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Tissue morphogenetic remodeling plays an important role in tissue repair and homeostasis and is often governed by mechanical stresses. In this study, we integrated an in vitro mesenchymal tissue experimental model with a volumetric contraction-based computational model to investigate how geometrical designs of tissue mechanical constraints affect the tissue remodeling processes. Both experimental data and simulation results verified that the standing posts resisted the bulk contraction of the tissues, leading to tissue thinning around the posts as gap extension and inward remodeling at the edges as tissue compaction. We changed the geometrical designs for the engineered mesenchymal tissues with different shapes of posts arrangements (triangle vs. square), different side lengths (6 mm vs. 8 mm), and insertion of a center post. Both experimental data and simulation results showed similar trends of tissue morphological changes of significant increase of gap extension and deflection compaction with larger tissues. Additionally, insertion of center post changed the mechanical stress distribution within the tissues and stabilized the tissue remodeling. This experimental-computational integrated model can be considered as a promising initiative for future mechanistic understanding of the relationship between mechanical design and tissue remodeling, which could possibly provide design rationale for tissue stability and manufacturing. 

Bacterial colonization of biotic and abiotic surfaces and antibiotic resistance are grand challenges with paramount societal impacts. However, in the face of increasing bacterial resistance to all known antibiotics, efforts to discover new classes of antibiotics have languished, creating an urgent need to accelerate the antibiotic discovery pipeline. A major deterrent in the discovering of new antibiotics is the limited permeability of molecules across the bacterial envelope. Notably, the Gram-negative bacteria have nutrient specific protein channels (or porins) that restrict the permeability of non-essential molecules, including antibiotics. Here, we have developed the Computational Antibiotic Screening Platform (CLASP) for screening of potential drug molecules through the porins. The CLASP takes advantage of coarse grain (CG) resolution, advanced sampling techniques, and a parallel computing environment to maximize its performance. The CLASP yields comprehensive thermodynamic and kinetic output data of a potential drug molecule within a few hours of wall-clock time. Its output includes the potential of mean force profile, energy barrier, the rate constant, and contact analysis of the molecule with the pore-lining residues, and the orientational analysis of the molecule in the porin channel. In our first CLASP application, we report the transport properties of six carbapenem antibiotics—biapenem, doripenem, ertapenem, imipenem, meropenem, and panipenem—through OccD3, a major channel for carbapenem uptake in Pseudomonas aeruginosa . The CLASP is designed to screen small molecule libraries with a fast turnaround time to yield structure–property relationships to discover antibiotics with high permeability. The CLASP will be freely distributed to enable accelerated antibiotic drug discovery. 

Within developing embryos, tissues flow and reorganize dramatically on timescales as short as minutes. This includes epithelial tissues, which often narrow and elongate in convergent extension movements due to anisotropies in external forces or in internal cell-generated forces. However, the mechanisms that allow or prevent tissue reorganization, especially in the presence of strongly anisotropic forces, remain unclear. We study this question in the converging and extendingDrosophilagermband epithelium, which displays planar-polarized myosin II and experiences anisotropic forces from neighboring tissues. We show that, in contrast to isotropic tissues, cell shape alone is not sufficient to predict the onset of rapid cell rearrangement. From theoretical considerations and vertex model simulations, we predict that in anisotropic tissues, two experimentally accessible metrics of cell patterns—the cell shape index and a cell alignment index—are required to determine whether an anisotropic tissue is in a solid-like or fluid-like state. We show that changes in cell shape and alignment over time in theDrosophilagermband predict the onset of rapid cell rearrangement in both wild-type andsnail twistmutant embryos, where our theoretical prediction is further improved when we also account for cell packing disorder. These findings suggest that convergent extension is associated with a transition to more fluid-like tissue behavior, which may help accommodate tissue-shape changes during rapid developmental events. 

The fluidity of biological tissues – whether cells can change neighbors and rearrange – is important for their function. In traditional materials, researchers have used linear response functions, such as the shear modulus, to accurately predict whether a material will behave as a fluid. Similarly, in disordered 2D vertex models for confluent biological tissues, the shear modulus becomes zero precisely when the cells can change neighbors and the tissue fluidizes, at a critical value of control parameter s 0 * = 3.81. However, the ordered ground states of 2D vertex models become linearly unstable at a lower value of control parameter (3.72), suggesting that there may be a decoupling between linear and nonlinear response. We demonstrate that the linear response does not correctly predict the nonlinear behavior in these systems: when the control parameter is between 3.72 and 3.81, cells cannot freely change neighbors even though the shear modulus is zero. These results highlight that the linear response of vertex models should not be expected to generically predict their rheology. We develop a simple geometric ansatz that correctly predicts the nonlinear response, which may serve as a framework for making nonlinear predictions in other vertex-like models.