Intermediate cell states in epithelial-to-mesenchymal transition

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The transition of epithelial cells into a mesenchymal state (epithelial-to-mesenchymal transition or EMT) is a highly dynamic process implicated in various biological processes. During EMT, cells do not necessarily exist in 'pure' epithelial or mesenchymal states. There are cells with mixed (or hybrid) features of the two, which are termed as the intermediate cell states (ICSs). While the exact functions of ICS remain elusive, together with EMT it appears to play important roles in embryogenesis, tissue development, and pathological processes such as cancer metastasis.

Single-cell analysis reveals fibroblast heterogeneity and myeloid-derived adipocyte progenitors in murine skin wounds

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During wound healing in adult mouse skin, hair follicles and then adipocytes regenerate. Adipocytes regenerate from myofibroblasts, a specialized contractile wound fibroblast. Here we study wound fibroblast diversity using single-cell RNA-sequencing. On analysis, wound fibroblasts group into twelve clusters. Pseudotime and RNA velocity analyses reveal that some clusters likely represent consecutive differentiation states toward a contractile phenotype, while others appear to represent distinct fibroblast lineages.

Bridging Multiple Scales in Modeling Targeted Drug Nanocarrier Delivery

The vascular administration of targeted nanocarriers enables precise delivery of drugs to diseased or inflamed endothelial cells. The primary therapeutic goal we are pursuing is to optimize endothelial delivery of antioxidant and antiinflammatory agents for alleviation of acute pulmonary inflammation and oxidative stress through multiscale modeling with validating experimentation.

Low resolution models for mesoscale structure and thermodynamics of soft materials

Abstract: Low resolution coarse-grained (CG) models are extensively employed for investigating mesoscale phenomena in soft materials.  Nevertheless, it remains challenging to determine CG models that accurately describe both structure and thermodynamic properties since coarse-graining necessarily transfers entropy and information from the microstate distribution into the effective interactions between the remaining mesoscale degrees of freedom.  We employ a simple analytic model in order to examine the intrinsic consequences of coarse-graining as a function of model re

Multiscale Structural and Functional Assessments of Healthy vs. Asthmatic Subjects via Computed Tomography Imaging Metrics - Bridging Individual and Population Scales

This study aims to explore structural and functional differences between healthy subjects and asthmatics via a refined and expanded set of quantitative computed tomography (QCT) imaging metrics at local (segmental) and global (lobar) scales. This set of multiscale imaging-based metrics is then employed to perform clustering analysis for the derivation of sub-asthma groups. We further explore the association of the imaging-based clusters with clinical metrics to establish the link between imaging and clinical phenotypes.

Agent-based modeling of cell-matrix interactions

Cell-populated extracellular matrix gels were one of the first approaches to tissue engineering and they are still used in this context. In addition, cell-populated gels are used as in vitro experimental models to explore in vivo processes such as tissue development and wound healing. A number of mathematical and computational models have been developed to describe cell-populated matrix gels. A limitation of many these models, however, is that they cannot explicitly handle the dynamic nature of cell-matrix interactions where cell repetitively bind to matrix, exert traction, and release.

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