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16 protocols using ds 5m camera

1

Aortic Sinus Histomorphometric Analysis

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Serial 6 μm thick cross-sections were made of the aortic sinus area on a cryotome (Reichert HistoStat, Cryostat Microtome). From the first cross-section in which the leaflets of the aortic valves appeared upward, 63 serial cross-sections were obtained, covering the entire aortic sinus area. Of every 3 consecutive cross-sections, they were subjected to anti-CD68 immunohistochemical staining, hematoxylin phloxine saffron (HPS)-staining, and Oil Red O-staining. HPS (HPS, polyscientific) and Oil Red O-staining (Fisher Scientific) were done with standard methods. Anti-CD68-staining was done with a protocol previously reported37. The sections were blocked with rabbit serum (Vectorlabs), incubated for 1 hour with rat anti-mouse CD68 primary antibody (Abdserotec, 1:250 dilution), 10 minutes with biotinylated rabbit anti-rat antibody (Vectorlabs, 1:200 dilution), thereafter 5 minutes with VECTASTAIN ABC-alkaline phosphatase solution (Vectorlabs), and finally for 17 minutes with Vector Red solution (Vectorlabs).
All cross-sections were digitally imaged with a Nikon eclipse E400 microscope, with a 10x eyepiece and 10x lenses, a Nikon DS-U1 camera box and Nikon DS-5M camera. We used NIS-Elements F3.0 software, and imaged at a 1/350s exposure time, 2560 × 1920 pixels, and pixel size of 1.46 μm2/ pix. Software written in Matlab was developed to facilitate automated image analysis.
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2

Morphological Assessment of New Species

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The morphological assessments of the new species were carried out on our field collections and on herbarium specimens deposited at BOL, NBG (including SAM and STE vouchers) and PRE (codes as indicated by Thiers 2022 ), as well as online voucher materials (JSTOR 2022). Micromorphological characters were observed using a hand lens (10×) or under stereomicroscope Leica S9i with Nikon DS-5M Camera attached. The holotype of T.muasyae was deposited at BOL and duplicates distributed to NBG, PRE and K. Morphological terms were adopted from the recent Thesium taxonomic treatments of García et al. (2018) (link), Zhigila et al. (2020) (link) and Lombard et al. (2021) (link).
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3

Aortic Sinus Histomorphometric Analysis

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Serial 6 μm thick cross-sections were made of the aortic sinus area on a cryotome (Reichert HistoStat, Cryostat Microtome). From the first cross-section in which the leaflets of the aortic valves appeared upward, 63 serial cross-sections were obtained, covering the entire aortic sinus area. Of every 3 consecutive cross-sections, they were subjected to anti-CD68 immunohistochemical staining, hematoxylin phloxine saffron (HPS)-staining, and Oil Red O-staining. HPS (HPS, polyscientific) and Oil Red O-staining (Fisher Scientific) were done with standard methods. Anti-CD68-staining was done with a protocol previously reported37. The sections were blocked with rabbit serum (Vectorlabs), incubated for 1 hour with rat anti-mouse CD68 primary antibody (Abdserotec, 1:250 dilution), 10 minutes with biotinylated rabbit anti-rat antibody (Vectorlabs, 1:200 dilution), thereafter 5 minutes with VECTASTAIN ABC-alkaline phosphatase solution (Vectorlabs), and finally for 17 minutes with Vector Red solution (Vectorlabs).
All cross-sections were digitally imaged with a Nikon eclipse E400 microscope, with a 10x eyepiece and 10x lenses, a Nikon DS-U1 camera box and Nikon DS-5M camera. We used NIS-Elements F3.0 software, and imaged at a 1/350s exposure time, 2560 × 1920 pixels, and pixel size of 1.46 μm2/ pix. Software written in Matlab was developed to facilitate automated image analysis.
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4

Histological Stages of Spermatogenesis

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The formalin-fixed mid-part testis samples were dehydrated in ethanol, embedded in paraffin, sectioned to 5-10 µm thickness with a Shandom Hypercut manual microtome (Shandon, Southern Products Ltd., England), and stained using the haematoxylin and eosin method of National Diagnostic (www.nationaldiagnostics.com/histology/article/staining-procedures). Five slides per fish were observed with a Nikon Eclipse E-400 microscope, and pictures were taken with a Nikon DS-5M camera attached to the microscope (Nikon, Tokyo, Japan). The stages of spermatogenesis were determined according to the germ cell types present in the testis (Miura and Miura, 2001; Leal et al., 2009) their relative abundance, the degree of development of the seminal tubules and the sperm production of the male at the time of sacrifice (Morini et al., submitted) . The stages considered were: Stage SPGA:
dominance of A spermatogonia, B spermatogonia present in low numbers; Stage SPGB/SPC: dominance of B spermatogonia and spermatocytes, in some cases low numbers of spermatids; Stage SD: dominance of spermatids, in some cases a small number of spermatozoa; Stage SZ: dominance of spermatozoa (Fig. 1).
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5

