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9 protocols using digital sight ds l3

1

Histological Processing and Imaging of Larvae

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Larvae were treated in parallel with the GFR assay, then fixed overnight at 4°C in 4% paraformaldehyde (PFA) in PBS. Larvae were then pre-embedded in 1.5% Ultrapure low-melting point agarose (Sigma Aldrich), to allow for alignment of the larvae for easy coronal cross-sectioning. Pre-embedded larvae were fixed in 10% neutral buffered formalin for between 1 and 3 days, then embedded in Surgipath Paraplast (LEICA) with the Tissue Tek Embedding Station, Model TEC EMA-1 (Sakura Finetek USA Inc). Larvae were then sectioned to 4 μm with a Nikon Eclipse Ni manual microtome with Nikon Plan Fluor objectives (Nikon), and stained with H and E with a Tissue-Tek Prisma automated slide stainer. Slides were preserved with the Tissue-Tek Glas g2 automated cover-slipper (Sakura Finetek USA Inc). Slides were examined and imaged with the Nikon Digital Sight DS-L3 (Nikon).
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2

In Vitro Angiogenesis Assay

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Matrigel® surfaces were prepared by the addition of 50 μl of neat Matrigel® (Corning, U.S.A.) into each well of a 96-well plate and made to solidify at 37 °C for 1 hour. 22.5 × 103 of live ECs were seeded into each well. About 200 μl of EGM-2 medium was added into each well and cells were left to form tubes at 37 °C for 2–3 h. Brightfield images were taken using the Nikon Digital Sight DS-L3 camera (Nikon, Japan). Quantitative analysis of tube characteristics was performed by online software WimTube (Wimasis Image Analysis, Córdoba, Spain, http://www.wimasis.com).
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3

Breast Cancer Cell Culture Protocols

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Experimental cultures of breast (MDA-MB-231,
MCF-7, and MCF-10A) were obtained from the American Type Culture Collection
(ATCC) and cultured in tissue culture dishes (Corning, NY) at 37 °C
in 5% CO2 atmosphere. Phosphate-buffered saline was obtained
from Gibco. Experiments were performed on cells within 20 passages.
The breast cancer cells MDA-MB-231 and MCF-7 cells were maintained
in Dulbecco’s modified Eagle’s medium (DMEM; Biowest
L0106, France) supplemented with 10% FBS (Gibco, NY), 1% l-glutamine (PAA Laboratories, Austria), and 1% penicillin/streptomycin
(HyClone, UT). The MCF-10A cells were maintained in a DMEM-F12 medium
(Biowest L0093, France) supplemented with 7.5% FBS (Gibco, NY), epidermal
growth factor (Invitrogen), insulin (Sigma-Aldrich), hydrocortisone
(Sigma-Aldrich) and 0.4% gentamicin (Gibco, NY), and 1% penicillin/streptomycin
(HyClone, UT). Bright-field images of the adhered cells were taken
using a Nikon Eclipse TS100 inverted microscope, with a 10× objective
and Nikon digital Sight DS-L3 camera.
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4

In vivo Smooth Muscle Cell Migration Assay

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In vivo SMC migration was measured as described by Bendeck et al with minor modifications [21 (link)]. Briefly, 5 days after GI, the femoral arteries were dissected out and fixed in 4% PFA overnight at 4ºC. The middle of the injured femoral arteries was cut and fixed again in cold acetone for 10 min. The artery was then opened longitudinally and pinned down onto an agar plate with the luminal surface facing up. The arteries were rinsed with PBS and treated with 3% H2O2 for 15 min to block the endogenous peroxidase activity. After blocking in 5% goat serum in PBS for 30 min, the arteries were incubated with anti-rabbit SMCα-actin antibody (1:300) overnight at 4ºC, followed by incubation with biotinylated goat anti-rabbit IgG for 30 min. After rinsing with PBS for 5 min, peroxidase labelling was carried out using an ABC kit, and coveslips were placed. The luminal surface of the artery was examined under Nikon Eclipse 50i microscope with 40X/0.25 magnification and images were captured with Nikon Digital Sight DS-L3 color camera and the SMCα-actin-positive cells were counted.
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5

