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19 protocols using las af 6000

1

Quantifying Germ Line DNA Damage

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Images were collected using a Leica DM6 fluorescence microscope and Hamamatsu camera under the control of Leica LAS AF 6000 software. Images were deconvolved and analyzed using the Leica LAS AF 6000 software and Image J program. Quantitative analysis of RAD-51 foci and DAPI-stained bodies along the germ line were performed on z series. Optical sections were collected at 0.18 µm and 0.50 µm increments respectively. The t-Student test for independent samples was used for the analysis of apoptosis levels and RAD-51 foci. At least five gonads were quantified for each genotype or condition.
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2

Quantitative Analysis of RAD-51 Foci in C. elegans Germline

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Collection of images was performed using a Leica DM6 fluorescence microscope, Hamamatsu camera under the control of Leica LAS AF 6000 software. Images were processed using Leica LAS AF 6000 software and Image J/Photoshop programs. Quantitative analysis of RAD-51 foci and DAPI-stained bodies along the germline were performed on z series. Optical sections were collected at 0.18 µm and 0.50 µm increments respectively.
The quantitative analysis of RAD-51 foci was performed by dividing the germline into seven 36 × 36 μm zones (mitotic tip, mitotic zone, transition zone, early pachytene, middle pachytene, late pachytene diplotene stage), beginning from the distal tip18 (link).
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3

Quantitative GFAP Immunofluorescence Analysis

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Brain sections taken from the lesion tip area were fixed for 20 min in ice-cold acetone at 4 °C. After three washes in PBS, brain sections were incubated in blocking solution (5% normal goat serum (NGS)-PBS in 0.3% Triton X-100, 1 h at room temperature). The sections were then treated with anti-GFAP primary antibody (1:100, 1 h at room temperature), incubated with FITC-anti-mouse secondary antibody (1:100, 1 h at room temperature), rinsed in PBS and counterstained with DAPI. Samples were mounted and examined using a Leica (LEITZ DMRB) light microscope equipped with epifluorescence. Z-stack images (no. steps: ~20; Z-step size: ~1 μm; Z-volume: ~19) were acquired using the Leica Application Suite Advanced Fluorescence 1.8.0 build 1346 (AF6000_DFC) and analysed using Leica microsystem LAS AF-6000 software. GFAP was semi-quantified as immunoreactivity area (mm2) normalized to the total number of cells and expressed as a percentage of controls (animals injected with endotoxin-free saline).
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4

Anatomical Delineation of the Suprachiasmatic Nucleus

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At the end of experiment, mice were intracardially perfused with saline followed by 4% paraformaldehyde. Brains were removed, postfixed overnight at 4°C and cryoprotected using 30% sucrose in phopshate‐buffered saline (PBS). Brains were cut (40 μm) on a freezing microtome at a coronal plane. Immunofluorescence labelling for arginine vasopressin (AVP) was performed to delineate SCN anatomical boundaries. Briefly, following washes in 0.1 m PBS and 0.1% Triton X‐100 in PBS, sections were blocked for 1 h in 5% normal donkey serum. Then, they were incubated with primary antibody (dilution 1:5000; AVP Rabbit; AB1565; Millipore, Burlington, MA, USA) for 2 days at 4°C. After washing, sections were incubated with Alexa Fluor 488 Donkey anti‐Rabbit IgG (dilution 1:800; A‐21 206; Invitrogen, Thermo Fisher Scientific) overnight at 4°C. Finally, sections were mounted onto gelatine coated slides and cover‐slipped using ProLong Gold Antifade Mountant (Molecular Probes, Invitrogen; Thermo Fisher Scientific). Photos were taken using a DFC365 FX camera (Leica, Wetzlar, Germany) connected to a DM2500 microscope (Leica) using LAS AF6000 software (Leica). Recording sites were estimated based on stereotaxic notes, CM‐DiI marks and AVP staining in accordance with atlas of Paxinos & Franklin (2001).
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5

Quantifying Ocular Neural Crest Cells

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Whole embryos were analyzed using a M205FA combi-scope (Leica Microsystems CMS GmbH, Germany, Wetzler, Germany). Images were obtained using brightfield DFC290 (Leica) and fluorescent ORCA-ER (Hamamatsu, Hamamatsu City, Japan) cameras. The sections were imaged using a DM6000B upright microscope (Leica) equipped with a DFC500 camera (Leica). The images were processed and analyzed using Adobe Photoshop (San Jose, CA, USA), LAS X (Leica) and/or LAS AF6000 software (Leica). The images shown are representative of all experiments. For quantifying the number of foxd3-positive periocular mesenchymal and ocular neural crest cells, z-stacks that ranged from the lateral edge of the cornea to 100 μm medial to the medial edge of the eye were obtained. The z-stacks were deconvolved and maximally projected in order to obtain a single image. The number of foxd3-positive cells was manually counted. Eye size was measured from the dorsal to ventral border in a lateral view and from the anterior to posterior border in a ventral view. Measurements were obtained from bilateral eyes of 4–6 embryos at each time point for each group. The data were statistically analyzed using ANOVA with Tukey’s post-hoc analysis, and p<0.05 was considered statistically significant.
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6

