C. Forbes Dewey

Vascular Endothelial Cells Respond to Spatial Gradients in Fluid Shear Stress by Enhanced Activation of Transcription Factors

The vascular endothelium is exposed to a spectrum of fluid mechanical forces generated by blood flow; some of these, such as fluid shear stress, can directly modulate endothelial gene expression. Previous work by others and in our laboratory, using an in vitro uniform laminar shear stress model, has identified various shear stress response elements (SSREs) within the promoters of certain endothelial genes that regulate their expression by interacting with various transcription factors, including nuclear factor-kappaB (NF-kappaB), early growth response-1 (Egr-1), and activator protein-1 (AP-1, composed of c-Jun/c-Jun and c-Jun/c-Fos protein dimers). In the current study, we have examined the topographical patterns of NF-kappaB, Egr-1, c-Jun, and c-Fos activation in a specially designed in vitro disturbed laminar shear stress model, which incorporates regions of significant spatial shear stress gradients similar to those found in atherosclerosis-prone arterial geometries in vivo (eg, arterial bifurcations, curvatures, ostial openings). Using newly developed quantitative image analysis techniques, we demonstrate that endothelial cells subjected to disturbed laminar shear stress exhibit increased levels of nuclear localized NF-kappaB, Egr-1, c-Jun, and c-Fos, compared with cells exposed to uniform laminar shear stress or maintained under static conditions. In addition, individual cells display a heterogeneity in responsiveness to disturbed flow, as measured by the amount of NF-kappaB, Egr-1, c-Jun, and c-Fos in their nuclei. This differential regulation of transcription factor expression by disturbed versus uniform laminar shear stress indicates that regional differences in blood flow patterns in vivo-in particular, the occurrence of spatial shear stress gradients-may represent important local modulators of endothelial gene expression at anatomic sites predisposed for atherosclerotic development.

Apparatus for subjecting living cells to fluid shear stress

This apparatus subjects cultured cell specimens to controlled levels of fluid shear stress in vitro. The cone‐plate geometry permits long term (≳7 days) investigation of the effects of external fluid forces on living cells.

Evaluation of Carotid Stenosis by Phonoangiography

Quantitative spectral (frequency) analyses were performed on 60 carotid bruits in 48 patients with suspected carotid stenosis. The technic was totally noninvasive. Bruits were recorded at the skin surface, analyzed by a minicomputer, and the degree of arterial stenosis estimated using a recently derived theory of sound production by turbulent blood flow. This method has been named phonoangiography. Fifty of the 60 bruits (83 per cent) had spectrums characteristic of turbulent blood flow, and a residual lumen diameter could be calculated. Results from the noninvasvie technic compared well with data obtained from radiographic carotid arteriograms in the 50 bruits with internal carotid artery stenosis. The residual lumen diameter estimated from phonoangiography differed from the radiographic value by less than 1 mm in 83 per cent and less than 1.5 mm in 92 per cent of the studies. Phonoangiography appears to be a useful method for assessment of carotid artery stenosis.

Mechanical Remodeling of the Endothelial Surface and Actin Cytoskeleton Induced by Fluid Flow

Objective: The mechanism by which cultured endothelial cells respond to shear stress is controversial. The cell surface and cytoskeleton are involved, but their roles are undefined. In this study, previously unknown changes in the surface detail and actin cytoskeleton of bovine aortic endothelial cells were identified.

Cell-delivery therapeutics for liver regeneration☆

For acute, chronic, or hereditary diseases of the liver, cell transplantation therapies can stimulate liver regeneration or serve as a bridge until liver transplantation can be performed. Recently, fetal hepatocytes, stem cells, liver progenitor cells, or other primitive and proliferative cell types have been employed for cell transplantation therapies, in an effort to improve the survival, proliferation, and engraftment of the transplanted cells. Reviewing earlier studies, which achieved success by transplanting mature hepatocytes, we propose that there is a switch-like regulation of liver regeneration that changes state according to a stimulus threshold of extracellular influences such as cytokines, matrices and neighboring cells. Important determinants of a successful clinical outcome include sufficient quantities and functional levels of the transplanted cells (even for short periods to alter the environment), rather than just engraftment levels or survival durations of the exogenously transplanted cells. The relative importance of these determining factors will impact future choices of cell sources, delivery vehicles, and sites of cell transplantation to stimulate liver regeneration for patients with severe liver diseases.