Ki67 Immunohistochemistry for Tissue Analysis

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Immunohistochemistry for Ki67 was performed on 4% PFA or Carnoy fixed paraffin-embedded tissues. Tissue sections were deparaffinized in xylene and hydrated through graded alcohol series. Antigen unmasking was performed using Tris-EDTA pH 9 at 95 °C for 50 min (PFA) or Citrate Buffer pH 6 (Carnoy) at 95 °C for 20 min, followed by quenching of endogenous peroxidases using 3% H2O2. Sections were then incubated with primary rabbit polyclonal antibody against Ki67 (ab15580, ABCAM) for 1 h at room temperature and with secondary antibody ready to use (DAKO Envision system HRP rabbit) for 20 min at room temperature. Tissue sections were then washed and incubated with peroxidase (DAB, DAKO) solution. Slides were then counterstained with hematoxylin. Images were acquired using Olympus BX51 Widefield microscope connected to a Nikon DS-5M camera. Ki67 staining was quantified by using ImageJ software and Immunoratio plugin46 (link).
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6

Cell Migration and Invasion Assay

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Cell migration was determined by wound healing assay. Briefly, transfected cells were seeded on six-well plates and cultured to confluence. A wound was created by manually scraping the cell monolayer with a sterile 200 μl pipette tip. Cells were washed twice with PBS to remove floating cells and incubated in medium containing 1% FBS for 24 h. The wounds were imaged at two time points (0 and 24 h) with a phase-contrast microscope (Leitz, Germany) equipped with a Nikon DS-5M camera. Cell migration was calculated as percentage of healed distance relative to the initial wounds over 24 h.
Cell invasion was analyzed using Transwell invasion chambers (Corning, U.S.A.). Briefly, 3 × 104 transfected cells in serum-free DMEM were added onto the upper chambers of 8-μm diameter Transwell inserts precoated with Matrigel (R&D Systems, U.S.A.), and 0.5 ml of DMEM with 10% FBS was added to the lower chamber. After 48 h incubation at 37°C, cells on the bottom chamber were fixed with 70% ethanol, stained with 0.1% Crystal Violet, and photographed under an inverted microscope. The numbers of cells in five random fields per well were counted and averaged as the invading cell number.
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7

Microscopic Techniques for Fluorescence and Imaging

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Bright-field and differential interference contrast microscopy were performed using a Nikon Eclipse 90i microscope (Nikon, Düsseldorf, Germany), equipped with DS-5 M camera. Aniline blue and 3,3′-diaminobenzidine (DAB) stainings were performed as described (De Neergaard, 2005 ).
Fluorescence microscopy was performed, using a Nikon Eclipse 90i confocal laser scanning microscope (Nikon, Düsseldorf, Germany), equipped with D-Eclipse C1-SHV camera and a pinhole diameter of 30 μm. For detection of eGFP fluorescence, an excitation wavelength of 488 nm and a 535/550 nm detection channel were employed.
Fluorescence intensity was measured using the EZ-C1 software (Nikon, Düsseldorf, Germany) as described before (Albarouki and Deising, 2013 (link)).
Image processing was done with Adobe Photoshop CS (Adobe Systems, San Jose, CA, USA).
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8

Endothelial Cell Migration Assay

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MS-1 cells (8×104 total cells) were seeded into silicone culture inserts (Ibidi, Martinsried, Germany) for 24 h in a humidified 5% CO2 incubator at 37°C to create a standardized wound. After removal of the silicone inserts and washing, fresh serum-free media was added to each well to assure that cell proliferation did not skew the migration data [35 (link), 36 ]. The endothelial cells were then treated with 40 μM of scrambled control peptide or RD-p9, or a dose response of 40, 20, 10, or 4 μM p296c-s. In some experiments, 0.5 μM anti-sFlt-1 Ab (Fisher Scientific, Waltham, MA) was added with the peptide. At 0 and 48 h, microphotographs (minimum of 4 per wound per time point) were acquired along the length of the wound with a Nikon DS-5M camera using DS-L2 software at 100x magnification. The area of the wound was calculated using ImageJ and the MRI Wound Healing Tool (http://dev.mri.cnrs.fr/projects/imagejmacros/wiki/Wound_Healing_Tool). The endothelial cell migration quantification was based on the amount of regrowth across the area of the wound compared to wound size at the 0-time point.
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9

Brightfield and DIC Microscopy Analysis

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Brightfield and differential interference contrast (DIC) microscopy was performed with a Nikon Eclipse 600 microscope (Nikon, Düsseldorf, Germany). Digital images were taken using a DS-5M camera (Nikon, Düsseldorf, Germany). Image processing was done with the software package Lucia 4.61 (Nikon GmbH, Düsseldorf, Germany). Image analysis was performed using ImageJ [23 (link)].
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10

Multicolor Fluorescence Microscopy Imaging

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Sections were observed and images obtained with a dual bright-field and fluorescence microscope Nikon Eclipse TE300 (Nikon, Tokyo, Japan) with objective lenses (CFI plan-achromat 10x/0.30, CFI plan-achromat 40x/0.60, and CFI plan-achromat 100x/1.3 Oil) and filter cassette with fluorescent filters: UV-2A (Ex: 330–380 nm; Em: 420 nm) for DAPI, B-2A (Ex: 450–490 nm, Em: 520 nm) for Alexa Fluor 488 and G-2A (Ex: 510–560 nm; Em: 590 nm) for Alexa Fluor 555. We used a DS-5M camera (Nikon, Tokio, Japan) to take 2560 × 1920 pixels images and we used NIS-Elements (F3.22.00) as imaging software.
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