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382 protocols using eclipse ni

1

Histological Analysis of Leech Tissue

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Leech tissue samples, dissected from differently treated leech body walls, were embedded in Polyfreeze tissue freezing medium (OCT, Polysciences, Eppelheim, Germany) and immediately frozen in liquid nitrogen. Cryosections (7 µm) were obtained with a cryotome (Leica CM1850, Wetzlar, Germany), collected on gelatinous slides and counterstained with crystal violet and basic fuchsin for morphological analysis. All samples were mounted with Cityfluor (Cityfluor Ltd., London, UK) and examined with a Nikon Eclipse Ni (Nikon, Tokyo, Japan) light microscope. Data were recorded with a Nikon digital sight DS-SM (Nikon).
For ACP assay, cryosections were rehydrated with PBS and incubated with sodium acetate-acetic acid 0.1 M buffer for 5 min, followed by incubation with reaction mixture (sodium acetate-acetic acid 0.1 M buffer, 0.01% naphtol ASBI phosphate, 2% NN-dimethylformamide, 0.06% Fast RedViolet LB and MnCl2 0.5 nM) for 90 min at 37 °C. After several washings in PBS, slides were mounted with PBS/glycerol and observed with a Nikon Eclipse Ni (Nikon) as above.
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2

Root Hair Deformation and Rhizobial Infection Analysis

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For root hair deformation assays, germinated WT (A17) and spd1+/− seedlings were grown on BNM plates for 3 d, and then incubated with NF from S. meliloti 2011 or the rhizobia themselves for 24 to 36 h before analysis. Images were taken using a Nikon Eclipse Ni light microscope with a Nikon DS-Fi2 camera.
For rhizobial infection analysis, M. truncatula seedlings were transferred into a vermiculite and perlite mixture (1:1) and inoculated with S. meliloti 1021 carrying HemA:LacZ 5 to 7 d after germination. The infection and nodulation phenotypes were analyzed at the indicated time points by light microscopy (Eclipse Ni, Nikon) after histochemical root staining using X-gal.
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3

Cultivation of Freshwater Cable Bacterium

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For cultivation of the freshwater cable bacterium Electronema aureum GS (Thorup et al., 2021 (link)) on natural sediment, about 50 mg (wet weight) of an already growing culture was transferred with an inoculation pen to the surface of freshly prepared sediment. In this work, a starter culture of E. aureum was kindly supplied by Lars Peter Nielsen (Center for Electromicrobiology). The provided culture is a stable single strain culture of E. aureum, which, however, still contains other microorganisms than cable bacteria, occurring with E. aureum in its natural environment. This culture was then used to inoculate, respectively, prepared sediment from Lake Gelterswoog. Inoculated sediment was kept in a sterile cultivation box in an incubation cabinet at 22°C. The cultivation box was filled with ambient air. A thin layer of ~5 mm of supernatant over the sediment prevented the samples from drying out. If necessary, more supernatant was added during cultivation. After 2 weeks and always before further use of the cultures, sediment was checked for cable bacteria microscopically (Nikon Eclipse Ni; Nikon).
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4

Construction of GFP-Pcf1 Fusion Protein

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A GFP fusion protein vector, pKD8B-GFP-PCF1, was constructed using a high-throughput gene knockout system as described previously [30 (link)]. Briefly, the fragment of PCF1 coding sequence was amplified from the M. oryzae genome was co-transformed into Saccharomyces cerevisiae strain FY834 with a linearized pKD8B-GFP that was digested by XbaI and SalI [30 (link)]. The plasmids of yeast transformants were extracted using TIANprep yeast plasmid DNA kit (Tiangen Biotech, Beijing, China) and transformed into Escherichia coli strain DH5α. After confirming the correctness of the vector, pKD8B-GFP-PCF1 and pKD9-H2B-mCherry [41 (link)] was co-transformed into the wild-type strain through Agrobacterium tumefaciens-mediated transformation (ATMT) [30 (link)]. Transformants that were expressing both GFP-Pcf1 and H2B-mCherry were screened on CM plates that were supplemented with 200 μg/mL hygromycin and 50 mg/mL G418 sulfate. The colocalization of GFP-Pcf1 and H2B-mCherry and the fluorescence intensity of GFP-Pcf1 in M. oryzae transformants were observed using fluorescence microscopy (Nikon Eclipse Ni) (Nikon, Tokyo, Japan) under the same exposure conditions. The primers for PCF1 amplification are listed in Supplemental Table S1.
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5

