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23 protocols using polybead

1

Laser Trapping of Actin Filaments

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Before being coated with nitrocellulose, the glass coverslips were sprayed with 4.5 μm polystyrene microspheres (171355; Polybead; Polysciences) to create pedestals (Roman et al., 2014 (link)). Trapping was performed with 3-μm amino polystyrene microspheres (171455; Polybead; Polysciences) coated with gelsolin according to Suzuki et al. (1996) (link), except that the time of suspension/gentle mixing of the microspheres in glutaraldehyde was increased to 15 h and the amount of protein dissolved in 0.5 ml of solution B was 27 μg gelsolin, 424 μg BSA, and 27 μg G-actin. Proteins and solutions were prepared and perfused in the assay chamber in the same manner as for the in vitro motility assay described above, with the exception that (gelsolin-coated) microsphere-tailed actin filaments were added to the laser trap assay buffer. The microsphere-tailed actin filaments were prepared according to Suzuki et al. (1996) (link) with the following modifications: 5 μM TRITC-labeled actin was used, and the suspension was diluted 1:10 with laser trap assay buffer to be perfused in the assay chamber.
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2

Microfluidic Device Particle Focusing

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To evaluate the performance of the microfluidic device for particle focusing, 10-µm polystyrene particles (Polybead, Polysciences, 10.0 ± 1.0 µm, ~ 1.05 g/cm3) at an initial concentration of 4.55 × 107 particles/mL and 4.5-µm polystyrene particles (Polybead, Polysciences, 4.5 ± 0.2 µm, ~ 1.05 g/cm3) at an initial concentration of 4.99 × 108 particles/mL were used. The particle suspensions were stored at a 4 °C and diluted to 5.0 × 105 particles/mL with pure water just before experiments.
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3

Cardiac Cell Isolation and Characterization

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After perfusion with PBS, the mice heart was excised and digested in HBSS medium containing 2.5 mg/ml collagenase D (Roche, Meylan, France) for 30 min at 37 °C, with stirring.
Erythrocytes were lysed by using red blood cell lysis buffer (MiltenyiBiotec, Paris, France). Samples were blocked with Fc block (Ebioscience, Paris, France) prior to labeling with antibodies and propidium iodide (PI). Cytometry data were acquired on an LSR Fortessa cytometer. After gating on CD45+ cells, doublets were excluded and live cells were analyzed (PI exclusion). Cardiac cell numbers were quantified using polybeads (Polysciences, Le-Perray-en-Yvelines, France). Data were analyzed with FlowJo software (Tree Star).
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4

Microscopic Imaging of C. elegans

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For all observations, animals were mounted on 2% agarose dry pads with 4% polystyrene beads (Polybeads, Polysciences) in M9 buffer. For images corresponding to Figures 1a, 2 and 5, and Figure S1, worms were observed using an Andor spinning disk system (Oxford Instruments) installed on a Nikon‐IX86 microscope (Olympus) equipped with a 40x/NA 1.3 and a 60×/NA 1.42 oil‐immersion objectives and an Evolve electron‐multiplying charge‐coupled device camera. Each animal was imaged with IQ software (APIS Informationstechnologien) as a stack of optical sections (0.3 μm apart) across the whole thickness of the worm (Figure 1a and Figure S1a) or across a specific tissue (Figures 2 and 4). All images were processed using the Fiji (ImageJ) software and correspond to the sums of the same number of slices (for each strain with or without auxin) except for images of the intestine (Figure 2g and Figure S1h) which correspond to z projection of maximum intensity. For fluorescence quantification, images covering the whole head including the most posterior pharyngeal bulb were summed (85 slices) and a ROI (180 × 230 pixels) was positioned relative to the middle of the most posterior part of the pharynx.
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5

Ultrasound-Mediated Microbubble Characterization

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17 μL of activated RN18 MBs was added to 1.7 mL of PBS in TPX microcentrifuge tubes. These tubes were then exposed to ultrasound identically to our in vitro protocol. The MBs used for each experimental tube were drawn from the same pool of activated RN18 MBs. After completion of ultrasound exposure, MBs were analyzed using flow cytometry and their sizes and concentrations were calibrated using known dilutions of polybeads (Polysciences Inc., Warrington, PA) on the same day. Run times were fixed and the number of events gathered was allowed to vary. Total events of US exposed MBs were compared to a control tube without US exposure. Consistent cytometer flow rate was verified by comparing dilutions of polybeads and untreated RN18 MBs from the start and end of each experiment.
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6

