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5 protocols using applications suite

1

Quantifying Cell Proliferation and Migration

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Cell proliferation was monitored every 24h for 144 hours by manual cell counting using a 1/4002 haemocytometer (Hawksley, Lancing, UK). Tumour cell invasion was assessed using 6mm Transwell plates with an 8.0μM pore size (Costar; Corning Incorporated, NY, USA) coated with basement membrane matrix (20% Matrigel; Invitrogen, Paisley, UK). Cells were seeded into the inner chamber at a density of 2.5×105 for MDA-MB-231-IV and 5×105 for MCF7 in RPMI without FCS and 5×105 HS5 bone marrow cells in RPMI supplemented with 10% FCS were added to the outer chamber. Cells were removed from the top surface of the membrane 24 and 48 hours after seeding, and cells that have invaded through the pores were stained with haematoxylin and eosin before being imaged on Leica DM7900 light microscope and manually counted.
Migration of cells was investigated by analysing wound closure: Cells were seeded onto 0.2% gelatine in 6-well tissue culture plates (Costar; corning incorporated); once confluent, 10ug/ml mitomycin C was added to inhibit cell proliferation and a 50uM scratch made across the monolayer. The percentage of wound closure was measured 24 and 48 hours using a CTR7000 inverted microscope and LAS-AF v2.1.1 software (Leica Applications Suite; Leica Microsystems, Wetzlar, Germany).
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2

Histological Lipid Analysis of Liver Sections

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Tissue Tek-embedded livers were cut with a cryostat CM3050S (Leica, Wetzlar, Germany) to obtain 14 µm sections which were mounted on SuperFrost Plus adhesion slides (Thermo Fisher Scientific, Waltham, MA, USA), air-dried overnight, and stored at room temperature until use. For hepatic neutral lipid staining, liver sections were fixed in 4% neutral buffered formalin, washed with tap water, and rinsed with 60% isopropanol. Hepatic lipids were stained with Oil Red O (Polysiences Inc., Warrington, FL, USA) for 15 min. Next, the liver sections were rinsed with 60% isopropanol, lightly stained with hematoxylin, and covered with a coverslip. Digital images of the sections were obtained using a Leica DMLB microscope (Leica Microsystems, Rijswijk, The Netherlands) equipped with software from the Leica Applications Suite (Leica Microsystems, Rijswijk, The Netherlands).
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Quantifying Calcium and Mineralization

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Calcium AS FS (DiaSys Diagnostic Systems, Holzheim, Germany) was used to quantify calcium content (normalized to the cell number per well) after cell lysis. OsteoImageTM mineralization assay (Lonza, Basel, Switzerland) applied according to the manufacturer’s instructions, allowed for hydroxyapatite visualization and quantification via the high resolution fluorescence scanner. Cells were stained with Alexa Fluor 568 phalloidin and examined using a Leica SP5X laser scanning confocal microscope (Leica, Wetzlar, Germany) for qualitative assessment. Leica Applications Suite was used to obtain images.
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Intestinal Tissue Immunohistochemistry

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Using immunohistochemical staining concentration of 3-nitrotyrosine (3-NT), inducible NO-synthase (iNOS), occludin and zonula occludens-1 (ZO-1) in proximal small intestinal tissue were evaluated as detailed previously [14] (link), [32] (link), [33] (link). In brief, just prior to incubation with primary specific polyclonal antibodies (3-NT: Santa Cruz Biotechnology, Dallas, TX, USA; iNOS: Thermo Fisher Scientific, Waltham, MA, USA; occludin and ZO-1: Invitrogen, Carlsbad, CA, USA), deparaffinated tissue sections were incubated with protease (occludin, ZO-1) or heated in mono-sodium citrate buffer and blocked using bovine serum albumin solution (3-NT, iNOS). Sections were than incubated with peroxidase-linked secondary antibodies and diaminobenzidine (Peroxidase Envision Kit, DAKO, Hamburg, Germany). Staining was evaluated using analysis system (Leica Applications Suite, Leica, Wetzlar, Germany) integrated in a microscope (Leica DM6 B, Leica, Wetzlar, Germany) as described previously [32] (link), [33] (link).
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5

Immunohistochemical Analysis of Liver and Intestinal Markers

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Immunohistochemical staining methods were used to measure concentration of 4-HNE, iNOS and MyD88 in paraffin embedded liver sections as well as of MMP13, Occludin and ZO-1 in small intestinal tissue sections as previously described7 (link),19 (link),22 (link). In brief, after treating sections with citrate buffer (MMP13) or incubating with protease (occludin, ZO-1) and blocking tissue sections with bovine serum albumin solution (iNOS, MMP13, MyD88), they were incubated with specific primary antibodies (4-HNE: AG Scientific, San Diego, CA, USA; iNOS: Thermo Fisher Scientific, Waltham, MA, USA; MMP13: LifeSpan BioSciences, Seattle, WA, USA; MyD88: Santa Cruz Biotechnology, Dallas, TX, USA; Occludin and ZO-1: Invitrogen, Carlsbad, CA, USA). Subsequently, sections were incubated with peroxidase-linked secondary antibodies followed by diaminobenzidine (Peroxidase Envision Kit, DAKO, Hamburg, Germany). Staining was evaluated using a camera integrated in a microscope (Leica DM4000 B LED, Leica, Wetzlar, Germany) and an analysis system (Leica Applications Suite, Leica, Wetzlar, Germany) as described previously19 (link),42 (link).
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