Quantifying Spinal Cord Gliosis and Inflammation

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Digital images of spinal cord sections were captured at 10× magnification using a Nikon Eclipse Ni fluorescent and brightfield microscope system (Nikon, Tokyo, Japan). Image analysis software (Image J; National Institutes of Health, Bethesda, MD) was used to quantify IBA1, GFAP and CCR2 immunostaining in a minimum of 4 randomly selected lumbar spinal cord sections [38 ] from each animal. For analysis of IBA1 and GFAP immunostaining, a square with a fixed area (200 × 200 mm2) was positioned in the medial, central, and lateral third of the dorsal horn. The number of pixels occupied by immunostaining within a defined threshold was measured. The upper and lower threshold optical densities were adjusted to match positive immunoreactivity and the determined thresholds were applied uniformly to all sections. Results from the three sampled regions of the dorsal spinal cord were summed for each section and expressed as total number of pixels (# pixels) in the area. For CCR2, sampling area was confined to superficial laminae (I–II) of the spinal cord [38 ]. The data were presented as fractional area reflecting the percent of the sampled area that fell within a defined immunodensity threshold. The individuals who quantified the images were blind to the experimental conditions.
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6

Detailed Macro- and Micromorphological Analysis

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Morphological external and internal macro-/micro-structures were noted per Wanasinghe et al. [16 (link)]. Macro- and micromorphological features were photographed using an Olympus SZ61 Series and a Nikon ECLIPSE Ni (Nikon Instruments Inc., Melville, NY, USA) compound microscope. Macroscopic images of colonies were documented using an iPhone XS Max (Apple Inc., Cupertino, CA, USA) with daylight. At least 20 measurements were taken for each structure using the Tarosoft (R) Image Frame Work program. All photographs were arranged using Adobe Photoshop CS6 (Adobe Systems, San Jose, CA, USA).
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7

Ovarian Ultrastructural Analysis

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The ovaries were dissected under a Nikon SMZ1500 stereoscopic microscope (Nikon, Japan). They were fixed in a mixture of 2 % formaldehyde and 2.5 % glutaraldehyde in 0.1 M phosphate buffered saline (PBS), pH 7.3, for several days. Isolated ovarioles were rinsed and postfixed in 2 % osmium tetroxide and 0.8 % potassium ferrocyanide in the same buffer for 30 min at 4 °C. After dehydration in a series of ethanol and acetone, the material was embedded in Glycid Ether 100 (Epon 812) resin (Serva, Heidelberg, Germany). Semithin sections (0.7 μm thick) were stained with 1 % methylene blue and examined under a Leica DMR (Heidelberg, Germany) or Nikon Eclipse Ni (Nikon) light microscopes. Ultrathin sections (80 nm thick) were contrasted with uranyl acetate and lead citrate according to standard protocols and analyzed with a Jeol JEM 2100 transmission electron microscope (TEM) at 80 kV.
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8

Cell Counting for Squamous Cytology

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Cytological samples were captured horizontally from left to right at ×100 magnification using a microscope (Nikon Eclipse Ni; Nikon, Tokyo, Japan) equipped with a digital camera (Olympus DP74; Olympus Corporation, Tokyo, Japan). At least 100 well-isolated squamous cells from over three captured images were counted on each slide using e-Cynuc2 cell counting software (e-Path, Kanagawa, Japan). Subsequently, since the area of the ×100 magnification fields seen through the eyepieces (field number=22) of the microscope was 3.9 mm2 and the area of the captured image was 1.6 mm2, the average number of cells per capture image was multiplied by 3.1 to estimate the average number of cells per ×100 magnification fields.
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9

Quantifying TNFα in Spinal Cord Laminae

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Images of spinal cord sections were acquired at 10x magnification using a Nikon Eclipse Ni fluorescent and brightfield microscope (Nikon, Tokyo, Japan). The Image J software (National Institutes of Health, Bethesda, MD) was used to quantify TNFα immunostaining in the superficial laminae (I-II) of four randomly selected lumbar spinal cord sections from each animal. The data were presented as the fractional area, which reflects the percentage of the sampled area that fell within a defined density threshold. The individual who analyzed the images was blind to the experimental conditions.
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10

Immunohistochemistry and Immunofluorescence Assays

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The application of these two methods to cells was as previously described 14 (link),15 (link). Briefly, cells transferred onto glass slides were washed with PBST (PBS + 0.05% Tween 20) 3 times and permeabilized with 0.1% Triton X-100 in PBS for 15 min. Cells are blocked with normal serum or 5% bovine serum albumin for 1 h, and then incubated with an appropriate dilution of primary antibodies at 4 °C overnight. After three washes with PBST for 15 min, cells are incubated for 1 h with horseradish peroxidase-conjugated secondary antibody at room temperature. Cells are then developed with chromogen (DAB) for 5–10 min at room temperature after three washes are counterstained with hematoxylin. The slides are dehydrated and mounted with liquid mounting media. For immunofluorescence detection, cells are processed with the same procedure as above but incubated for 1 h with fluorophore-conjugated secondary antibodies (usually diluted 1:400) instead and covered with mounting medium with 4’−6-diamidino-2-phenylindole (DAPI). All stained slides are examined and photographed using a Nikon fluorescence microscope (Nikon Eclipse Ni, Tokyo, Japan) with a Wide Zoom Camera.
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