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25 protocols using ds l2

1

Quantitative Analysis of Lung Histopathology

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Murine lungs were fixed with 10% paraformaldehyde and then embedded in paraffin for sectioning, according to standard methods. In order to correlate the presence of histologic lesions with acid-fast bacilli (AFB), replicas 3 μm sections were cut and stained with both Haematoxyline and Eosin (HE) and Ziehl–Neelsen (ZN), following standard techniques. The lesions morphology and distribution were evaluated by light microscopy. At least 6 lung sections for all mice of the 5 groups were analyzed in different points (24 lung sections per experimental group in total). For each section the number of ZN positive cells, the total surface area and the area with lesions were measured at 400x magnification and averages calculated for each section and group. Slides were imaged using Nikon Eclipse 80i microscope and digital computer images were recorded with a Nikon DS-L2 camera control unit and the Nikon dedicated software 3422.1001.1798.080117. Cellular automatic count and histological measurements were carried out using the dedicated software Axiovision ver. 4.4 (Zeiss) by two independent researchers on two independent photo series.
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2

Spleen Histopathology of Euthanized Pigeons

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Following the euthanasia of pigeons, tissue samples from the spleen were collected. The extracted tissue samples were fixed in 10% phosphate buffer formalin solution and embedded in paraffin. For histopathological examination, hematoxylin-eosin was used to stain 5 µm thick tissue samples. The samples were examined under a light microscope, and images were obtained using a Nikon DS-L2 camera unit connected to a Nikon Eclipse E-200 microscope.
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3

Colony Formation Assay of Transfected Cells

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U251- and U343-transfected cells (siRNA control and SERBP1) were harvested using trypsin and re-plated in 6-well plates (5000 cells/well). Cells were kept in culture for 10–14 days until colonies were clearly visible. Colonies were fixed with 4% paraformaldehyde solution and visualized by staining with 1% crystal violet. Microscopic images were taken with a Nikon Eclipse TS100 inverted microscope equipped with a DS-L2 camera control unit (Nikon Instruments, Melville, NY) at × 20 magnification. Crystal violet was dissolved from stained plates and optical density was measured with a microplate reader at 570 nm. All experiments were performed with technical triplicates.
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4

Measurement of Wound Epithelial Regeneration

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The H&E-stained slides were also used for the measurement of RE. The wound edge and RE tip judgment were conducted in images at x400 magnification, which were captured using a digital camera (Nikon DS-L2). The lengths of the curved lines from both wound edges to the RE tips and the wound gap between the RE tips were also measured. The %RE of the wound was calculated using the following equation: %RE=distance covered by epithelium/distance between wound edges) x100 (5 (link),16 (link)).
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5

Senescence Induction in DIPG Cells

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Adherently growing DIPG 4 cells were plated at a density of 100,000 cells per well in a 6-well plate and allowed ~24 h in which to develop adhesion before subjecting them to experimental conditions. Cells were treated for two days with 50 nM, 500 nM or 5 µM of AZD2014 or everolimus, along with DMSO control. After two days of incubation, the cells were placed into normal growth media for five days. Staining for β-galactosidase was performed using a Senescence β-galactosidase Staining kit (Cell Signaling Technology, Inc.) according to the manufacturer's instructions. Cells were washed with 2 ml of PBS, followed by a 15-min incubation using 1X fixative. Cells were again washed twice with PBS and then incubated with 1 ml of β-galactosidase staining solution. The cells were incubated overnight in a dry 37°C incubator without CO2. Senescencent cells were imaged via brightfield microscopy (Nikon DS-L2).
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6

Immunohistochemical Staining of Leptin Receptor

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Paraffin-embedded specimens were deparaffinized in ethanol and xylene and incubated with 3% H2O2 for 5 min to quench endogenous peroxidase activity. After microwave treatment (for 20 min with Novocastra Epitope Retrieval Solutions pH 6, Novocastra; Leica Microsystems, Wetzlar, Germany), the sections were incubated in blocking solution (Block Ace; DS Pharma Biomedical, Osaka, Japan) for 30 min before incubation with a primary antibody. Then the sections were incubated with mouse anti-leptin receptor for 15 min, washed, and incubated with a horseradish peroxidase-conjugated anti-mouse secondary antibody (EnVision/HRP; Dako, Glostrup, Denmark) for 8 min. A further washing in PBS was followed by developing in DAB (Dako) as a chromogen for signal visualization. Anti-mouse IgG (Leica, Wetzlar, Germany) was used for a negative control. The slides were counterstained with Mayer's haematoxylin and coverslipped using mounting medium. Consecutive sections of human lymphatic ducts were stained with hematoxylin and eosin (Sakura Finetek Japan, Tokyo, Japan) according to the manufacturer’s instructions. Images were acquired using a TS100 confocal microscope and DS-L2 (Nikon, Tokyo, Japan).
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7

