space and time with appropriate force vectors so as to cause chemical transformations or physical changes of a substrate or a bound ligand. So defined, conformons provide a plausible molecular means to link the genetic information stored in DNA and its ultimate expression, namely networks of coupled intracellular biochemical reactions and physical processes maintained by a continuous dissipation of free energy--dissipative structures of Prigogine. The proposed model of the living cell appears to possess the potential for bridging the gap between molecular biology and the biology of multicellular systems.     

Plant‐facilitated effects of exotic earthworm Pontoscolex corethrurus on the soil carbon and nitrogen dynamics and soil microbial community in a subtropical field ecosystem

Earthworms and plants greatly affect belowground properties; however, their combined effects are more attractive based on the ecosystem scale in the field condition. To address this point, we manipulated earthworms (exotic endogeic species Pontoscolex corethrurus) and plants (living plants [native tree species Evodia lepta] and artificial plants) to investigate their combined effects on soil microorganisms, soil nutrients, and soil respiration in a subtropical forest. The manipulation of artificial plants aimed to simulate the physical effects of plants (e.g., shading and interception of water) such that the biological effects of plants could be evaluated separately. We found that relative to the controls, living plants but not artificial plants significantly increased the ratio of fungal to bacterial phospholipid fatty acids (PLFAs) and fungal PLFAs. Furthermore, earthworms plus living plants significantly increased the soil respiration and decreased the soil NH₄⁺‐N, which indicates that the earthworm effects on the associated carbon, and nitrogen processes were greatly affected by living plants. The permutational multivariate analysis of variance results also indicated that living plants but not earthworms or artificial plants significantly changed the soil microbial community. Our results suggest that the effects of plants on soil microbes and associated soil properties in this study were largely explained by their biological rather than their physical effects.     

Elevated expression of pp60c-src alters a selective morphogenetic property of epithelial cells in vitro without a mitogenic effect.

Madin-Darby canine kidney (MDCK) cells are highly differentiated and have retained the morphogenetic properties necessary to form polarized, multicellular epithelial structures (cysts) in vitro that resemble epithelial tissues in vivo. We introduced the c-src gene into MDCK cells to elevate the level of the plasma membrane-associated cellular tyrosine kinase, pp60c-src, to levels two- to ninefold higher than that expressed in parent MDCK cells. Our results revealed a highly discriminatory biological action of pp60c-src on the morphogenetic properties of MDCK cells. Elevated expression of pp60c-src conferred on MDCK cells the ability to undergo dramatic changes of cell shape that includes the formation of long cell processes (100 to 200 microns), never observed in control MDCK cells. The morphogenesis of multicellular epithelial cysts was altered by elevated levels of pp60c-src and led to predictable distortions of their three-dimensional architecture. However, these cells established morphologically normal cell polarity, formed adhesive epithelial cell-cell contacts indistinguishable from those of control MDCK cells, and exhibited neither focus-forming ability or anchorage-independent growth potential. Finally, we showed that MDCK cells expressing elevated levels of pp60c-src exhibit increased phosphorylation of a more limited number of phosphotyrosine-containing proteins than MDCK cells expressing pp60v-src. We suggest that a natural function of pp60c-src is to regulate the morphogenetic properties which determine the shape of differentiated cells and multicellular structures.     

Bio-soliton model that predicts non-thermal electromagnetic frequency bands,that either stabilize or destabilize living cells

Solitons, as self-reinforcing solitary waves, interact with complex biological phenomena such as cellular self-organization. A soliton model is able to describe a spectrum of electromagnetism modalities that can be applied to understand the physical principles of biological effects in living cells, as caused by endogenous and exogenous electromagnetic fields and is compatible with quantum coherence. A bio-soliton model is proposed, that enables to predict which eigen-frequencies of non-thermal electromagnetic waves are life-sustaining and which are, in contrast, detrimental for living cells. The particular effects are exerted by a range of electromagnetic wave eigen-frequencies of one-tenth of a Hertz till Peta Hertz that show a pattern of 12 bands, and can be positioned on an acoustic reference frequency scale. The model was substantiated by a meta-analysis of 240 published articles of biological electromagnetic experiments, in which a spectrum of non-thermal electromagnetic waves were exposed to living cells and intact organisms. These data support the concept of coherent quantized electromagnetic states in living organisms and the theories of Fröhlich, Davydov and Pang. It is envisioned that a rational control of shape by soliton-waves and related to a morphogenetic field and parametric resonance provides positional information and cues to regulate organism-wide systems properties like anatomy, control of reproduction and repair.     

