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14 protocols using lsm 5 pascal system

1

Viability and Morphology of Encapsulated Cells

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The viability and morphology of encapsulated IDG-SW3 cells were assessed using a live/dead assay based on Calcein AM (Corning), which stains the cytosol of live cells, and ethidium homodimer (Corning), which enters the nucleus of compromised cells and stains DNA. Hydrogels were incubated with 4 μM Calcein AM and 2 μM ethidium homodimer for 10 minutes. The GFP expression could not be distinguished from the cytosolic stain of Calcein, but the latter will stain all live cells. Qualitative assessment of dead cells was not affected by GFP expression. Intact hydrogels were imaged by confocal microscopy (Zeiss LSM 5 Pascal system using a Zeiss Axiovert microscope).
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2

Fabrication of Composite Hydrogel Materials

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Patterned material #1 was soaked in 70% Ethanol for 48 hours followed by equilibrium swelling in diH2O or PBS. Depending on the experiment, the precursor solution for material #2 was introduced either into one side of the reservoirs in the 1D experiment or by submerging the material #1 in the precursor solution of material #2. The submerged samples were later photopolymerized to lock the material #2 in place. The composite samples were swelled to equilibrium in diH2O and then imaged. For the experiments in Figure 7b, images were acquired VersaDoc MP 4000 Molecular Imaging System. For all other experiments, images were acquired using confocal fluorescence microscopy (Zeiss LSM5 Pascal system) with a water immersed 10X objective lens. NIH ImageJ software was used to determine distances of overlapping fluorescence.
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3

Astrocyte Quantification in GFAP-GFP Mice

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GFAP-GFP transgenic mice were anesthetized with isoflurane during cardiac perfusion of PBS followed by 4% paraformaldehyde (PFA, Electron Microscopy Science). Brains were then dissected out and post-fixed in 4% PFA overnight at 4°C followed by 30% sucrose dehydration. Coronal brain sections (45 μm in thickness) were prepared by frozen sectioning, and were blocked in PBS solution with 10% goat serum/1% BSA/0.3% Triton X-100 for 1 hour at room temperature. Glial fibrillary acid protein (GFAP) is a specific marker for astrocytes. The brains sections were incubated in the primary antibody (anti-GFAP, mouse, 1:2000, Cell Signaling) overnight at 4°C, and secondary antibody (CY3 goat-anti-mouse, 1:1000) at room temperature for 4 hr. For GFAP positive astrocyte counting, confocal images were taken with Zeiss LSM 5 PASCAL system coupled to Zeiss Axiovert 200 microscope. Comparable sections from different mice were chosen for comparison. A 0.3 mm2 area of each side of cerebral cortex was analyzed for GFAP positive astrocyte counting in a blinded fashion.
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4

Amyloid and ApoE Co-Staining in Mouse Brain

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Brain sections from 10-month-old 5XFAD/apoEm/4 or 85-day-old APPPS1-21/apoEm/4 mice were co-stained for fibrillar amyloid, mouse apoE, and apoE4 using X-34, anti-mouse apoE monoclonal antibody HJ6.3-Alexa Fluor 568 (generated in-house) and anti-human apoE monoclonal antibody HJ15.7-Alexa Fluor 488 (generated in-house), respectively. For quantification of apoE/CAA or apoE/plaque co-staining in 10-month-old 5XFAD/apoEm/4 mice, brain sections were imaged using a Zeiss LSM 5 PASCAL system coupled to a Zeiss Axiovert 200 M confocal microscope. Three sections from each mouse were used and five fields containing CAA and five fields containing plaques on each section were imaged. Images were thresholded for corresponding colors and the degree of co-localization was analyzed with ImageJ. Percent area of CAA or plaque covered by mouse apoE or apoE4 was calculated and the average from the 3 sections/mouse was used to represent each mouse. For quantification of apoE/plaques in 85-day-old APPPS1-21/apoEm/4 mice, which were at the initiation of plaque deposition, all the plaques in the cortical area were counted under Nikon Eclipse 80i fluorescent microscope and the apoE co-staining status for each individual X-34 plaque was recorded. The average of 3 sections from each mouse was used to represent each mouse.
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5

