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10 protocols using cf633

1

Fluorescent Antibody-based Detection of Protein Aggregates

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Fluorescent antibodies were used for microscopy-based detection of aggregates. The mouse monoclonal anti-α-synuclein Syn211 antibody (Santa Cruz Biotechnology, Inc., Dallas, USA) was labeled with CF633 and CF488A (Biotium, Freemont, USA) and the anti-Aβ IC16 (Heinrich-Heine University, Düsseldorf, Germany) antibody was labeled with CF633 (Biotium, Freemont, USA)40 (link),44 (link). The labeling process was performed according to the manufacturer’s protocol. The dyes with activated succinimidyl esters were mixed with the antibody in carbonate buffer to react covalently with the amines of the antibody. The labeled antibody was purified using a polyacrylamide bead suspension (Bio-Gel P 30 Gel, Bio-Rad Laboratories, Inc., Hercules, USA). The concentration and degree of labeling were determined according to the manufacturer’s protocol.
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2

Engineered Protein Hydrogel Synthesis

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GM-0111 was purchased from GlycoMira Therapeutics, Inc. (Salt Lake City, UT). Poloxamer 407 was purchased from Spectrum Chemical Mfg. Corp. (New Brunswick, NJ). Poly(lactic acid)-co-(glycolic acid)-block-poly(ethylene glycol)-block-poly(lactic acid)-co-(glycolic acid) (PLGA-PEG-PLGA) was purchased from Sigma Aldrich (St. Louis, MO). CF™633 was purchased from Biotium (Fremont, CA). SELP-815K and SELP-415K were produced and characterized as previously described[45 (link),50 (link)–52 (link)]. Post purification shear processing was performed on SELPs to normalize and enhance material properties[51 (link)].
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3

Fluorescent Tau13 Antibody Western Blot

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For western blots, a fluorescent anti-tau antibody was used. Therefore tau13 (Biolegend, San Diego, USA) was labelled with CF633 (Biotium, Freemont, USA), and the labelling process was performed as described previously [37 (link)]. 2N4R tau recombinant protein samples were prepared in Laemmli buffer (final 1× composition: 20 mM Tris, pH 6.8, 2% SDS, 6% glycerol, 1% β-ME, 0.002% Bromophenol Blue). All samples were heated at 95°C for 5 min and separated using SDS PAGE (15%). Proteins were then transferred to a polyvinylidene fluoride (PVDF) membrane (Thermo Fisher Scientific, Waltham, USA) at 500 mA for 40 min. After a washing step for 15 min in Tris-buffered saline tween buffer (TBS-T) (20 mM Tris, 150 mM NaCl, 0.1% Tween 20), the membrane was blocked for 1 h with 2.5% milk powder/TBS-T. Next, the membrane was washed with TBS-T, 2 × 5 min and in the last step for 15 min. tau13 stocks were 1 mg/ml and were diluted in TBS-T (1:5000). The membrane was incubated with the antibody for 1.5 h. at RT. After a final wash step (2 × 5 min and 1 × 10 min), TBS-T was performed. Detection based on the CF633 fluorescence of the labelled tau13 antibody. Bio-Rad universal hood II and Chemidoc XRS camera and Quantity One 4.6.5 software enabled the visualisation and quantification of the protein bands.
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4

Visualizing Bone Vasculature and Microenvironment

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Tissue preparation, immunostaining and imaging of full-bone femoral sections was performed as previously described (Coutu et al., 2018 (link)). Briefly, bones were fixed overnight in 4% paraformaldehyde and decalcified using 10% ethylenediaminetetraacetic acid (EDTA, pH=8) for two weeks. Longitudinal bone sections were stained overnight at RT with primary [anti-CD31 (goat, R&D, Ref#AF3628), anti-IL6st (rat, eBiosciences, Ref#17–1302–82), anti-collagen type I (rabbit, Cedarlene, Ref#CL50151AP), anti-von Willenbrand factor (rabbit, Thermo Scientific, Ref#RB–281–AO), anti-Endomucin (rat, eBiosciences, Ref#14–5851–82)] and secondary antibodies (CF488, CF555, CF633 and CF680, Biotium). Detection of IL6st was performed by biotin-streptavidin CF555 amplification. Sections were then optically cleared using graded series of 2,2-thiodiethanol (TDE, Sigma).
Full-bone imaging was performed on a Leica TCS SP8 confocal microscope equipped with two photomultiplier tubes, three HyD detectors and three laser lines (405-nm blue diode, argon and white light) using type F immersion liquid (RI: 1.518) and 20× multiple immersion objective (NA 0.75, FWD 0.680 mm). Images were acquired at 8-bit, 400 Hz and 1024×1024 or 2048×2048 resolution with 2.49 μm z-spacing.
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5

Focal Dendritic Stimulation of Pyramidal Neurons

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Focal synaptic stimulation at apical and basal dendrites of pyramidal neurons was performed using theta-glass pipette (borosilicate; Hilgenberg), placed in close proximity (5–10 µm) to the desired dendritic segment guided by the fluorescent image of the dendrite and Dodt contrast image of the slice. The theta-stimulation electrodes were filled with CF 633 (0.1 mM; Biotium) diluted with filtered ACSF. Current was delivered through the electrode (short bursts of three pulses at 50 Hz) at varying intensities using a stimulus isolator (ISO-Flex; AMPI). The efficacy and location of the stimulation was verified by simultaneous calcium imaging evoked by small EPSPs and their localization to a small segment of the stimulated dendrite.
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6