Polystyrene Bead Dispersion and Cell Culture

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We dispersed nonfluorescent polystyrene beads of 6, 10, and 15 µm (Polybeads; Polysciences, Warrington, PA) and fluorescent beads of 10 µm (Fluoresbrite; Polysciences) in medium (Dulbecco's phosphate-buffered saline [DPBS] 1×; Thermo Fisher Scientific, Waltham, MA). We then measured the resistivity of this medium (electrical resistivity ρ = 0.65 Ωm). We diluted the beads to a working concentration of 10 4 /mL for the particle size assay and 5 × 10 3 /mL for the particle dispensing assay. We cultured murine fibroblast (3T3-J2) cells as previously described. A Single Epidermal Stem Cell Strategy for Safe Ex Vivo Gene Therapy. EMBO Mol. Med. 2015; 7: 380-393 Google Scholar
We detached adherent cultured cells with trypsin/EDTA (Sigma-Aldrich, St. Louis, MO), filtered using a 40 µm cell strainer (BD) and then diluted to a final concentration of 10 4 cells/mL. As the suspending medium, we used Hank's balanced salt solution (HBSS; Gibco-Thermo Fisher Scientific, Waltham, MA) complemented with 3% bovine serum (BS; Gibco-Thermo Fisher Scientific).
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7

Polystyrene Beads Coupling Protocol

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First 1-μm polystyrene beads containing a reactive amine blue dye were purchased from a commercial source (polybeads; Polysciences, Warrington, PA). In pilot experiments, it was discovered that simple adsorption provided comparable adhesion compared to attempted carboxylate/phosphate coupling using 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride. For the reactions shown in Fig. 5, microspheres were diluted to 1/10th their stock concentration in CA buffer, and 200 μl were mixed with 1 ml of CAP dialysates, incubated overnight at room temperature, and then vortexed with an additional 1 ml of CA buffer prior to centrifugation. Subsequent dilutions in CA buffer were used to assess any influence of sample viscosity.
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8

Phenotypic Analysis of Neuronal Development

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For phenotypic analysis of neuronal development, animals were anaesthetized on 5% agarose pads containing 20 mM NaN3. Images were taken using an automated fluorescence microscope (AXIO Imager M2; Carl Zeiss) and Zen 2012 software, equipped with objectives (EC Plan-NeoFluor 20x/0.5 and 40x/0.75 and Plan Apochromat 63x/1.4 oil DIC and 100x/1.4 oil DIC; Carl Zeiss) and an ORCA-R2 camera (C10600; Hamamatsu Photonics). For in vivo calcium imaging, C. elegans in L4 stage expressing the Ca2+ sensor Cameleon YC3.60 were immobilized with 0.10 µM polystyrene microspheres (Polybead; Polysciences Inc.) on a glass slide coated with a 10% agarose pad. The rab-3::cameleonYC3.60 strain was obtained from N. Ringstad (New York University Langone Medical Center, New York, NY).Temperature was maintained at 25°C during which two ventral motor neurons, most anteriorly and posteriorly to the vulva, were imaged. Calcium imaging was performed as described in the In vitro calcium imaging section. Post-acquisition analysis was performed using Volocity 3D analysis software 6.3 (PerkinElmer).
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9

Multimodal Optoacoustic Mesoscopy of Zebrafish

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We characterized the MORSOM imaging performance in terms of resolution, SNR, and overall image quality using a phantom consisting of 10-μm spheres that were randomly dispersed in agar gel and juvenile Zebrafish at 21 dpf. At 21 dpf, Zebrafish have a length of ~10 mm and diameters ranging from 1 to 2 mm (Supplementary Fig. S4). These dimensions are not accessible by optical or optoacoustic microscopy techniques, such as SPIM18 (link) or multiview optical resolution photoacoustic microscopy6 (link), 19 (link), 20 (link), and correspond to dimensions for which optoacoustic mesoscopy may be ideally suited. Zebrafish were embedded in low melting agar (Sigma-Aldrich, St Louis, MO, USA) and imaged ex vivo, consistent with the current regulations and processes allowed by the Government of Upper Bavaria for adult Zebrafish. The agar was mixed with ~10 μm diameter black microspheres (black polystyrene microspheres, Polybead, Polysciences Inc., Warrington, PA, USA), which we use as fiducial markers to confirm the exact alignment of the different RSOM projections onto the common MORSOM image reconstruction scheme. The Zebrafish/agar specimen was mounted on a syringe, as previously described for SPIM21 , and placed in a water bath for acoustic coupling.
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10

Immobilizing Hermaphrodite Worms for Imaging

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One-day-old adult hermaphrodites were mounted for imaging by placing a single worm on an agar pad (10% agarose dissolved in M9 buffer) on a microscope slide with 1.6 µL of a solution containing equal measures of polystyrene beads (Polybead, Cat# 00876-15, Polysciences Inc) and 30 mM muscimol (Cat# 195336, MP Biomedicals). Once the muscimol slowed worm movement (~5 min), a coverslip was dropped onto the agar pad, physically restraining the worm. The worm’s orientation was manually adjusted by sliding the coverslip to reorient the positioning of the AVA interneurons for imaging (Doser et al., 2023 (link)).
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