Quantitative Nuclear Analysis of Adult Worms

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Synchronized adult worms were transferred to glass slides in 15 μl of M9 solution. Samples were permeabilized, fixed and washed with absolute ethanol, then 15 μl of a 2 ng/μl solution of 4′, 6′-diamidino-2-phenylindole hydrochloride (DAPI) diluted in M9 was added. Quantitative analysis was performed on z series of images acquired using a Leica DM6000 fluorescence microscope, Leica DC 350 FX camera under the control of Leica LAS AF 6000 software. Optical sections were collected at 0.50 μm increments.
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7

Live-Cell Imaging of Axon Dynamics

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Cultured DRGs were imaged at 2 DIV in Hibernate A low-fluorescence medium (Brain Bits) inside a 37°C chamber. For transport assays, neurons were observed at 63x using a DMI6000B epifluorescence microscope with a CTR7000 HS control box run by LAS-AF6000 software (Leica) and a C10600 Orca-R2 camera (Hamamatsu); images were acquired at 3 seconds per frame for 3 minutes. For axon tip biogenesis and distal axon exit assays, GFP-LC3 neurons were observed at 100x with the 488-nm and 562-nm laser on an Ultraview Vox spinning-disk confocal system (PerkinElmer) on an inverted Ti microscope (Nikon); images were acquired at 1–2 seconds per frame for 5–10 minutes. Frame rates were optimized for each experimental approach (epifluorescence versus confocal) to capture events with high time resolution while minimizing photobleaching; within an experiment all conditions were imaged with the same paradigm.
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8

In Vitro and In Vivo Analysis of H5-Derived Fusion Proteins

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Whole overnight inducted E. coli BL21(DE3) cells were collected and the expression of the H5-derived fusion proteins was analysed by an in vitro assay with the fluorescent SNAP-Vista Green™ substrate (New England Biolabs, Ipswich, MA; hereinafter BG-FL), as previously described58 (link),64 . The in vivo imaging was carried out as described by Merlo et al.58 (link). Briefly, bacterial cells expressing the H5-SspCA onto cell surface were washed twice in PBS 1× and resuspended in 50.0 μl of the same buffer supplemented with 5.0 μM of the BG-FL. After incubation at 37.0 °C for 30.0 min, cells were washed twice, resuspended, and again incubated for 30.0 min at 37.0 °C, to allow the external diffusion of the unreacted substrate. Images were collected using a DM6 fluorescence microscope and Hamamatsu camera under the control of Leica LAS AF 6000 software; excitation and emission wavelengths used suitably for AlexaFluor488 dye were λex = 490 nm; λem = 525 nm, respectively.
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9

Live Imaging of LRRK2 Dynamics

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Live cell imaging of HEK293T/17 cells transfected with GFP-tagged wild-type LRRK2 was performed on cells grown on glass-bottom dishes (IBIDI) in full medium without phenol red. Live images were acquired 48 h after transfection on a Leica TCS-SP5 confocal microscope using a 63× 1.4 NA oil UV objective (HCX PLAPO CS). LRRK2-IN1 (1 μM final concentration) was added at time 0, and images collected using single excitation 488 nm Argon Laser line and a 495–575 nm emission band pass. The 488 nm Argon Laser line was set at 30%, with pinhole airy at 1. Contrast phase images of single stacks were simultaneously acquired. Fifteen image sections of selected areas were acquired every 45 s with a step size of 0.5 μm. Z-stack maximal intensity projection images were analyzed and processed using Leica Applied Systems (LAS AF6000) image acquisition software.
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10

In vivo E. coli BL21(DE3) Fluorescent Labeling

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For in vivo imaging, E. coli BL21(DE3) cells transformed with pET-22b/INPN-SspCA or pET-ASLtag plasmids were IPTG-inducted, grown overnight at 37.0 °C and finally diluted until OD600nm of 1.0. An amount of cells corresponding to a volume of 1.0 mL of the culture was washed twice in PBS 1× and finally resuspended in 50.0 μL of the same buffer supplemented with 5.0 μM of the BG-FL substrate. After an incubation at 37.0 °C for 30.0 min, cells were washed twice, resuspended and again incubated for 30.0 min at 37.0 °C, to allow the external diffusion of the unreacted substrate. Labelling was first verified by fluorescence gel-imaging on SDS-PAGE and then spotted on poly-L-lysine coated slides for microscopy analysis.
Images were collected using a DM6 fluorescence microscope and Hamamatsu camera under the control of Leica LAS AF 6000 software; excitation and emission wavelengths used suitably for AlexaFluor488 dye were λex = 490 nm; λem = 525 nm, respectively.
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