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72 protocols using polystyrene beads

1

Optimized Microscopy Sample Preparation

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For most experiments, early embryos were dissected from gravid hermaphrodites in 5-6 µl of M9 buffer (22 mM KH2PO4, 42 mM NaHPO4, 86 mM NaCl and 1 mM MgSO4) on a coverslip and mounted under 2% M9 agarose pads (Zipperlen et al., 2001 (link)). In some instances (Figs 1B,G, 3A,B,E and 4, and Fig. S1), to minimize eggshell autofluorescence that may be prominent with agarose mounts, embryos were dissected in 8-10 µl of egg buffer [118 mM NaCl, 48 mM KCl, 2 mM CaCl2 2 mM MgCl2 and 25 mM HEPES (pH 7.3)], and mounted with 20 µm polystyrene beads (Polysciences) between a slide and coverslip as described previously (Rodriguez et al., 2017 (link)).
To harvest late embryos (Fig. 6A-C), gravid worms were allowed to lay embryos for 4-5 h at 20°C. Embryos were collected and mounted in 8-10 µl of egg buffer supplemented with 18.8 µm polystyrene beads (Polysciences).
L1 larva (Fig. 6D) were collected from plates where gravid adult worms were allowed to lay eggs for 12-13 h at 20°C. Whole larva were then mounted between a 2% M9 agarose pad and coverslip in M9 containing 0.1 µm polystyrene beads (Polysciences) and 10 mM levamisole to induce worm paralysis (Reich et al., 2019 (link)).
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2

Culturing Trypanosoma brucei brucei

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Trypanosoma brucei brucei MiTat 1.2 bloodstream form trypanosomes were routinely grown in HMI-9 36 culture medium at 37 °C in a 95% air/5% CO 2 humidified atmosphere. Populations were kept below 10 6 cells per mL by repetitive splitting. After a maximum of 15 splittings, trypanosomes were discarded and fresh populations were defrosted. For experiments, 2 mL of trypanosomes in culture medium were centrifuged at 237 x g and washed once with 2 mL of culture medium and once with 2 mL culture medium with bovine serum albumin (BSA, 5 mg/mL). The supernatant was discarded and the cells were taken up into a 1 mL syringe (Braun) in 0.7 mL of culture medium with BSA (5 mg/mL). This comprised the cell solution, which was introduced into the device. The solution of culture medium and BSA was weekly prepared and stored at 37 °C and at 5% CO 2 in humid atmosphere to ascertain optimal conditions. For drug solutions of suramin, the drug was dissolved in 2 mL of culture medium and polystyrene beads (1 µμm diameter, Polysciences) solution 2 µμL/mL. For drug solutions of GA and 2DG, 2 mL of culture medium solvent contained additionally BSA (5mg/mL) and polystyrene beads (1 µμm diameter, Polysciences) solution 2 µμL/mL.
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3

Polyacrylamide Gel Synthesis and Actin Polymerization

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Gels consisting of 1.75 wt % PAAm were prepared with 30 wt % acrylamide/bis-acrylamide mixed solution (37.5:1, Wako Chemicals Inc.), polystyrene beads (Polysciences Inc., 2a = 2 μm diameter), and 0.033% ammonium persulfate. The solution was thoroughly degassed in a vacuum, and polymerization was initiated by adding 0.05% tetramethylethylenediamine. The solution was loaded into a glass chamber and polymerized at room temperature for several hours while the chamber was gently rotated. This thermal equilibrium sample was measured by feedback AMR with the following calibration values: kp = 9.4 × 10−7 N/m, kd = 5.8 × 10−6 N/m, and τ = 3.8 × 10−2 s (I = 2 s−1, C = 4.1 × 10−7 m/V, B = 5.4 × 10−6 m/V).
G-actin was prepared from rabbit skeletal muscle according to standard protocols (72 ) and was stored at −80°C in G-buffer [2 mM tris-Cl, 0.2 mM CaCl2, 0.5 mM DTT, and 0.2 mM ATP (pH 7.5)]. G-actin was diluted into F-buffer [1 mM Na2ATP, 2 mM Hepes, 1 mM EGTA, 2 mM MgCl2, and 50 mM KCl (pH 7.5)] to initiate actin polymerization. An F-actin solution (1 mg/ml) including polystyrene beads (Polysciences Inc., 2a = 1 μm diameter) was directly infused into sample chambers. Polymerization occurred at room temperature for about 30 min. The thermal equilibrium sample was then measured by feedback PMR with the following calibration values: kt= kp= 4.8 × 10−6 N/m and τ = 0.024 s.
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4

