Flowtrace: simple visualization of coherent structures in biological fluid flows

Gilpin, William; Prakash, Vivek N.; Prakash, Manu

doi:10.1242/jeb.162511

Cited by 43 publications

(40 citation statements)

References 46 publications

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“…Fluorescence imaging was performed using a B2 filter which allows differentiating the fluorobead and the rest of rotifer. The particle displacement image stacking was performed using Image J software and Flow trace plug in . The enzymes lysozyme and organophosphorus hydrolase were functionalized into the carboxylated fluorobeads, via activation of the carboxylic moieties using a NHS (20 × 10 −3 m )/EDC (10 × 10 −3 m ) in 0.1 m MES buffer (pH 6.5) for 30 min.…”

Section: Methodsmentioning

confidence: 99%

Rotibot: Use of Rotifers as Self‐Propelling Biohybrid Microcleaners

Soto

Lopez‐Ramirez

Jeerapan

et al. 2019

Adv Funct Materials

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Self-propelled biohybrid microrobots, employing marine rotifers as their engine, named "rotibot," are presented and their practical utility and advantages for environmental remediation are demonstrated. Functionalized microbeads are attached electrostatically within the rotifer mouth and aggregated inside their inner lip. The high fluid flow toward the mouth, generated by the strokes of rotifer cilia bands, forces an extremely efficient transport of the contaminated sample over the active surfaces of the functionalized microbeads. The reactive particles confined around the rotifer's lip are thus exposed to a high flow rate of the pollutant solution, resulting in dramatically accelerated decontamination processes, without external mixing or harmful fuels. Theoretical simulations, modeling the greatly enhanced fluid dynamic associated with such built-in mixing effect, correlate well with the experimental observations. The rotibot thus proves to be an effective, versatile, and robust dynamic microcleaning platform for removing diverse environmental pollutants. Microbeads functionalized with lysozyme and organophosphorus hydrolase enzymes are shown to be extremely useful for enzymatic biodegradation of Escherichia coli and the nerve agent methyl paraoxon, respectively, while ligand (meso-2,3-dimercaptosuccinic acid) modified beads are used for removing heavy metal contaminants. Rotifer-based biohybrid microrobots hold considerable promise as self-propelling dynamic pumps for diverse large-scale environmental remediation applications.

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Section: Methodsmentioning

confidence: 99%

Rotibot: Use of Rotifers as Self‐Propelling Biohybrid Microcleaners

Soto

Lopez‐Ramirez

Jeerapan

et al. 2019

Adv Funct Materials

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“…We used different computational analysis techniques to quantify the experimental time-lapse datasets. The dorsal layer datasets with sticky-microbeads tagging were visualized using Flowtrace 65 , a simple tool for visualizing coherent structures in biological fluid flows (in ImageJ). The Flowtrace algorithm generates pathlines of particles with a given input projection time (here we chose 5 seconds).…”

Section: Methodsmentioning

confidence: 99%

“…7, Methods). (i) Flowtrace 65 visualizations reveal bead trajectories in a region of local shear-induced fracture (zoom-in insets (C)). (ii) The internal strain rate (with peak ∼0.2 s - 1 ) contours from a PIV analysis overlaid on the velocity vectors.…”

Section: Figurementioning

confidence: 99%

“…Right Insets display control experiments demonstrating that microspheres bind on cell membrane. (B) Computational data analysis techniques: We employ Flowtrace 65 for visualization of particle trajectories, Particle tracking for quantitative non-affine motion analysis, and Particle Image Velocimetry to measure velocity fields and internal strain rate.…”

Section: Extended Data Figurementioning

confidence: 99%

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Motility induced fracture reveals a ductile to brittle crossover in the epithelial tissues of a simple animal

Prakash

Bull

2019

Preprint

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8Animals are characterized by their movement, and their tissues are continuously subjected to dynamic force loading while they crawl, walk, run or swim 1 . Tissue mechanics fundamentally determine the ecological niches that can be endured by a living organism 2 . While epithelial tissues provide an important barrier function in animals, they are subjected to extreme strains during day to day physiological activities, such as breathing 1 , feeding 3 , and defense response 4 . However, failure or inability to withstand to these extreme strains can result in epithelial fractures 5, 6 and associated diseases 7, 8 . From a materials science perspective, how properties of living cells and their interactions prescribe larger scale tissue rheology and adaptive response in dynamic force landscapes remains an important frontier 9 . Motivated by pushing tissues to the limits of their integrity, we carry out a multi-modal study of a simple yet highly dynamic organism, the Trichoplax Adhaerens 10-12 , across four orders of magnitude in length (1 µm to 10 mm), and six orders in time (0.1 sec to 10 hours). We report the discovery of abrupt, bulk epithelial tissue fractures (∼10 sec) induced by the organism's own motility. Coupled with rapid healing (∼10 min), this discovery accounts for dramatic shape change and physiological asexual division in this early-divergent metazoan. We generalize our understanding of this phenomena by codifying it in a heuristic model, highlighting the fundamental questions underlying the debonding/bonding criterion in a soft-active-living material by evoking the concept of an 'epithelial alloy'. Using a suite of quantitative experimental and numerical techniques, we demonstrate a force-driven ductile to brittle material transition governing the morphodynamics of tissues pushed to the edge of rupture. This work contributes to an important discussion at the core of developmental biology 13-17 , with important applications to an emerging paradigm in materials and tissue engineering 5, 18-20 , wound healing and medicine 8, 21, 22 . 9 Tissues are the paragon example of a 'smart material'. Cells within a tissue may dynamically 10 reconfigure under stress 15, 23 , exhibit superelastic responses by localizing strain 19 , contract to actively 11 avoid rupture 10 , locally reinforce regions of tissue through recruitment 24 and other forms of mechanically 12 regulated feedback 25, 26 . Harnessing these properties promises valuable insights for synthetic adaptable 13 materials 18, 20, 27 . Many of these phenomena illustrate the role of mechanical feedback in service of tissues 14 maintaining their integrity under large strains. Here, we address the question -how do cellular tissues 15 behave on the threshold of failure? What determines if a tissue fractures or if it flows? We investigate this 16 question in a 'minimal tissue system' that is capable of highly adaptive and fast plastic deformation. 17 We experimentally study the dynamic epithelial tissues in the marine animal, the Trichoplax adhaerens. 1...

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“…In our recent work [1], we found that these vortex structures work in tandem with swimming to enhance each larva's ability to intercept and ingest algae, their primary food source. Immobilization of the swimmer combined with computational reconstruction of the pathlines of tracer particles [2,3] allows straightforward visualization of the elegant and dynamic array of vortices that forms around the body.…”

mentioning

confidence: 99%