Conjugation of Fluorescent Dyes with BG-NH2

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Benzylguanine-conjugated Alexa Fluor 647 (#S9136S) and benzylguanine-conjugated Dyomics 649P1 (#S9159S) were purchased from New England BioLabs. Alexa Fluor 647 (#A20006), Alexa Fluor 680 (#A20008) and DyLight 650 (#62265) conjugated with succinimidyl ester (NHS ester) were purchased from Thermo Scientific. Atto 647N NHS ester (#18373) and Atto 655 NHS ester (#76245) were purchased from ATTO-TEC. Cy3B NHS ester (#PA63101), Cy5 NHS ester (#PA15101), and Cy5.5 NHS ester (#PA15601) were purchased from GE Healthcare. CF633 (#92133), CF647 (#92135), CF660C (#92137), and CF660R (#92134) conjugated with NHS ester were purchased from Biotium. Dyomics 654 conjugated with NHS ester (#654-01) was purchased from Dyomics (Jena). Each dye with NHS ester was reacted with BG-NH2 (#S9148S, New England Biolabs) in anhydrous dimethylformamide (DMF, #227056, Sigma-Aldrich) at 30 °C overnight according to the manufacturer's instructions (New England Biolabs).
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7

Fluorescent Antibody Detection of Protein Aggregates

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For microscopic detection of aggregates, we used fluorescent antibodies. The mouse anti-aSyn monoclonal antibody 211 (Santa Cruz Biotechnology, Inc., Dallas, USA) was labeled with CF633 (Biotium, Freemont, USA), whereas the anti-tau Tau5 antibody (Biolegend, San Diego, USA) was labeled with CF488A (Biotium, Freemont, USA). The labeling process was performed as described in the manufacturer’s protocol. The dyes were activated as succinimidyl esters to react covalently with the amines of the antibody in carbonate buffer. For purification of each labeled antibody, a polyacrylamide bead suspension (Bio-Gel P-30 Gel, Bio-Rad Laboratories, Inc., Hercules, USA) was used. The concentration and the degree of labeling was determined according to the manufacturer’s protocol.
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8

Focal Dendritic Stimulation in Pyramidal Neurons

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Focal synaptic stimulation, at apical dendrites of PCx pyramidal neurons was performed via a theta-glass (borosilicate; Hilgenberg) pipettes located in close proximity to the selected dendritic segment guided by the fluorescent image of the dendrite and the DIC image of the slice. The theta-stimulating electrodes were filled with CF-633 (Biotium; 0.2 mM). Current was delivered through the electrode (short burst of 3 pulses at 50 Hz), via stimulus isolator (ISO-Flex; AMPI). The efficacy and location of the stimulation was verified by simultaneous calcium imaging evoked by small EPSPs and their localization to a small segment of the stimulated dendrite.
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9

Multicolor 3D Bone Imaging

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Femoral sections were prepared, immunostained and imaged as previously described (Coutu et al., 2018 (link)). Bones were fixed in 4% paraformaldehyde overnight, and decalcified using 10% ethylenediaminetetraacetic acid (EDTA, pH=8) for two weeks. Longitudinal bone sections were stained overnight at RT with primary [anti-LepR (R&D systems, AF497), anti-Sca-1 (Biolegend, 122502), anti-collagen type I (Cedarlene, CL50151AP) and anti-GFP (Aves, GFP-1020)], secondary antibodies (CF488, CF633 and CF680, Biotium) and DAPI. Detection of LepR was performed by biotin-streptavidin CF555 amplification. Finally, sections were optically cleared using graded series of 2,2-thiodiethanol (TDE, Sigma). Three-dimensional full-bone imaging was performed using type F immersion liquid (RI: 1.518) and 20X multiple immersion objective (NA 0.75, FWD 0.680 mm) on Leica TCS SP8 confocal microscope equipped with two photomultiplier tubes, three HyD detectors and three laser lines (405-nm blue diode, argon and white light). 8-bit images were acquired at 400 Hz and 1024 × 1024 resolution (2.49 μm z-spacing) and stitched together.
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10

Transparent Mouse Brain Clearing

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Transparent mouse brains were generated by the ScaleS method as previously described23 (link). In brief, ScaleS solutions were made using urea crystals (Wako Pure Chemical Industries, 217–00615), D(−)-sorbitol (Wako Pure Chemical Industries, 199–14731), methyl-β-cyclodextrin (Tokyo Chemical Industry, M1356), γ-cyclodextrin (Wako Pure Chemical Industries, 037–10643), N-acetyl-L-hydroxyproline (Skin Essential Actives, Taiwan), dimethyl sulfoxide (DMSO) (Wako Pure Chemical Industries, 043-07216), glycerol (Sigma, G9012), and Triton X-100 (Nacalai Tesque, 35501-15). A mouse brain of a human mutant APP knock-in mouse22 (link) was fixed at indicated ages and cleared with ScaleS. For immunohistochemistry, the following fluorophore-conjugated antibodies (Abs) were used: mouse monoclonal antibody to amyloid-β conjugated to Alexa Fluor-488 (Covance; SIG-39347, 1:200), rat Ab to pSer46-MARCKS conjugated to CF633 (Biotium) and goat synapsin-1 antibody conjugated to Oyster 550 (Luminartis). The images were acquired with a TPEFM system (Olympus FVMPE-RS) with 920-nm excitation and an objective lens (XLSLPLN25XGMP) with a numerical aperture (NA) = 1.0, working distance (WD) = 8 mm, refractive index (RI) = 1.41–1.52, a collection collar, and a z-drive. The z step was 2.0 μm.
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