Actin-Myosin Contractility Reconstitution

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Actin and myosin II were prepared from rabbit skeletal muscle according to published methods 26 . Actin was stored at -80°C in G-buffer (2 mM Tris-Cl, 0.2 mM CaCl 2 , 0.5 mM DTT, 0.2 mM ATP, pH 7.5) and myosin at -80°C in high salt buffer (0.6 M KCl, 50 mM KH 2 PO 4 , pH 6.5). Actin was biotinylated following a standard procedure 27 . Unlabeled actin, and biotinylated actin were mixed with probe particles and neutravidin (Molecular Probes) as a crosslinker, and copolymerized in F-buffer (2 mM HEPES, 2 mM MgCl 2 , 50 mM KCl,1 mM EGTA, pH 7.5) which was pre-mixed with myosin and ATP (3.5 mM). The ratio of normal actin: biotinylated actin: neutravidin was 180:5:2. The total concentration of actin was 1 mg/ml and of myosin 170 nM. Unless stated otherwise, 2a = 1.16 μm silica particles were used as probes for microrheology by laser interferometry and 1.1 μm diameter polystyrene beads (Polysciences) were used for video microscopy. Crosslinking prevented macroscopic phase separation (superprecipitation) 28 while the samples still exhibited vigorous non-thermal fluctuations. For control experiments, crosslinked actin gels were prepared following the same protocol, but leaving out myosin.
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5

Microscopic Imaging of C. elegans Embryos

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For ex utero imaging, embryos or oocytes were dissected from hermaphrodite worms into Shelton’s Growth Medium [64 (link)], supplemented with 20 μm polystyrene beads to act as spacers between glass slide and coverslip. For in utero imaging, whole worms were mounted between a 10% M9 agarose pad and coverslip, in M9 containing either 0.1 μm polystyrene beads (Polysciences), or 5% tetramisole in order to immobilize the worms.
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6

Phage Display of Single-Domain Antibodies Against Alpha-Synuclein and Tau

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Phage displaying sdAbs were rescued from individual libraries with helper phage M13K07 and subjected to biopanning in two different ways: solid-phase and solution-phase panning. For solid-phase panning, rec α-syn or rec tau was adsorbed on 2-μm-diameter polystyrene beads (Polysciences Inc.), blocked with PBS-T containing 5% non-fat dried milk, and incubated with 2 × 1011 phage in 1 ml of PBS-T/milk for 1 hour at room temperature. For solution-phase panning, rec α-syn or rec tau were biotinylated using Lightning-Link Rapid Biotin (Innova Biosciences), and 1 μg of biotinylated α-syn or tau was incubated with 2 × 1011 phage in 1 ml of PBS-T/milk for 1 hour at room temperature. polystyrene beads were captured by centrifugation and washed extensively with PBS-T. Biotinylated α-syn or tau bound to phage was captured with streptavidin (SA)–coated magnetic Dynabeads (Life Technologies) and extensively washed with PBS-T. For both the solid- and solution-phase approaches, bound phage was eluted with both high pH (100 mM triethylamine, pH ~10) and low pH (100 mM glycine, pH ~2.5) for 5 min and neutralized with 1 M tris (pH 7.5). E. coli strains TG1 and SS320 were then infected with eluted phage and used for a subsequent round of panning (TG1) or to express antibodies (SS320).
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7

