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7 protocols using alex fluor 555

1

Conformational dynamics of Hsp90 by FRET

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The conformational change rate of Hsp90 was measured by a FRET-based assay[41 (link)]. Briefly, D61C or E329C mutation was introduced into Hsc82 for labeling with Alex Fluor 647 or Alex Fluor 555 (Life Technologies) respectively. Labeled Hsp90 populations were mixed to produce Hsp90 heterodimers. The conformational change of Hsp90 was initiated by adding AMP-PNP (1 mM) in the presence of compounds. The fluorescence from different dyes was monitored on a microplate spectrophotometer with excitation/emission wavelength as follows: Ex525/Em568 (AF555), Ex525/Em668 (AF647). The assay was carried out at room temperature in the same buffer as Hsp90 ATPase assay.
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2

Immunofluorescence Staining of Paraffin-Embedded Tissues

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4-µm paraffin-embedded tissue samples were incubated with 10 mM sodium citrate buffer (pH 6.0) and autoclaved for 15 min for antigen retrieval. The samples were then blocked with PBS-based mixture of 5% bovine serum albumin (BSA; Affymetrix, CA) and 1% normal goat serum (NGS, Vector Laboratories, CA) for 30 min. After Blocking, sections were incubated with GFP (Santa Cruz Biotechnology, sc53882, 1:100), β-catenin (Abcam, ab2365, 1:100), CD44 (Proteintech, #15675-1-AP, 1:100), CD133 (Miltenyi Biotec, #130-108-062, 1:50), and CD166 (Abbiotec, #251619, 1:100) primary antibody overnight at 4 °C, followed by incubation with anti-mouse Alexa Fluor 488 (Life Technologies, CA, A11008; 1:500) or anti-rabbit Alex Fluor 555 (Life Technologies, A21428; 1:500) secondary antibodies for 1 h at room temperature. The samples were then counterstained with 4′, 6-diamidino-2-phenylindole (DAPI; Sigma-Aldrich) and mounted in Gel/Mount media (Biomeda Corporation, CA). All incubations were conducted in dark, wet chambers. The fluorescence signal was visualized using a confocal microscope (LSM510; Carl Zeiss, Germany) and analyzed by using Zen software V3.1 (Carl Zeiss).
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3

Histological Evaluation of Cardiac Fibrosis and Immune Cells

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Formalin-fixed, paraffin-embedded hearts from sham and HF mice were sectioned at 5 μm thickness, deparaffinized, and rehydrated. Histological staining was performed as previously described.6 (link), 21 (link), 23 (link) Masson’s trichrome was used to evaluate tissue fibrosis and Alexa Fluor 488–conjugated wheat germ agglutinin (Invitrogen) to assess myocyte area, as quantified from 5 to 6 high-power fields per section in non-infarcted myocardium using Metamorph software version 6.3r5 (Molecular Devices).
To evaluate for tissue abundance of CD4+ and CD8+ T-cells, heart sections were embedded in OCT compound (Tissue-Tek OCT), and then kept at −80°C until sectioning. Sections (7 μm thickness) were fixed with 4% paraformaldehyde in PBS, and labeled with either rat anti-mouse CD4 (Clone GK1.5; eBiosciences) or CD8 antibody (Clone 4SM15; eBiosciences). Goat anti-rat antibody conjugated with Alex Fluor 555 and 488 (Life Technologies) were used as secondary antibodies for CD4 and CD8, respectively, and fluoroshield-containing DAPI (Sigma-Aldrich) was used as the mounting medium. CD4+ or CD8+ cells were quantified using confocal microscopy from 5–6 sections and 3–4 mice from each group. All measurements were conducted in a blinded manner. Confocal microscopy was performed on an LSM710 microscope (Zeiss).
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4

Immunofluorescent Analysis of 3D Spheroid Cultures

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Spheroids were harvested at day 5 of spheroid culture, fixed with acetone, and embedded in 1% agarose. 1% Agarose blocks were dehydrated and embedded into a paraffin block. Paraffin-embedded spheroid sections (4 μm thick) were rehydrated, permeabilized with 0.1% triton X-100, blocked with 5% bovine serum albumin (BSA), and incubated with the primary antibodies: anti-GFP (Santa-Cruz Biotechnology), anti-panRAS (Millipore), anti-β-catenin (BD Bioscience), anti-CD44 (ProteinTech), anti-CD133 (ABBIOTEC), and anti-CD166 (ABBIOTEC). For secondary antibodies, Alexa Fluor 488 (Life Technologies) or Alex Fluor 555 (Life Technologies) was used. Counterstaining was done with 4′6’-diamidino 2-phenylindole (DAPI; Sigma). Gel/Mount media (Biomeda Corporation) was used for mounting. Immunofluorescent images were captured using confocal microscopy (LSM 700, Carl Zeiss). At least five fields per section were analyzed.
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5

