291 research outputs found
Raw data: Jiang et al. Plos Computational Biology
No full textRaw data files associated with the publication
Fine-grained, Nonlinear Registration of Live Cell Movies Reveals Spatiotemporal Organization of Diffuse Molecular Processes
Xuexia Jiang, Tadamoto Isogai, Joseph Chi, Gaudenz Danuser*
Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
*Correspondence: [email protected]
The data is organized figure by figure. Time lapse image sequences are contained in folders of .tif series
Computer Vision in Cell Biology
No full textComputer vision refers to the theory and implementation of artificial systems that extract information from images to understand their content. Although computers are widely used by cell biologists for visualization and measurement, interpretation of image content, i.e., the selection of events worth observing and the definition of what they mean in terms of cellular mechanisms, is mostly left to human intuition. This Essay attempts to outline roles computer vision may play and should play in image-based studies of cellular life
High-resolution analysis of F-actin meshwork kinetics and kinematics using computational Fluorescent Speckle Microscopy
No full text
Automated profiling of growth cone heterogeneity defines relations between morphology and motility.
No full textGrowth cones are complex, motile structures at the tip of an outgrowing neurite. They often exhibit a high density of filopodia (thin actin bundles), which complicates the unbiased quantification of their morphologies by software. Contemporary image processing methods require extensive tuning of segmentation parameters, require significant manual curation, and are often not sufficiently adaptable to capture morphology changes associated with switches in regulatory signals. To overcome these limitations, we developed Growth Cone Analyzer (GCA). GCA is designed to quantify growth cone morphodynamics from time-lapse sequences imaged both in vitro and in vivo, but is sufficiently generic that it may be applied to nonneuronal cellular structures. We demonstrate the adaptability of GCA through the analysis of growth cone morphological variation and its relation to motility in both an unperturbed system and in the context of modified Rho GTPase signaling. We find that perturbations inducing similar changes in neurite length exhibit underappreciated phenotypic nuance at the scale of the growth cone
Lamellipodia as Proliferation Machines: How Branched Actin Based Feedback Loops Allow Melanoma to Evade Growth Inhibition
No full textThe general metadata -- e.g., title, author, abstract, subject headings, etc. -- is publicly available, but access to the submitted files is restricted to UT Southwestern campus access and/or authorized UT Southwestern users.Spatial regulation of Rac1 activity is well-characterized and important for several cellular functions, including building and sustaining protrusive branched actin networks at the cell edge. High Rac1 activity sits atop a dense cytoskeletal scaffold that drives the extension of a flat lamellipodium, whose tightly packed volume forms a microdomain of enhanced signaling activity with elevated transduction efficiency. Cancer cells can coopt this mechanism to drive proliferation and survival signaling. For example, the hyperactive Rac1P29S mutation found in 10% of melanoma patients is associated with advanced disease, increased resistance to MAPK pathway inhibitors, and decreased patient survival. Previous work demonstrated that these clinical phenotypes correlate at a cellular level with sustained proliferation under drug challenge and is linked to a cell's ability to build extended lamellipodia. Using FRET- and localization-based biosensors for Rac1 activity, we observe larger and more potent microdomains in melanoma cells expressing Rac1P29S. The resultant branched actin network provides abundant binding sites for the tumor suppressor NF2/merlin. Superimposition of heightened Rac1 activity poises the Rac1 effector kinase PAK to inactivate merlin through phosphorylation. Displacement of merlin from the lamellipodia by a competitive actin-binding peptide interrupts this phospho-inactivation, re- sensitizing melanoma cells to MAPK inhibition. However, merlin plays an additional role upstream of the Rac1 signaling domain. Merlin recruitment to the cell edge limits protrusion formation. Knockout of merlin recapitulates the Rac1P29S-induced phenotype, producing enhanced lamellipodia with elevated wildtype Rac1 activity upon MAPK-inhibition. Breaking merlin's inhibition of the branched actin network similarly allows for enhanced lamellipodia formation, and ultimately merlin phospho-inactivation. Together these data support a double-negative feedback--Rac1 microdomains inactivate merlin localized to the dense branched-actin networks; active merlin, in turn, attenuates microdomain formation through inhibition of branched actin polymerization. This localized signaling feedback is thus prone, when perturbed, to produce self-sustaining patterns of signaling activity, allowing for MAPK-inhibited melanoma to escape merlin-mediated growth control
Total internal reflection fluorescence microscopy and bead flow assay: Two techniques for investigating dynamics of protein- and cell-surface interactions
No full textNEUBIAS TS7 - data used in the workflow deconstruction session on quantifying monolayer cell migration
No full text<p>Training session details (including slides): https://github.com/miura/NEUBIAS_AnalystSchool2018/tree/master/Assaf</p>
<p>Matlab source code: https://github.com/assafzar/MonolayerKymographs</p>Assaf Zaritsky was supported by the National Institute of Health Grant to Gaudenz Danuser (P01 GM103723). The workflow deconstruction session was developed as part of the Network of European BioImage Analysts (NEUBIAS) TS7, funded by COST Action CA15124
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