Confocal Microscopy Imaging and Colocalization Analysis

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Confocal images were generated on an LSM 5 Pascal system (Zeiss) equipped with 40× 1.3 NA and 63× 1.4 NA objectives. All figures were maximum projections except Figures 3E and 10. Image maximum projections were compiled from Z-stacks of 30-50 sections with intervals ranging from 0.3-0.4 μm and a Z distance of 10-14μm. Confocal images for all figures, except Figure 10, were deconvolved using AutoQuant X AutoDeblur Gold CF (Media Cybernetics, Inc.). Manders colocalization coefficients were determined using unbiased automatic thresholding (Imaris 7.3) on deconvolved Z-stack images, and reported in the value range 0 1 (0: no colocalization, 1: all pixels colocalize) directly from the software analysis. Three-dimensional surface renderings of deconvolved images were done with Imaris 7.3 (Bitplane AG).
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6

Confocal Imaging of Xenopus Embryos

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Image acquisition was performed using an LSM710 system (×40, NA 1.2 water immersion objective or ×63, NA 1.4 oil immersion objective; Zeiss), an LSM5 PASCAL system (×63 NA 1.2 and ×20 NA 0.60; Zeiss), an A1Rsi system (×63 NA 1.3 water immersion objective; Nikon) or a TSC SP8 system (×40, NA 1.10 water immersion objective; Leica). Bright field images were acquired by detecting transmitted light (488 or 552 nm). For live-imaging, Xenopus gastrula embryos were embedded with 1.5% LMP agarose (#16520-050; Invitrogen) gel in 1/10× Steinberg’s solution on 35 mm glass-based dishes (Iwaki) or mounted in a house-made imaging chamber. For confocal imaging of immunostaining, stained embryos were mounted in shallow wells on 2% agarose plate, flattened with a coverslip. Images were cropped and/or processed with Photoshop CS4 (Adobe) or ImageJ (NIH). Fluorescent intensity was measured using Image J (NIH) or Zen (Zeiss).
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7

Confocal Imaging Protocol: LSM 5 Pascal

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Confocal images were generated on an LSM 5 Pascal system (Zeiss, Thornwood, NY, USA) equipped with 40X 1.3 NA and 63X 1.4 NA objectives.
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8

Live/Dead Cell Viability Assay

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Cell viability (n=2) was qualitatively assessed on day 1 and 28 by live/dead assay based on Calcein AM, which stains the cytosol of live cells, and ethidium homodimer, which enters the nucleus of compromised cells and stains DNA. Hydrogel constructs were incubated in osteogenic media with 4 μM Calcein AM for 10 minutes, after which ethidium homodimer was incorporated at 2 μM and hydrogels were incubated for another 10 minutes. Hydrogels were immediately imaged using confocal microscopy (Zeiss LSM 5 Pascal system using a Zeiss Axiovert microscope) with either a 10x or 40x objective. Cell shape (n=2) was quantified from the live/dead confocal microscopy images using NIH Image J and the particle analyzer measurement for circularity. A minimum threshold was set for area to remove cells that were out of plane in the image. Aggregates of cells were not counted.
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9

Time-lapse Imaging of GFP-DMP1 Hydrogels

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GFP-expressing DMP-1 was monitored over culture time up to 30 days by fluorescence microscopy (EVOS FL Imaging System; Life Technologies) and image acquisition using a camera (Sony ICX445 monochrome CCD camera) in the 2D cultures. At day 28, intact hydrogels were imaged by confocal microscopy (Zeiss LSM 5 Pascal system using a Zeiss Axiovert microscope). In the 2D culture experiment, the corresponding bright field images were also acquired.
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10

Immunocytochemical Analysis of HSV-1 Infection

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HFFs were seeded in 4-well chamber slides to a confluence of approximately 70%. They were mock-infected or infected with HSV-1 at an MOI of 3. After 1 h, the inoculum was replaced by medium with 0.1% DMSO or 10 µM NFV, and the cultures were returned to the incubator. Sixteen hours after infection, the cells were fixed in 4% paraformaldehyde in phosphate-buffered saline. Cells were then permeabilized with 0.2% Tween-20. Endogenous peroxidase activity was inhibited with 3% H2O2. The cells were then incubated with 10% nonfat dry milk containing 1% normal goat serum (blotto/NGS; Jackson) to block nonspecific binding. Primary antibody binding was revealed with anti-mouse IgG-HRP (Jackson) followed by a 10-minute TSA amplification with TSA-594 (Life Technologies). The nuclei were stained with TO-PRO 3. Slides were mounted after addition of SlowFade (Life Technologies) and analyzed by confocal microscopy. Confocal images were generated on an LSM 5 Pascal system (Zeiss).
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