Electrochemical Imaging of Polystyrene Beads

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To compare the experimental and simulation results for validation of the simulation analysis, 90 μm diameter polystyrene beads (Polysciences Inc., USA) were used (Fig. 2(A)). A solution containing 0.1 M KCl and 1.0 mM ferrocenemethanol (FcCH2OH) was introduced onto the device, and FcCH2OH was oxidized at 0.50 V to acquire electrochemical images. Then, the polystyrene beads were scattered randomly into the solution, and FcCH2OH was oxidized at 0.50 V to investigate the blocking influence. Average currents of between 116.0 and 118.8 s with a potential step to 0.50 V were used for electrochemical images.
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8

Calcium Imaging of Neurons in C. elegans

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We generated animals expressing the calcium indicator YCX1.6 (Madisen et al. 2015 (link)) in the AFD and AIY neurons. The YCX1.6 in AFD was localized to the nucleus to separate the signals from AFD and AIY. The animals were cultivated at 20°C and were immobilized by placing on a 10% agarose pad with polystyrene beads (Polysciences), which were then covered by a cover slip. The samples were placed on a Peltier device used for the temperature control, and the YFP and CFP images were captured using epi-fluorescent microscope equipped with SOLA light engine (Lumencore) as a light source and were recorded at 1 frame per second with 400 ms exposure. Image processing was performed by MetaMorph software (Molecular Devices), and the fluorescent intensities of YFP and CFP were determined. The ratio change was calculated as (RtR0)/R0, where Rt represents the ratio of YFP to CFP of each frame, and R0 the mean ratio of the first 10 frames.
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9

Antibody and Reagent Sources

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Mouse anti-human ICAM-1 clone R6.5 (anti-ICAM) was from ATCC (Manassas, VA). Mouse IgM anti-ceramide was from Sigma-Aldrich (Saint Louis, MO). Rabbit anti-human PKC (H-300), rabbit anti-human GAPDH, and FITC-labeled goat anti-mouse IgM were from Santa Cruz Biotechnology (Dallas, TX). Rabbit anti-phosphorylated human PKCα (phospho T638) was from Abcam (Cambridge, United Kingdom). HRP-linked anti-rabbit IgG was from GE Healthcare (Pittsburgh, PA). Mouse IgG and fluorescently-labeled secondary antibodies were from Jackson Immunoresearch (West Grove, PA). Polystyrene beads were from Polysciences (Warrington, PA). 125Iodine (125I) was from Perkin-Elmer (Waltham, MA) and Pierce iodination tubes were from Thermo Scientific (Rockford, IL). Precast 4–15% polyacrylamide gels were from Biorad (Hercules, CA) and PVDF membranes were from Pall Life Sciences (Port Washington, NY). Unless noted, all other reagents were from Sigma-Aldrich.
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10

Droplet Microscopy Analysis Protocol

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Droplets were analyzed by transmission and epifluorescent microscopy. A 70x50x1 mm glass slide (Paul Marienfeld, GmbH & Co. K.G., Germany) was made hydrophobic by pouring 3 mL Novec 1720 (3M) and baked for 1 minute at 100 °C on a heating plate. Polystyrene beads (Polysciences, Inc., PA, USA) slightly larger than the droplets, used as hard spheres spacers, were spotted on the glass slide and left for evaporation at 100 °C. The emulsion was deposited on the glass slide and covered with a 22x22 mm coverslip (VWR) treated with Novec 1720. For Figures 4, 5 and6 a minimum of 5,000, 5,000 and 10,000 droplets were analyzed respectively. The coverslip was gently pressed to obtain a monolayer array of close-packed droplets. The chamber was sealed with an epoxy glue (Sader) and images were acquired using an epifluorescence microscope Nikon Eclipse Ti equipped with a motorized XY stage (Nikon), a camera Nikon DS-Qi2 and a CoolLed pE-4000 illumination source. Depending on the droplet size, apochromatic 10X (N.A. 0.45, WD 4.0) or 20X (N.A. 0.75, WD 1.0) objectives were used. False-color images were generated with the open source ImageJ software.
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