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25 protocols using lasersharp 2000

1

Monitoring Autophagy in H. pylori Infection

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AGS cells were transfected with GFP-MAP1LC3B or RFP-MAP1LC3B plasmid for 24 h, following H. pylori infection for another 24 h. Radiance 2000 laser scanning confocal microscope detected the images of the cells, and image analysis with LaserSharp 2000 software (Bio-Rad, San Francisco, CA) as our previous study (Tang et al., 2016 (link)). According to methods for monitoring GFP-LC3 and mRFP-GFP-LC3 puncta formation assays (Klionsky et al., 2007 (link); Mizushima et al., 2010 (link)), the average number of MAP1LC3B puncta per cell in GFP-MAP1LC3B or RFP-MAP1LC3B-positive cells (200 cells per sample) was determined (Pattingre et al., 2005 (link)).
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2

Visualizing Tight Junctions and F-Actin

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Cells grown on filters were washed three times with PBS, and incubated in 2% BSA in PBS for 30 min. on ice. Cells were incubated with FITC-conjugated anti-ZO-1 or anti-occludin antibodies diluted 1:20 in 0.2% BSA in PBS for 1 hr on ice. After two washes in PBS, cells were fixed in 3% PFA, 2% sucrose for 10 min. In separate experiments, cells were stained with 20 nM phalloidin-TRITC to visualize F-actin. After three washes in PBS, filters were excised and placed side up on a glass slide, and overlaid with a drop of Mowiol (Calbiochem, San Diego, CA, USA) followed by a coverslip. Cells were analysed by using a Nikon TE2000 microscope coupled to a Radiance 2100 confocal dual-laser scanning microscopy system (Bio-Rad, Segrate, Italy). Specimens were viewed through a 60× oil immersion objective, with a 2.5 zooming in some analyses. Digital images were processed by using the program Laser Sharp 2000 (Bio-Rad). XY planes are shown at 5–6 slices from the apical level.
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3

Multimodal Fluorescence Microscopy Imaging

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Images were captured on a fluorescence microscope (Nikon E90i or Nikon E1000) equipped with a Nikon Intensilight C-HGFI source or an X-Cite 120 illuminator (EXFO), respectively, using high numerical aperture optics and a cooled CCD camera (ANDOR or Q-Imaging, respectively) running NIS Elements software (Nikon) or Velocity software (Improvision, Lexington, MA).
Five-channel confocal imaging was performed at the Harvard Center for Biological Imaging on a Zeiss 710 inverted confocal microscope equipped for spectral unmixing and for acquisition of confocal montages of entire tissue sections, running ZEN software (Zeiss). Other confocal images were obtained using a BioRad Radiance 2100 Rainbow laser-scanning confocal system based on a Nikon E800 microscope with LaserSharp 2000 imaging software (Bio-Rad Laboratories). Some images were subsequently processed for 3D reconstruction in Imaris (Bitplane). For an optimal visual reproduction of the data, images were adjusted for contrast, brightness, color balance, and size in Photoshop CS3 (Adobe, San Jose, CA), and assembled in Power Point for Mac 2011 (Microsoft Corporation, Redmond, WA), and in Illustrator CS3 (Adobe, San Jose, CA).
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4

Confocal Microscopy of Fluorescently Labeled Proteins

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Images of single optical sections were collected on a Bio-Rad Radiance 2100 laser-scanning confocal microscope (Bio-Rad, Hercules, CA) mounted on a Nikon TE2000-U microscope (Nikon, Melville, NY) using a 100× (1.4 numerical aperture) Plan-Apochromat oil-objective lens at room temperature (zoom = 3). Bio-Rad LaserSharp 2000 software was used during image collection. Images were processed with Photoshop (Adobe, San Jose, CA), and image figures were constructed in Adobe Illustrator. Supplemental Figure S5 shows diagrams of sarcomeres indicating the expected locations of the various fluorescently labeled proteins in Figures 4–8.
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5

Multicolor Immunostaining of Isolated Islets

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Immunostaining was conducted on isolated islets, fixed in 4% paraformaldehyde before being permeabilised using 0.1% Triton X-100 (Sigma). After blocking with 5% goat serum, islets were incubated overnight (4°C) with primary antibodies before incubation with secondary antibodies. Fluorescent staining was visualised using a laser-scanning confocal microscopy (BioRad) controlled by LaserSharp2000 (BioRad).
Antibodies used in this study were: rabbit FITC 495-conjugated anti-GFP (1:250; DS-PB-00926; InsightBio, Wembley, United Kingdom), mouse anti-glucagon (1:1000; G2654; Sigma), guinea-pig anti-insulin (1:400; A0564; Dako, Santa Clara, California, United States), goat anti-somatostatin (1:100; sc-7819; Santa Cruz Biotechnology, Dallas, Texas, United States); Alexa Fluor 633 goat anti-mouse IgG (1:500; A-21052; ThermoFisher); Alexa Fluor 594 goat anti-guinea pig IgG (1:500; A-11076; ThermoFisher); and Alexa Fluor 546 donkey anti-goat IgG (1:100; A-11056; ThermoFisher).
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6

Confocal Fluorescence Microscopy Imaging

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Confocal fluorescence microscopy images were acquired on a Bio-Rad (Zeiss) Radiance 2100 Rainbow laser scanning confocal microscope with LaserSharp 2000 software (Bio-Rad, Hercules, CA), or an Olympus FV1000 laser scanning confocal microscope with Fluoview Viewer software (Olympus, Center Valley, PA), both equipped with 60× oil immersion objectives. Images were processed with Fiji software.67 (link)
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7

