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10 protocols using af1494

1

Quantitative Western Blot Analysis of BDNF and TrkB

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HIP and PFC samples (20 µg total protein) were separated on 10% criterion TGX gels (Bio-Rad) and transferred to nitrocellulose membranes. The samples were then blocked in odyssey blocking buffer (LI-COR, Lincoln, NE, USA) and probed with the primary antibodies: rabbit anti-BDNF (Sigma AV41970; 1:2000), mouse anti-β-actin (926-42212, LI-COR; 1:3000), goat anti-TrkB (AF1494, R&D Systems, Minneapolis, MN, USA; 1:500), and rabbit anti-TrkB(Y817) (ab81288, Abcam, Cambridge, UK; 1:1000) overnight at 4 °C. This was followed by incubation with the appropriate IRDye conjugated secondary antibody for 1 h at RT: IRDye 800CW donkey anti-goat IgG, IRDye 680RD donkey anti-rabbit IgG, IRDye 800CW goat anti-rabbit IgG, or IRDye 680RD goat anti-mouse IgG, all in 1:15,000 dilution (LI-COR). Infrared signals were detected using the Odyssey CLx infrared imaging system (LI-COR, and bands were quantified using Image Studio software (LI-COR).
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2

Immunohistochemical Staining of TrkB and Tubulin

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For immunohistochemical stainings the following primary antibodies were used: Goat anti-TrkBECD (R&D, AF1494, 1:100); Mouse anti-tubulin βIII (R&D, TUJ-1 clone/catalog, 1:500). Fluorescent secondary antibodies were purchased from Jackson Immunoresearch: donkey anti-goat Cy3 (1:200), and goat anti-mouse Cy3 (1:200). Phalloidin-Rhodamine was used at 1 ug/ml (Sigma-Aldrich, P1951).
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3

Quantifying TRKB Surface Levels in Cortical Neurons

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Cortical neurons were cultured in 96-well plates (60,000 cells/well, 100 μL/well of medium, DIV8) and treated with C21 (0, 0.1, 1, 10 μM/15 min) and surface levels of TRKB was determined as previously described [23 (link),43 (link)]. Briefly, after drug administration, the wells were washed three times with cold PBS and fixed with 4% PFA for 20 min at room temperature (RT) under agitation. The cells were washed again three times with PBS for 5 min at RT and blocked for 1 h at RT (5% nonfat dry milk, 5% Bovine Serum Albumin-BSA-in PBS). Primary antibody against the extracellular portion of TRKB (R&D; #AF1494; 1:500) was added and incubated overnight (ON) at 4 °C. Following wash with PBS, the cells were incubated with anti-goat IgG HRP-conjugated antibody (Invitrogen; #61-1620; 1:5000) for 1 h at RT. The cells were washed four times with PBS (10 min at RT for each wash) and then ECL (1:1) was added to detect the signal by the plate reader (Varioskan Flash, Thermo Scientific, Waltham, MA, USA). The signal from the samples, after blank subtraction, were normalized by the average of the control group (C21 = 0) and expressed as percentage from control.
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4

Investigating Neural Crest Cell Migration

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Embryos were injected and electroporated with an EGFP plasmid (pMES) at HH St 10 and incubated for 72 hours. Embryos were then sectioned transversely, using a feather blade (~150um thick), between the fore- and hindlimbs and placed on a Millicell culture insert (EMD Millipore, Billerica, MA). BDNF- (Peprotech, Rocky Hill, NJ) or PBS- soaked Affigel beads (Bio-Rad, Hercules, CA) were placed in the slices along the dorsal migratory path of neural crest cells but in ectopic locations that the cells normally avoid (i.e. adjacent to notochord, ventral to spinal nerve, dorsal aorta), using fine glass pipettes and tungsten needles. The Millipore filter was then placed in a glass bottom petri dish and tissue time-lapse imaged. For function blocking experiments, trunk transverse tissue sections were cultured as above and the following function blocking antibodies were added to the culture media: anti-BDNF (1:500; Millipore, #AB1513P), anti-trkB (1:500; R and D systems, #AF1494) or CHEX, anti-p75 (1:1,000; kind gift of F. Lefcort/L. Reichardt, MSU).
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5

Elucidating Neurotrophic Factor Roles in PC12 Survival

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Neutralization experiments using specific blocking antibodies were conducted to determine which neurotrophic factors were involved in mediating PC12 cell survival and neurite outgrowth. PC12 was cultured with 50% DPSCs-CM in the presence of anti-NGF antibody (0.25 µg/mL; Cat# MAB556, R&D Systems), anti-GDNF antibody (1 µg/mL; Cat# AF212, R&D Systems), anti-BDNF antibody (2 µg/mL; Cat# AF1494, R&D Systems), anti-NT-3 antibody (2 µg/mL; Cat# AF1404, R&D Systems) or in the presence of mixture of all antibodies using the concentrations stated earlier.
At the beginning of each experiment, cells were washed twice with PBS and all experiments were performed in absence of serum. The cultures were maintained under the same conditions as previous experiments for 8 days, followed by quantification of neurite outgrowth and the number of survived neurons.
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6