A unified model for the origin of DNA sequence-directed curvature

The fine structure of the DNA double helix and a number of its physical properties depend upon nucleotide sequence. This includes minor groove width, the propensity to undergo the B-form to A-form transition, sequence-directed curvature, and cation localization. Despite the multitude of studies conducted on DNA, it is still difficult to appreciate how these fundamental properties are linked to each other at the level of nucleotide sequence. We demonstrate that several sequence-dependent properties of DNA can be attributed, at least in part, to the sequence-specific localization of cations in the major and minor grooves. We also show that effects of cation localization on DNA structure are easier to understand if we divide all DNA sequences into three principal groups: A-tracts, G-tracts, and generic DNA. The A-tract group of sequences has a peculiar helical structure (i.e., B*-form) with an unusually narrow minor groove and high base-pair propeller twist. Both experimental and theoretical studies have provided evidence that the B*-form helical structure of A-tracts requires cations to be localized in the minor groove. G-tracts, on the other hand, have a propensity to undergo the B-form to A-form transition with increasing ionic strength. This property of G-tracts is directly connected to the observation that cations are preferentially localized in the major groove of G-tract sequences. Generic DNA, which represents the vast majority of DNA sequences, has a more balanced occupation of the major and minor grooves by cations than A-tracts or G-tracts and is thereby stabilized in the canonical B-form helix. Thus, DNA secondary structure can be viewed as a tug of war between the major and minor grooves for cations, with A-tracts and G-tracts each having one groove that dominates the other for cation localization. Finally, the sequence-directed curvature caused by A-tracts and G-tracts can, in both cases, be explained by the cation-dependent mismatch of A-tract and G-tract helical structures with the canonical B-form helix of generic DNA (i.e., a cation-dependent junction model).     

Regional requirements for Dishevelled signaling during Xenopus gastrulation: separable effects on blastopore closure, mesendoderm internalization and archenteron formation

During amphibian gastrulation, the embryo is transformed by the combined actions of several different tissues. Paradoxically, many of these morphogenetic processes can occur autonomously in tissue explants, yet the tissues in intact embryos must interact and be coordinated with one another in order to accomplish the major goals of gastrulation: closure of the blastopore to bring the endoderm and mesoderm fully inside the ectoderm, and generation of the archenteron. Here, we present high-resolution 3D digital datasets of frog gastrulae, and morphometrics that allow simultaneous assessment of the progress of convergent extension, blastopore closure and archenteron formation in a single embryo. To examine how the diverse morphogenetic engines work together to accomplish gastrulation, we combined these tools with time-lapse analysis of gastrulation, and examined both wild-type embryos and embryos in which gastrulation was disrupted by the manipulation of Dishevelled (Xdsh) signaling. Remarkably, although inhibition of Xdsh signaling disrupted both convergent extension and blastopore closure, mesendoderm internalization proceeded very effectively in these embryos. In addition, much of archenteron elongation was found to be independent of Xdsh signaling, especially during the second half of gastrulation. Finally, even in normal embryos, we found a surprising degree of dissociability between the various morphogenetic processes that occur during gastrulation. Together, these data highlight the central role of PCP signaling in governing distinct events of Xenopus gastrulation, and suggest that the loose relationship between morphogenetic processes may have facilitated the evolution of the wide variety of gastrulation mechanisms seen in different amphibian species.     

Orexin modulation of adipose tissue

The orexins are neuropeptides with critical functions in the central nervous system. These neuropeptides have important roles in energy balance and obesity, and therefore on the accumulation of adipose tissue. Rodents lacking orexins, typically through genetic knockouts, experience increased weight gain and accumulation of adipose tissue. Evidence indicates that the lack of the orexins increase adiposity as a result of decreased energy expenditure, principally through a reduction of physical activity. Different lines of evidence suggest that other mechanisms are likely also in play, and neural influences on both white and brown adipose tissues remain to be fully and functionally defined. In addition, the orexin peptides and their receptors are expressed in adipose tissue, with little available information as to their significance. This review summarizes our current understanding of how the orexin peptides affect adipose tissue. We provide a brief introduction to the physiology of orexins and their effects on white and brown adipose tissues in the context of energy balance. We conclude this review by integrating this information in the context of the known physiology of the orexins. This article is part of a Special Issue entitled: Modulation of Adipose Tissue in Health and Disease.     

The Drosophila shell game: patterning genes and morphological change

What are the mechanisms that convert cell-fate information into shape changes and movements, thus creating the biological forms that comprise tissues and organs? Tubulogenesis of the Drosophila dorsal eggshell structures provides an excellent system for studying the link between patterning and morphogenesis. Elegant genetic and molecular analyses from over a decade provide a strong foundation for understanding the combinatorial signaling events that specify dorsal anterior cell fates within the follicular epithelium overlying the oocyte. Recent studies reveal the morphogenetic events that alter that flat epithelial sheet into two tubes; these tubes form the mold for synthesizing the dorsal appendages--eggshell structures that facilitate respiration in the developing embryo. This review summarizes the mutant analyses that give insight into these patterning and morphogenetic processes.