Fluorescence Imaging of Cellular Iron Transport

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TOPRO-3, ProLong Antifade kit, calcein, Alexa 546-conjugated dextran (M.W. 10,000), Alexa 594-conjugated-Tf, and non-essential amino acid solution (10 mM) were from Invitrogen (Carlsbad, CA). Fetal bovine serum (FBS) was from Atlanta Biologicals (Lawrenceville, GA). DMEM was from Mediatech (Herndon, VA) or Sigma Aldrich (St. Louis, MO). Paraformaldehyde was from Fisher Scientific (Pittsburgh, PA). HEPES, Antibiotics, Chelex resin, ascorbate, ferric chloride, hemin and 2,2'-dipyridyl (DPD) were from Sigma Aldrich. All other chemicals of analytical grade were from Sigma Aldrich. Anti-DMT1 antibody (iron-responsive element, IRE) was described previously.(14 (link)) The Caco-2 cell line (HTB-37) was from American Type Culture Collection (Rockville, MD). The Millicell electrical resistance system and Millicell 6-well cell culture inserts with 0.4 µm pore size membranes were from Millipore (Bedford, MA). Transwell clear inserts for 24-well plates were from Corning (Lowell, MA). The collagen solution (rat tail Type I) was from Boehringer-Manheim (Manheim, Germany) and Becton Dickinson (San Diego, CA). DRAQ5 was from AXXOLA (San Diego, CA). The Bio-Rad Radiance 2000 Laser scanning microscope and Lasersharp 2000 were from Bio-Rad (Hercules, CA). The LSM 510 META Confocal microscope was from Carl-Zeiss (Thornwood, NY). Glass-bottom dishes were from Mat-Tek (Ashland, MA).
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8

Immunostaining of Drosophila Embryos and Imaginal Discs

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Embryos were dechorionated and fixed for 20 minutes in 10% formaldehyde overlayed with n-heptane at room temperature. Devitellinisation was achieved by adding chilled methanol and shaking vigorously. Embryos were washed twice with methanol before rehydrating in a step-wise manner with PBS and blocked with 4% normal goat serum. Imaginal discs from third instar larvae were fixed in 4% formaldehyde for 20 minutes before blocking.
Immunostaining of embryos was performed over night with anti-H B (directed against C-terminal fragment of H) and of wing discs with anti-H A (directed against central H fragment)22 (link), with anti-Phospho-Histone H3 (Ser28) (#9713, Cell Signaling Technology, Massachusetts, USA), and anti-GFP (sc-8334, Santa Cruz Biotechnology, Inc., Texas, USA). Secondary antibodies fused to FITC, Cy3 and Cy5 respectively were used (Jackson ImmunoResearch, Pennsylvania, USA). Embryos and imaginal tissue were mounted in VectaShield (Vector Laboratories, California, USA) before being imaged on a Bio-Rad MRC1024 system running LaserSharp 2000 imaging software (Bio-Rad Laboratories, California, USA) coupled to a Zeiss Axioskop (Carl Zeiss AG, Oberkochen, Germany). Figures were assembled using Corel Draw and Photo Paint software.
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9

Multicolor Imaging of Muscle Structure

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Antibody-labeled muscles were pinned down on Sylgard-bottomed petri dishes containing PBS and placed on the stage of an upright microscope (BX51WI, Olympus, Japan) equipped with a tunable Chameleon Ti/Sapphire laser (Coherent) and a Radiance 2000 Scanning Head (Bio-Rad, UK). Images were acquired with a ×20, 0.95 NA (Olympus XLUMPLANFL) water-immersion objective. Muscles labeled with Alexa 488 alone or Alexa 488 and Texas Red were excited with a laser wavelength of 840 nm. Images were simultaneously acquired using the following filter combinations (band-pass/dichroic/band-pass, in nm): second harmonic generation (SHG) and Alexa 488 emission (410-490//495//500-530), Alexa 488 and Texas Red emission (500-530//550//620-660), and SHG and Texas Red emission (402-446//495//615-645). Images were analyzed using commercial (LaserSharp 2000, Bio-Rad, UK) and/or public-domain image analysis software package (ImageJ).
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10

Multimodal Fluorescence Microscopy Imaging

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Images were captured on a fluorescence microscope (Nikon E90i or Nikon E1000) equipped with a Nikon Intensilight C-HGFI source or an X-Cite 120 illuminator (EXFO), respectively, using high numerical aperture optics and a cooled CCD camera (ANDOR or Q-Imaging, respectively) running NIS Elements software (Nikon) or Velocity software (Improvision, Lexington, MA).
Five-channel confocal imaging was performed at the Harvard Center for Biological Imaging on a Zeiss 710 inverted confocal microscope equipped for spectral unmixing and for acquisition of confocal montages of entire tissue sections, running ZEN software (Zeiss). Other confocal images were obtained using a BioRad Radiance 2100 Rainbow laser-scanning confocal system based on a Nikon E800 microscope with LaserSharp 2000 imaging software (Bio-Rad Laboratories). Some images were subsequently processed for 3D reconstruction in Imaris (Bitplane). For an optimal visual reproduction of the data, images were adjusted for contrast, brightness, color balance, and size in Photoshop CS3 (Adobe, San Jose, CA), and assembled in Power Point for Mac 2011 (Microsoft Corporation, Redmond, WA), and in Illustrator CS3 (Adobe, San Jose, CA).
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