CytoSolve: A Scalable Computational Method for Dynamic Integration of Multiple Molecular Pathway Models

A grand challenge of computational systems biology is to create a molecular pathway model of the whole cell. Current approaches involve merging smaller molecular pathway models’ source codes to create a large monolithic model (computer program) that runs on a single computer. Such a larger model is difficult, if not impossible, to maintain given ongoing updates to the source codes of the smaller models. This paper describes a new system called CytoSolve that dynamically integrates computations of smaller models that can run in parallel across different machines without the need to merge the source codes of the individual models. This approach is demonstrated on the classic Epidermal Growth Factor Receptor (EGFR) model of Kholodenko. The EGFR model is split into four smaller models and each smaller model is distributed on a different machine. Results from four smaller models are dynamically integrated to generate identical results to the monolithic EGFR model running on a single machine. The overhead for parallel and dynamic computation is approximately twice that of a monolithic model running on a single machine. The CytoSolve approach provides a scalable method since smaller models may reside on any computer worldwide, where the source code of each model can be independently maintained and updated.

Measuring actin dynamics in endothelial cells

Cytoplasmic actin distributes between monomeric and filamentous phases in cells. As cells crawl, actin polymerizes near the plasma membrane of expanding peripheral cytoplasm and depolymerizes elsewhere. Thus, the finite actin filament lifetime, the diffusivity of actin monomer, and the distribution of actin between the polymer and monomer phases are key parameters in cell motility. The dynamics of cellular actin can be determined by following the evolution of fluorescence in the techniques of photoactivated fluorescence (PAF) or fluorescence recovery after photobleaching (FRAP) of microinjected actin derivatives. A mathematical model is discussed that measures monomer diffusion coefficients, filament turnover rates, and the fraction of actin polymerized from measurements of the evolution of fluorescence from a photoactivated band [Tardy et al. (1995) Biophys. J., 69:1674–1682; McGrath et al. (1998) Biophys. J., in press]. Applying this model to subconfluent endothelial cells shows that ∼40% of the actin is polymer and that these filaments turn over on average every 6 minutes. This report dicusses how PAF and FRAP can be combined with more traditional biochemistry to probe actin cytoskeleton remodeling in endothelial cells. Microsc. Res. Tech. 43:385–394

Three-dimensional reconstruction of the actin cytoskeleton from stereo images

In eucaryotic cells, actin filaments are abundant components in the cytoskeleton where they form a complex three dimensional (3D) structural network that provides the cell with its shape and mechanical properties. However, understanding the structural and mechanical properties of actin filaments composing the cell cytoskeleton is often hampered by the inability to faithfully reconstruct the three-dimensional geometric relationships. This paper presents a vision-based reconstruction approach that automatically reconstitutes the three-dimensional structures of cytoskeletal polymers from stereo image pairs taken at the different tilt angles. The approach finds corresponding points between two images and recovers the depth information about the structures. The computational process consists of three major procedures: feature representation, stereo matching, and disparity refinement, implemented in a multi-resolution manner based on a coarse-to-fine strategy. The reconstruction depicts the three-dimensional structure of cytoskeletal polymers and their geometric relationships. New and useful information becomes available and allows quantitative analysis of the structure. Measurement of the cytoskeleton geometrical properties and the filament concentration in a defined volume are obtained by direct calculation.

Fluid Flow Modulates Vascular Endothelial Cytosolic Calcium Responses to Adenine Nucleotides

Objective: To determine whether fluid flow influences the action of soluble vasoactive agonists on vascular endothelium.

TENET: topological feature-based target characterization in signalling networks

MOTIVATION Target characterization for a biochemical network is a heuristic evaluation process that produces a characterization model that may aid in predicting the suitability of each molecule for drug targeting. These approaches are typically used in drug research to identify novel potential targets using insights from known targets. Traditional approaches that characterize targets based on their molecular characteristics and biological function require extensive experimental study of each protein and are infeasible for evaluating larger networks with poorly understood proteins. Moreover, they fail to exploit network connectivity information which is now available from systems biology methods. Adopting a network-based approach by characterizing targets using network features provides greater insights that complement these traditional techniques. To this end, we present Tenet (Target charactErization using NEtwork Topology), a network-based approach that characterizes known targets in signalling networks using topological features. RESULTS Tenet first computes a set of topological features and then leverages a support vector machine-based approach to identify predictive topological features that characterizes known targets. A characterization model is generated and it specifies which topological features are important for discriminating the targets and how these features should be combined to quantify the likelihood of a node being a target. We empirically study the performance of Tenet from a wide variety of aspects, using several signalling networks from BioModels with real-world curated outcomes. Results demonstrate its effectiveness and superiority in comparison to state-of-the-art approaches. AVAILABILITY AND IMPLEMENTATION Our software is available freely for non-commercial purposes from: https://sites.google.com/site/cosbyntu/softwares/tenet CONTACT hechua@ntu.edu.sg or assourav@ntu.edu.sg SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.