Histological Analysis of Tissue Sections

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Fixed tissue sections were embedded longitudinally in paraffin wax and 4‐μm sections were cut longitudinally and mounted on polylysine slides. Proximal, middle and distal sections of each tissue were stained with hematoxylin and eosin (H&E), Alcian blue‐periodic acid Schiff (AB‐PAS) stain was used for detection of glycosaminoglycans (GAGs) (Bancroft & Gamble, 2008) and Miller's stain for elastic fibres (Miller, 1971). All histological sections were visualised using a Nikon eclipse 80i microscope and pictures were acquired with a Nikon DS‐L2 standalone control unit.
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8

Tracking Lifespan Movement Dynamics

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C. elegans movement was recorded for 45 seconds at different days of adulthood using a Nikon DS-L2 / DS-Fi1 camera and controller setup, attached to both a computer and a standard bright field microscope. Five plates of worms, with 10 worms per plate were measured in each condition. Fly movement was recorded by placing flies in a sealed chamber, tapping the chamber, and recording their movement as they naturally climb towards the top. For the tapping test, flies at the corresponding ages were recorded using a standard SLR camera with a Leica macro objective. The experiment was performed 3 times for each cohort with one minute recordings each, with a “tap” sending the flies to the bottom of the chamber every 10 seconds.
Using these video recordings, the movement traces of both worms and flies during all recording periods were calculated by following the organism centroids using a modified version of the Parallel Worm Tracker for MATLAB (Ramot et al., 2008 (link)). The distance covered during the recording periods was then averaged per plate and per condition.
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9

Immunohistochemical Analysis of Human and Mouse Tissues

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The human and mouse tissues were fixed in buffered formalin and the inclusion in paraffin was done according to the standard technical procedures. Histochemical and immunohistochemical studies were performed on formalin-fixed paraffin-embedded tissue sections. Sections were 2 microns (human ganglia) or 3-6 microns (mouse tissues) thick (for H&E) and 4 microns thick (for the immunohistochemical study). The following markers were used for immunohistochemistry– aminoethylcarbazole (AEC) and 3,3'-diaminobenzidine (DAB), accordingly to the usual technical procedure for the marker. For the immunohistochemical studies sections underwent antigenic recovery prior to incubation with primary antibodies – anti-CD68 (Dako; clone PG-M1; dilution 1/150) anti-human Slc6a2 (Mab Techonolgies, clone 3-6C1 sc H10; dilution 1/1000), anti-MAOa (Abcam, clone GR155892-5, dilution 1/50), anti-UCP1 (Abcam, dilution 1/500). Human tissues were analyzed under an optical microscope (Nikon Eclipse 50i) and iconography microscopic images captured using a coupled digital camera (DS Camera Control Unit DS-L2). Mouse tissues were analyzed using Leica DM LB2 microscope and images were captured with Leica DFC 250 camera.
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10

Light-Induced Stomatal Opening Protocol

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Epidermal strips were peeled from abaxial young, fully expanded leaves. Epidermal strips were floated in petri dishes (diameter, 9 cm) containing opening medium A [10 mM MES–KOH (pH 6.15), 50 mM KCl, 0.1 mM CaCl2] for Arabidopsis, or opening medium B [10 mM MES–KOH (pH 6.15), 50 mM KCl] for fava bean and were kept for 2 h at 23 °C under light (50 μmol m−2 s−1). The strips were then transferred to opening medium containing sodium glutamate, glycine, and/or the pharmacological reagents (AP-5, EGTA, BAPTA-AM) and kept for 3 h at 23 °C under light irradiation. For light-induced stomatal opening, Glu was applied to the epidermal strips after the 2 h of dark period and subsequently exposed to light for 3 h. Following treatment, the stomata were photographed under a microscope (Eclipse E600; Nikon Corp. Tokyo, Japan) using a digital camera (Ds-L2, Nikon Corp.). Inner widths of stomatal pores were measured using a digital micro-analyzer (Japan Polaroid Digital Products, Tokyo). At least four strips containing 20 stomata were measured for each treatment. Experiments were repeated at least three times, and Student’s t test was used to assess significant differences.
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