Characterizing Anti-TrkB Antibody Specificity

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Anti-TrkB antibody (R&D systems, AF1494, RRID:AB_2155264) produced against the extracellular domain (Cys32-His429) of recombined mouse TrkB. Based on manufacturers technical information the antibody detects mouse TrkB in direct ELISA and Western blot, and shows 25% cross reactivity with human TrkB, and less than 2% cross reactivity with recombined rat TrkA and TrkC. The antibody labels mechanoreceptors in the TGG as shown by Matsumoto et al., 2012 (link).
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7

Spinal Cord BDNF Injection Protein Analysis

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Spinal cords were extruded with ice-cold PBS (pH 7.4), 6 days after injury, and the dorsal horn of the lumbar enlargement corresponding to L3 to L5 was isolated. Following BDNF injections, spinal cords were extruded with ice-cold PBS (pH 7.4) at times 0 (no injection), 3, 6, and 24 hours, and the entire lower lumbar enlargement was used for WB. The tissue was lysed in standard Tris-NaCI-EDTA lysis buffer supplemented with protease and phosphatase inhibitors. Following SDS–polyacrylamide gel electrophoresis (PAGE) and blotting, the proteins were probed against NTSR-3 (1:1000; 61200, BD Biosciences), KCC2 (1:1000; 07-432, Millipore), TrkB (1:1000; AF1494, R&D Systems), ERK1/2 (1:1000; 4695, Cell Signaling Technology), pERK1/2 (1:1000; 9101, Cell Signaling Technology), Akt (1:500; 9272, Cell Signaling Technology), pAkt (1:300, 9275, Cell Signaling Technology), NKCC1 (1:1000; Lytle, C., Developmental Studies Hybridoma Bank, NICHD, The University of Iowa), pNKCC1 (1:1000; donated by B. Forbush, Yale University, New Haven, CT), and β-actin (1:5000; Sigma-Aldrich), visualized with horseradish peroxidase–conjugated secondary antibody (Dako) and ECL substrate (Amersham) by LAS 4000 (Fujifilm Life Science) and quantified using Multi Gauge version 3.2 (Fujifilm Life Science).
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8

Investigating Neural Crest Cell Migration Using BDNF Stimulation

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Embryos were injected and electroporated with an EGFP plasmid (pMES) at HH St. 10 and incubated for 72 h. Embryos were then sectioned transversely, using a feather blade (∼150-μm thick), between the fore- and hindlimbs and placed on a Millicell culture insert (EMD Millipore, Billerica, MA). BDNF- (Peprotech, Rocky Hill, NJ) or PBS-soaked Affigel beads (Bio-Rad, Hercules, CA) were placed in the slices along the dorsal migratory path of neural crest cells but in ectopic locations that the cells normally avoid (that is, adjacent to notochord, ventral to spinal nerve, dorsal aorta), using fine glass pipettes and tungsten needles. The Millipore filter was then placed in a glass bottom Petri dish and tissue time-lapse imaged. For function-blocking experiments, trunk transverse tissue sections were cultured as above and the following function blocking antibodies were added to the culture media: anti-BDNF (1:500; Millipore, #AB1513P) or anti-trkB (1:500; R and D systems, #AF1494).
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9

Immunohistochemistry of Neural Markers

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Primary antibodies used included the following: Elp1 (Sigma #SAB2701068, 1:500), Tubb3 (Abcam #ab78078, 1:1,000 for sections, 1:300 for whole-mount), Sox10 (R&D #AF2864, 1:200 or GeneTex #GTX128374, 1:500), TrkA (R&D #AF1056, 1:500 for sections, 1:200 for whole-mount), TrkB (R&D #AF1494, 1:300), TrkC (R&D #AF1404, 1:300), Six1 (Sigma #HPA001893, 1:500), Islet1 (DSHB #PCRP-ISL1-1A9, 1:500), Neuropilin2 (R&D cat. AF567, 1:500), Pax3 (DSHB, ‘Pax3’, 1:200), BFABP (Sigma, ZRB13190-25ul, 1:500), and RFP (Thermo, MA515257, 1:400). All species/isotype-specific, Alexa Fluor-conjugated secondary antibodies were purchased from Thermo Scientific and used at a dilution of 1:500 on sections or 1:300 in whole-mount.
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10

Vagal Ganglia Neuroreceptor Quantification

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Vagal ganglia were stained for immunoreactivity to TRPV1 (goat; 1:150; catalog #sc-12498, Santa Cruz Biotechnology), and the neurotrophin receptors tyrosine receptor kinase A (TRKA; rabbit; 1:300; catalog #06–574, Millipore) and tyrosine receptor kinase B (TRKB; goat; 1:300; catalog #AF1494, R&D Systems). Primary antibodies were visualized with the following secondary antibodies: chicken anti-goat 647 (1:300; catalog #A212345, Invitrogen) and donkey anti-rabbit 488 (1:300; catalog #A21206, Invitrogen). Images were taken with Olympus FV1200 laser-scanning confocal microscope equipped with 20× UPLAN SAPO, 0.75 numerical aperture. z-Stack images (each 20 μm) of four to six different ganglia were taken, and projection images were obtained using Fiji software. Cell counts and somal diameters were measured using Fiji software. Each somal diameter was calculated as the mean of the longest and shortest distances across the soma of a neuron identified in a z-stack projection (2D image). The diameters of various vagal afferent subpopulations were compared using ANOVA with Sidak’s multiple-comparisons test (GraphPad Prism version 7). A p value <0.05 was considered significant.
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