title: Automated analysis of cell-matrix adhesions in 2D and 3D environments.
abstract: Cell-matrix adhesions are of great interest because of their contribution to numerous biological processes, including cell migration, differentiation, proliferation, survival, tissue morphogenesis, wound healing, and tumorigenesis. Adhesions are dynamic structures that are classically defined on two-dimensional (2D) substrates, though the need to analyze adhesions in more physiologic three-dimensional (3D) environments is being increasingly recognized. However, progress has been greatly hampered by the lack of available tools to analyze adhesions in 3D environments. To address this need, we have developed a platform for the automated analysis, segmentation, and tracking of adhesions (PAASTA) based on an open source MATLAB framework, CellAnimation. PAASTA enables the rapid analysis of adhesion dynamics and many other adhesion characteristics, such as lifetime, size, and location, in 3D environments and on traditional 2D substrates. We manually validate PAASTA and utilize it to quantify rate constants for adhesion assembly and disassembly as well as adhesion lifetime and size in 3D matrices. PAASTA will be a valuable tool for characterizing adhesions and for deciphering the molecular mechanisms that regulate adhesion dynamics in 3D environments.
authors: Department of Biological Sciences and Vanderbilt Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, Tennessee 37235.
authors: Joshua A
authors: JA
authors: Broussard
authors: Department of Biological Sciences and Vanderbilt Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, Tennessee 37235.
authors: Nicole L
authors: NL
authors: Diggins
authors: Center for Cancer Systems Biology at Vanderbilt, Vanderbilt University, Nashville, Tennessee 37235.
authors: Stephen
authors: S
authors: Hummel
authors: 1] Center for Cancer Systems Biology at Vanderbilt, Vanderbilt University, Nashville, Tennessee 37235 [2] Vanderbilt Institute for Integrative Biosystems Research and Education (VIBRE), Vanderbilt University, Nashville, Tennessee 37235 [3] Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235.
authors: Walter
authors: W
authors: Georgescu
authors: 1] Center for Cancer Systems Biology at Vanderbilt, Vanderbilt University, Nashville, Tennessee 37235 [2] Vanderbilt Institute for Integrative Biosystems Research and Education (VIBRE), Vanderbilt University, Nashville, Tennessee 37235 [3] Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee 37235.
authors: Vito
authors: V
authors: Quaranta
authors: 1] Department of Biological Sciences and Vanderbilt Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, Tennessee 37235 [2] Vanderbilt Institute for Integrative Biosystems Research and Education (VIBRE), Vanderbilt University, Nashville, Tennessee 37235 [3] Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee 37235.
authors: Donna J
authors: DJ
authors: Webb
mesh_terms: D000465:Algorithms; D000818:Animals; D001331:Automation; D018929:Cell Culture Techniques / Q000379:methods*; D045744:Cell Line, Tumor; D021982:Cell-Matrix Junctions / Q000187:drug effects; D024042:Collagen Type I / Q000494:pharmacology; D049452:Green Fluorescent Proteins / Q000378:metabolism; D006801:Humans; D007091:Image Processing, Computer-Assisted; D051419:Paxillin / Q000378:metabolism; D051381:Rats; D015203:Reproducibility of Results; D059008:Time-Lapse Imaging
chemical_list: D024042:Collagen Type I; D051419:Paxillin; D049452:Green Fluorescent Proteins
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