Quantification of Adipocyte Differentiation by Oil-Red-O Staining

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Cells were stained with Oil-Red-O (Sigma–Aldrich) as described previously [30 (link)]. 3T3-L1 cells were plated on a 24-well plate and induced to differentiate using the DMI method described earlier. The cells were rinsed with phosphate-buffered saline (PBS), fixed with 4% paraformaldehyde (PFA; Wako) for 14 min, and then stained with 3 mg/mL Oil-Red-O (in 60% isopropanol) for 10 min at room temperature. After staining, cells were washed once with 60% aqueous isopropanol and twice with PBS. After washing, the cells were observed using an ECLIPSE Ti-U inverted microscope (Nikon, Tokyo, Japan). Cell images were captured with a CCD camera (digital sight DS-L3, Nikon). Additionally, after the dye was extracted for 10 min with isopropanol, the absorbance was measured at 490 nm using a DTX 880 Multimode Detector (Beckman Coulter, Brea, CA, USA). All experiments were performed at least three times.
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6

Immunohistochemical Analysis of PDH

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The intestinal tissues were fixed in buffered 10% formalin and then processed for standard (5 μm) paraffin sections. Then, sections were incubated for 30 min in 3% H2O2, and nonspecific binding was blocked with normal serum. The PDH was incubated with primary antibodies against PDH overnight at 4 °C. The same concentration of normal serum served as a negative control. The bound antibodies were eventually detected with the biotin-streptavidin peroxidase system. Then, samples were incubated with 3,3′-diaminobenzidine (DAB) peroxidase substrate solution, and the slides was counterstained with haematoxylin. The immunostained images were captured using a digital camera microscope (Nikon Digital Sight DS-L3, Tokyo, Japan).
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7

Bacterial Density and Live/Dead Assay

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A densitometer DEN-1 from the company Grant-bio was used to determine the McFarland value. A digital control heated water bath with in-built shaking tray from Thermoline Scientific was used to incubate the bacteria. The Foodsafer Vacuum sealer was used to prepare the sample for exclusion of oxygen. A Nikon digital sight DS-L3 at a 490 nm excitation wavelength and live-dead optical filters were used to take the fluorescence microscopy images. To measure the absorbance at 490 nm an ELx800 absorbance microplate reader from Bio-Tek with the corresponding software Gen5 was used. To measure the absorbance at 540 nm a Synergy HT multi-detection microplate reader from Bio-Tek with the appropriate software KC4 was used.
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8

Live Cell Imaging of Cultured Cells

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Cells were seeded in 12-well plates at a concentration of 1 × 105 cells/mL/well. After a 24 h-exposure, culture media were removed gently and replaced with the Live Cell Imaging Solution (Invitrogen, Burlington, Canada). Treated cells were observed with a Nikon TE300 microscope connected to a Nikon Digital Sight DS-L3 camera.
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9

Micromorphology of Fungal Specimens

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The studied specimens were deposited at the herbarium of the Institute of Microbiology, Beijing Forestry University (BJFC), with color terms following those outlined by Petersen (1996 ). Sections mounted in 5% KOH and 2% phloxine B (C20H2Br4Cl4Na2O5) were studied at a magnification of up to 1,000 × using a Nikon Eclipse 80i microscope and phase contrast illumination. A Nikon Digital Sight DS-L3 camera was used to photograph microscopic structures. We also used other reagents, including Cotton Blue and Melzer's reagent to observe micromorphology following Wu et al. (2022b (link)). To show the variation in spore sizes, 5% of measurements were excluded from each end of the range and shown in parentheses. At least thirty basidiospores from each specimen were measured. Stalks were excluded from basidia measurements, and the hilar appendage was excluded from basidiospore measurements. The following abbreviations were used: KOH, potassium hydroxide (5%); L, mean length (arithmetic average of all basidiospores length); W, mean width (arithmetic average of all basidiospores width); Q, L/W ratio for each specimen studied; n (a/b), number of basidiospores (a) measured from a given number of specimens (b).
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