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108 protocols using dfc350fx

1

Chromosome Spread Analysis by Fluorescence Microscopy

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Slides with chromosome spreads were analysed using a fluorescence microscope, Leica DM 4000, equipped with a monochrome digital camera DFC350 FX and filter cubes corresponding to fluorochromes Alexa488, Cy3, and DAPI (Leica-Microsystems). The LAS X core computer program was used to obtain and process colour images.
Analysis of the 3D morphology of the gonads and whole-mount FISH was performed by laser scanning confocal microscopy (using a Leica TCS SP5 based on the inverted microscope Leica DMI 6000 CS, Leica-Microsystems). Nuclei were scanned in XYZ planes using lens HC PL APO 40×. Images were obtained by the LAS AF program (Leica-Microsystems, Germany).
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2

Aortic Root Lesion Analysis in LDLR-Deficient Mice

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The aortic roots of ldlr−/− mice fed a high fat, high cholesterol diet for 24 weeks were dissected and embedded in Tissue Tek OCTTM (Sakura Finetek, Staufen, Germany). Within the aortic root, serial cryostat sections (6 μm, CM3050S, Leica Microsystems, Wetzlar, Germany) at the level of all 3 cusps were prepared. Lesion areas were analyzed for LCN2, endothelial cells (CD31), alpha smooth muscle cells (αSMA), monocytes/macrophages (MOMA-2) as well as the M1 macrophage marker inducible nitric oxide synthase (iNOS) and counterstained with hematoxylin (Carl Roth, Karlsruhe, Germany) for immunohistochemistry or 4',6-diamidino-2-phenylindole (DAPI, Life Technologies) for immunofluorescence, respectively. Visualization was performed with the appropriate VECTASTAIN ABC reagents for biotinylated antibodies and either ImmPACT DAB or VIP Peroxidase (HRP) Substrate (all from Vector Laboratories) according to the manufacturer’s protocol. For immunofluorescence Alexa Fluor 488 and 555 conjugated secondary antibodies were used (Life Technologies). Staining for collagen (Picrosirius Red) were assessed under polarized light. Pictures were captured using a DM4000 B microscope with a DFC320 camera for immunohistochemistry and a DFC350FX camera for immunofluorescence and QWin software (all Leica Microsystems).
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Germ Cell Quantification in Fetal Ovary

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For each germ cell marker (OCT4+ve; DAZL+ve; VASA+ve), four fields of view were captured across each section using a light microscope with a 5× objective (DM500B, Leica Microsystems) and camera (DFC350FX, Leica Microsystems). Germ cells (total number within ovigerous cords) were manually counted using the pointer tool (Image ProPlus) for each image. The mean germ cell count was calculated from the four fields of view across each section. This count was then repeated for every stained section across the whole fetal ovary. This was used to determine an overall mean count, density, and total number of germ cells. The ratio between the different germ cell markers was also calculated. The proliferation index was calculated as the proportion of all germ cells (within the ovigerous cord) which were Ki67+ve, while the apoptotic index was calculated as the proportion of germ cells which were caspase 3+ve.
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4

Fluorescent Liposome Imaging in 3D

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Stock suspensions of LPs, either filled with free-CF640R or empty, were diluted 1:400 v/v in 0.5% low gelling temperature agarose in Ames’ medium at 37 °C. A thin film was polymerized over a pure agarose meniscus in a Petri dish and covered with Ames’ medium. 3D image stacks were acquired with a 63x/0.9NA water immersion objective and a CCD camera (DFC350 FX, Leica Microsystems, Milan, Italy) in an upright widefield fluorescence microscope (DM LFSA, Leica Microsystems, Milan, Italy) using a Cy5 filterset (49,006; Chroma, Olching, Germany). Stacks were deconvolved and max projected along the z-axis using Fiji/ImageJ as detailed in Ref [68 (link)].
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5

Correlative Fluorescence Microscopy Setup

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Fluorescence images for correlative microscopy were recorded on a Leica DM6000B microscope (Leica Microsystems GmbH, Wetzlar, Germany), equipped with a CCD-camera (DFC350FX) and the following filter cubes.A4 (UV): Exc 360/40, Dichro 400, Suppres BP 470/40. GFP (blue): Exc 470/40, Dichro 500, Suppres BP 525/50. SFRED (red): Exc HQ 630/20x, Dichro Q649LP, Suppres HQ 667/30. Furthermore, this microscope allows imaging in brightfield and phase contrast microscopy.
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6

Viability Assay Using Calcein-AM and Ethidium Homodimer-1

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Culture medium was aspirated gently, the cells were rinsed briefly with 0.1% glucose–PBS, and incubated for 15 minutes in 2 µM ethidium homodimer-1 and 2 µM calcein-AM (Molecular Probes, Thermo Fisher Scientific, Waltham, MA, USA) diluted in 0.1% glucose–PBS under protection from light. Cells were then fixed, permeabilized, counterstained with 4′,6-diamidino-2-phenylindole (DAPI) (1 µg/mL in PBS), mounted in Mowiol as previously described,25 (link) and analyzed by fluorescence microscopy (Leica Microsystems, Wetzlar, Germany). Images of all the subgroups of a given experiment were acquired on the same day using a monochrome digital camera (DFC 350 FX; Leica Microsystems) attached to the microscope and the Leica Application Software (Advanced Fluorescence 2.3.0, build 5131) under identical settings for exposure time, gain, and intensity. Quantification of the staining intensity was performed using the ImageJ software (National Institutes of Health, Bethesda, MD, USA, http://imagej.nih.gov/ij/, 1997–2014) on the images having an area of 0.04 mm2. The viability index was calculated from the ratio of the intensities of calcein and ethidium homodimer-1 stainings.
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Quantifying Proliferation of Mesenchymal Cells

