Modeling the human cardiome in silico

Modeling Ca2+ signaling in the microcirculation: intercellular communication and vasoreactivity

A network of intracellular signaling pathways and complex intercellular interactions regulate calcium mobilization in vascular cells, arteriolar tone, and blood flow. Different endothelium-derived vasoreactive factors have been identified and the importance of myoendothelial communication in vasoreactivity is now well appreciated. The ability of many vascular networks to conduct signals upstream also is established. This phenomenon is critical for both short-term changes in blood perfusion as well as long-term adaptations of a vascular network. In addition, in a phenomenon termed vasomotion, arterioles often exhibit spontaneous oscillations in diameter. This is thought to improve tissue oxygenation and enhance blood flow. Experimentation has begun to reveal important aspects of the regulatory machinery and the significance of these phenomena for the regulation of local perfusion and oxygenation. Mathematical modeling can assist in elucidating the complex signaling mechanisms that participate in these phenomena. This review highlights some of the important experimental studies and relevant mathematical models that provide the current understanding of these mechanisms in vasoreactivity.

Calcium dynamics and signaling in vascular regulation: computational models

Calcium is a universal signaling molecule with a central role in a number of vascular functions including in the regulation of tone and blood flow. Experimentation has provided insights into signaling pathways that lead to or affected by Ca(2+) mobilization in the vasculature. Mathematical modeling offers a systematic approach to the analysis of these mechanisms and can serve as a tool for data interpretation and for guiding new experimental studies. Comprehensive models of calcium dynamics are well advanced for some systems such as the heart. This review summarizes the progress that has been made in modeling Ca(2+) dynamics and signaling in vascular cells. Model simulations show how Ca(2+) signaling emerges as a result of complex, nonlinear interactions that cannot be properly analyzed using only a reductionist's approach. A strategy of integrative modeling in the vasculature is outlined that will allow linking macroscale pathophysiological responses to the underlying cellular mechanisms.

Building the developmental oculome: systems biology in vertebrate eye development and disease

The vertebrate eye is a sophisticated multicomponent organ that has been actively studied for over a century, resulting in the identification of the major embryonic and molecular events involved in its complex developmental program. Data gathered so far provides sufficient information to construct a rudimentary network of the various signaling molecules, transcription factors, and their targets for several key stages of this process. With the advent of genomic technologies, there has been a rapid expansion in our ability to collect and process biological information, and the use of systems-level approaches to study specific aspects of vertebrate eye development has already commenced. This is beginning to result in the definition of the dynamic developmental networks that operate in ocular tissues, and the interactions of such networks between coordinately developing ocular tissues. Such an integrative understanding of the eye by a comprehensive systems-level analysis can be termed the 'oculome', and that of serial developmental stages of the eye as it transits from its initiation to a fully formed functional organ represents the 'developmental oculome'. Construction of the developmental oculome will allow novel mechanistic insights that are essential for organ regeneration-based therapeutic applications, and the generation of computational models for eye disease states to predict the effects of drugs. This review discusses our present understanding of two of the individual components of the developing vertebrate eye--the lens and retina--at both the molecular and systems levels, and outlines the directions and tools required for construction of the developmental oculome.

The developmental nephrome: systems biology in the developing kidney

PURPOSE OF REVIEW

A set of important genes and signaling pathways involved in kidney development is emerging from analyses of mutant mice, in-vitro models, and global gene expression patterns. Conversion of data into dynamic models or networks through the synthesis of information at multiple levels is crucial for a better understanding of kidney development.

RECENT FINDINGS

Genetic and in-vitro evidence is beginning to provide a limited sense of the network topology in stages of kidney development. Intriguing data from other fields suggest how, with the aid of large-scale gene expression studies, these stages might be represented as dynamic attractor states. It is also suggested how branching morphogenesis of the epithelial ureteric bud may be sustained by an autocatalytic set of proteins whose interactions lead to repeated rounds of tip and stalk generation. Accumulating data in lower organisms suggest network topologies may be quite flexible, and the implications of these results for varieties of tubulogenesis and renal regeneration after acute injury are discussed.

SUMMARY

Currently it may be feasible to build tentative dynamic multistage models of nephrogenesis that facilitate experimental thinking. As data accumulate, it may become possible to test their predictive value.

A strategy for integrative computational physiology

Organ function (the heart beat for example) can only be understood through knowledge of molecular and cellular processes within the constraints of structure-function relations at the tissue level. A quantitative modeling framework that can deal with these multiscale issues is described here under the banner of the International Union of Physiological Sciences Physiome Project.

Developing integrative computational models of pulmonary structure

Integrative computational modeling of the pulmonary system aims to incorporate interactions between the lung's subsystems by means of a hierarchy of structural and functional models. This requires detailed imaging-based data, along with a wide range of functional information from experiments. Advances in computed tomography imaging technology ensure that high-resolution data are now readily available upon which the structure of these models can be based. We present methods for constructing anatomically realistic finite element models of interrelated pulmonary structures from such data. Segmented human lung lobe data are fit to high-order (cubic Hermite) volume elements. Meshes for the conducting airways and pulmonary arteries and veins are constructed within the lobe mesh, using a combination of fitting to imaging data and a bifurcating-distributive algorithm. The algorithm generates an airway-consistent mesh within a host volume, and this airway mesh is then used as a template for generating blood vessel models. The lung parenchyma is modeled as a space-filling three-dimensional (3D) Voronoi mesh, with generated geometry consistent with the alveolated airway structure. Pulmonary capillaries are generated over the alveolar model, as a 2D Voronoi mesh. These structural models have been compared extensively with morphometric data to verify that their geometry is representative of the pulmonary system. The models are designed to be integrative: they relate multiple structural systems within the same individual, and their use as computational meshes allows application of spatially distributed properties.