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3 protocols using ab1954

1

Protein Extraction and Analysis from LV Tissue

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To extract protein from the LVI, LV tissue was homogenized in protein extraction reagent 4 (Sigma) with 19 protease inhibitor using the Power Gen 1000 Homogenizer (Fisher Scientific). The homogenized LV was centrifuged at 4700 rpm to remove debris. A Bradford assay (BioRad) was used to measure the concentration of protein. The extracted protein was stored at −80 °C.
SDS-PAGE and immunoblotting analysis of total protein (10 μg) were performed, as previously described [23 (link)]. Specific primary antibodies against Mac-3 (Cedarlane CL8943B, 1:500), collagen I (Cedarlane CL50141AP-1, 1:1000), collagen III (Cedarlane CL50341AP-1, 1:1000), fibronectin (Abcam ab1954, 1:2000), and hyaluronic acid (Abcam ab53842, 1:1000) were used. ImageQuant TL 8.1 analysis software (GE Healthcare, Waukesha, WI) was used to quantify densitometry. The intensity of every lane was normalized to the densitometry of the total protein for that lane, as an internal loading control.
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2

Visualizing Focal and Fibrillar Adhesions

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Cells were fixed with 4% paraformaldehyde for 5 min, rinsed in
1X phosphate buffered saline, incubated within 0.1% Triton X-100 solution
for 5 min, rinsed, and blocked by a 1% bovine serum albumin solution
(Millipore Sigma) for 30 min. Focal adhesions were visualized using
antibodies specific for vinculin (MAB3574; Millipore Sigma) and integrin
αvβ3 (MAB1976Z; Millpore Sigma). Fibrillar adhesions were
identified using specific antibodies to tensin-1 (NBP1–84129;
Novus biologicals, Toronto, ON), integrin β1 (MAB17781; R&D
Systems, Minneapolis, MN), and integrin α5 (ab150361; Abcam,
Waltham, MA). Extracellular matrix deposition was identified using
antibodies to fibronectin (ab1954; Abcam, Waltham, MA). F-actin was
labeled with rhodamine conjugated phalloidin (R415; Life Technologies,
Grand Island, New York), and nuclei were counterstained with Hoechst
(H3560; Invitrogen, Burlington, ON). Images were taken on a Carl Zeiss
Axio Imager M2m microscope (Zeiss Microscopes, North York, ON) under
reverse osmosis water immersion and processed using Zen Pro software.
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3

Quantitative Analysis of Recombinant Proteins

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Select strains were grown overnight in YPD and cell wall susceptibility assays were performed as described elsewhere (Ram & Klis, 2006). Congo red and Calcofluor white dyes (cat. nos. C6277 and F3543; Millipore Sigma) were added to final concentrations of 150 and 20 µg/mL, respectively.
Quantitative polymerase chain reaction (PCR) was performed according to PowerUp SYBR Green kit instructions (Thermo Fisher Scientific) using a Roche LightCycler 480. β‐Actin, rhGH, rhG‐CSF, and trastuzumab ORFs were PCR amplified and serially diluted to generate a standard curve (see Table S2 for primers). Experimental design and absolute copy number quantification were performed according to best practices (Abad et al., 2010)
Protein concentrations of rhGH and rhG‐CSF were determined using sandwich enzyme‐linked immunosorbent assay (ELISA) as described elsewhere (Crowell et al., 2018). rhGH‐specific antibodies were used at concentrations of 5 µg/ml capture (ab1954; Abcam, Cambridge, UK) and 0.6 µg/ml secondary/detection (ab1956; Abcam). rhG‐CSF‐specific antibodies were used at concentrations of 2 µg/ml capture (BVD13‐3A5; Biolegend, San Diego, CA), 0.4 µg/ml secondary (BVD11–37G10), and 0.2 µg/ml detection (ab7403; Abcam). Protein concentrations of trastuzumab were determined using a Human IgG1 ELISA kit (cat. no. RAB0242; Millipore Sigma).
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