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To assess cell proliferation, MD-ASC and ASC at the third passage in culture were plated at a density of 3.0 × 103 cells/cm2 in a 96-well plate. The medium was replaced with a fresh one every 4 days. Every 24 h for 7 days cells were stained with 1 µg/mL Hoechst 33,342, incubated for 15 min at 37 °C, and images were acquired using an epifluorescence Leica DMI 6000B microscope connected to a Leica DFC350FX camera (Leica Microsystems, Wetzlar, Germany). Cells at each time point were counted using ImageJ 1.52i software. Population doubling time (PDT) was calculated during exponential growth (log phase) with the following formula: PDT = T ln2/ln(Xe/Xb), where T is the time interval considered, Xb is the cell number at the beginning of the time interval, and Xe is the cell number at the end of the time interval. All experiments were performed in triplicate.
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8

Calculating Cell Population Doubling Time

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The cell population doubling time (PDT) was calculated by plating cells at the third passage at a density of 2 × 103 cells/cm2 into 96-well plates (BD FalconTM) in MC-conditioned medium (CM), obtained as follows: 1 × 106 cells/ml of the human MC line HMC-1 were cultured for 48 hr in the absence or presence of FICZ (300 nM) or, as a positive control, phorbol 12-myristate 13-acetate (PMA, 1 ng/ml) and ionomycin (200 ng/ml) (35 (link)), all from Sigma-Aldrich. HMC-1-derived medium was diluted (1:1) in stromal cell culture medium prior to incubation with stromal cells. CM was replaced every 4 days, and images of Hoechst 33342-labeled cells were acquired at different time points (1-2-3-5 days) using a Leica DMI 6000B microscope connected to a Leica DFC350FX camera (Leica Microsystems) and equipped with a 5X objective lens (numerical aperture: 0.12). Cell counts were performed using ImageJ. Experiments were performed in triplicate. PDT was calculated during the log-phase of growth.
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9

Inhibition of PLK-1 and c-Myc in D17 Cells

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The D17 cell line, known to overexpress PLK‐1 and c‐Myc proteins, was selected for inhibition experiments using BI 2536 (Boehringer Ingelheim, Ingelheim, Germany).32 A 10 mM stock solution of BI 2536 was prepared by resuspending the compound in dimethyl sulfoxide (DMSO). D17 cells treated with DMSO were used as control. First, 3 × 105 cells/well were seeded in six wells cell culture plates and were then treated with BI 2536 at 2.5, 5, 7.5, and 15 nM for 12 and 24 h. Morphological changes were evaluated with a Leica AF6000 LX (Leica Microsystems, Wetzlar, Germany) microscope equipped with a Leica DFC350FX digital camera controlled by the LAS AF software (Leica Microsystems). Based on morphological effect, viability assay was performed using CellTiter 96 AQueous One Solution Cell Proliferation Assay (Promega, Madison, WI) on 1 × 106 cells/well at 2.5, 5, 7.5, and 15 nM for 12 and 24 h. Similarly, caspase activity for apoptosis detection was evaluated using Caspase‐Glo 3/7 Assay System (Promega, Madison, WI) according to the datasheet after 12 and 24 h of treatment at 2.5, 5, and 7.5 nM. The untreated D17 cell line was used as control while the medium was used as blank to subtract background signal. All experiments were performed in triplicate and repeated three times.
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10

Neuronal Culture and Imaging on Patterned Substrates

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The use of animals and all protocols were approved by the University of Iowa Institutional Animal Care and Use Committee. Dissociated SGN and TGN cultures from P3–5 rat pups were prepared as previously described (Hansen, et al., 2001a (link), Hansen, et al., 2001b (link), Roehm, et al., 2008 (link), Tuft, et al., 2013 (link)) and plated onto patterned and unpatterned methacrylate thin-films. Neurotrophin-3 (NT-3, 50 ng/ml) and brain derived neurotrophic factor (BDNF, 50 ng/ml) were added to SGN cultures and NGF (50ng/ml) was added to TGN cultures to support neuronal survival and neurite growth. After 72 h, the cultures were fixed and immunostained with anti-neurofilament 200 (NF200) antibodies (1:400, Sigma-Aldrich), which detects neurites in SGNs and TGNs, as previously described (Hansen, et al., 2001a (link)). Alexa 488 conjugated secondary antibody (1:800, Invitrogen) was used to detect the primary antibody immunolabeling. Digital epifluoresencent images were captured of the entire polymer surface using the scan slide application of Metamorph software (Molecular Devices) on a Leica DMIRE2 microscope (Leica Microsystem) with a Leica DFC350FX digital camera.
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