Detailed Immunofluorescence Staining Protocol

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Experimental plates were cultured for 24 hours and 4% paraformaldehyde was then applied for 15 minute. Wells were then washed in PBS three times with PBS cells prior to incubation in blocking solution (PBS + 0.2% Tritonx-100, 5% BSA and 10% FBS) for 30 minutes. Phalloidin alexafluor 488 was made up in 0.2% triton in PBS (1 in 500 in block solution; Life Technologies) and added to the slides. For tubulin and actin imaging; cells were incubated in 4% paraformaldehyde (made up in PHEM buffer; 60 mM PIPES, 25 mM HEPES, 10 mM EGTA, 2 mM MgCl2, pH6.9) for 15minutes. Phalloidin Alexfluor 488 was added in addition to anti alpha tubulin (mouse; 1 in 500) for 1 hr. Coverslips were washed three times with PBS. For tubulin imaging anti-mouse Alexfluor 555 (1 in 10000, Life Technologies) was added in PBS 0.2% triton X-100). Coverslips were washed three times with PBS. Coverslips were removed and placed on slides with Fluorsave (DAPI containing, Sigma). Slides were imaged using a Leica SPE Confocal Microscope.
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6

Immunohistochemistry of Inner Ear and Eye

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E16.5 inner ears or eyes were fixed for 1 hour in PFA 4%, equilibrated in sucrose 20% overnight and embedded in a 1:1 mixture of sucrose 20%: OCT (Tissue-Tek). Cryosections (12μm) were stored at −80C, thawed, and processed for citrate antigen retrieval (boiled five times for 1 minute in 10mM citrate with cooling intervals). The sections were then permeabilized and blocked in 0.5% Triton X-100 and 1% BSA, and incubated with the primary antibodies overnight (NR2F1: R&D Systems PPH813299, mouse monoclonal clone H8132 (1:100); SOX2: Santa Cruz Biotechnology sc-17320, goat polyclonal (1:100)). Secondary antibodies were donkey anti-mouse conjugated to Alex Fluor 555 and donkey anti-goat conjugated to Alex Fluor 647 (Thermofisher). Nuclei were stained with Hoechst 33342 (Thermofisher). For the quantifications in Fig. 3D, a 25×25 μm region of interest was defined to match the organ of Corti, and signal intensity was measured separately for the SOX2 and NR2F1 channels using ImageJ (IntDens). For whole-mounts at birth (Fig. 5), inner ears were fixed 1 hour in 4% PFA, the sensory epithelia were exposed, permeabilized in 0.5% Triton X-100, stained with phalloidin conjugated to Alexa Fluor 488 (Thermofisher), and mounted flat. Images were acquired with a Zeiss LSM800 confocal microscope.
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7

Investigating BLA-vHPC Neural Activity in Fearful Behavior

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To examine the neural activity of BLA-projecting vHPC neurons during Exp OF, we bilaterally injected Cholrea Toxin Subunit B (CTB) conjugated to AlexFluor-555 (200 nL per side, 100 nL / min, ThermoFisher Scientific) in BLA aimed at the following coordinates relative to bregma: AP: −1.40 mm; ML: ±3.40 mm; DV: −5.00 mm. Mice were allowed to recover for 3 days before returning to group housing with cagemates. On Day 1, observers were subjected to CFC. On Day 2, we then tested observers for Exp OF with a familiar demonstrator (W/+/+) or with stranger demonstrator (W/+/−). 1 hour after behavioral testing, mice were perfused and immunostained for Arc and NeuN. We collected 2–4 vHPC coronal sections (AP; −3.20 mm) per mouse. In Figure 7B, we examined a total of 12,872 (W/+/−: 5,943, W/+/+: 6,929) NeuN+ cells. The percentage of total Arc+CTB+ neurons was calculated out of total CTB+ cells ( Total Arc+CTB+cellsTotal CTB+cells*100% ). Fold change analysis (normalized by the average of the control W/+/− group) was compared between groups. The percentage of total Arc+CTB neurons was calculated out of total CTB cells ( Total Arc+CTBcellsTotal CTBcells *100% ). Fold change analysis (normalized by the average of the control W/+/− group) was compared between groups. Quantification of NeuN, CTB, and Arc positive cells in vHPC was conducted using the Cell Counting plugin in ImageJ.
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