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57 protocols using a1 hd25

1

Visualizing NPR1 Subcellular Localization

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The expression of NPR1 tagged with either GFP (NPR1-GFP) or cyan fluorescent protein (CFP) (NPR1-CFP) was investigated in both intact leaves and protoplasts of stable NPR1-GFP transgenic plants. Confocal laser scanning microscopes (A1 HD25 from Nikon, Japan; FluoView 300 from Olympus, Tokyo, Japan; and STELLARIS 8 from Leica, Wetzlar, Germany) and a fluorescence microscope (THUNDER Imager from Leica, Wetzlar, Germany) equipped with a high-resolution CCD camera (A1 HD25 from Nikon, Tokyo, Japan) were used to visualize the GFP and CFP fluorescence in the cells. Excitation and emission were set at 488 and 520 nm, respectively, for GFP, and at 450 and 470 nm, respectively, for CFP. Red chlorophyll fluorescence was visualized by exciting at 458 nm and a detecting emission at 647–720 nm. The intensity of fluorescence was quantified using the Image J software (https://imagej.nih.gov/ij/, accessed on 15 March 2023). Thirty images were acquired per independent experiment, and each experiment was repeated more than three times (n = 30, N > 3).
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2

Subcellular Localization of HvFRF9 Protein

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The coding sequence of HvFRF9 gene (stop codon removed) was amplified using the intermediate vector, pEASY-Blunt-HvFRF9, and ligated into SUPER1300-35S-GFP and P131-35S-YFP vectors, respectively. The ligation products were used to transform competent E. coli Trans1-T1 cells, and positive clones were obtained and sequenced. SUPER1300-35S-HvFRF9-GFP and P131-35S-HvFRF9-YFP of subcellular localization vector were obtained from the plasmids of the correctly sequenced clones (to ensure that there was no frame shift and the complete fusion protein could be translated). SUPER1300-35S-HvFRF9-GFP, nuclear localization marker, arabidopsis protoplasts, and PEG4000 solution were mixed and placed in water bath for 15 min. Protoplasts were collected after washing with W5 solution (154 mM NaCl, 125 mM CaCl2, 5 mM KCl, 5 mM glucose, and 2 mM MES). The fluorescence distribution was observed under a laser confocal microscope (A1 HD25, Nikon, Tokyo, Japan). P131-35S-HvFRF9-YFP plasmid was transferred into Agrobacterium tumefaciens EHA105, which was used to infect tobacco (Nicotiana benthamiana) at the 4–5 leaf stage. Between 36 and 72 h after infection, undamaged tobacco leaves were selected to make sample slides. The fluorescence distribution was observed under a laser confocal microscope (A1 HD25, Nikon, Tokyo, Japan). The culture conditions for tobacco were 24°C/26°C, 16 h/8 h, day/night.
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3

Immunofluorescence Analysis of Chicken Blastoderm

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For analysis of the chicken blastoderm, at least 10 blastoderms were pooled together and centrifuged at 2000 × g for 5 minutes. The resulting tissue masses were paraffin-embedded, and then 4-μm thick sections were cut and placed on slides. Tissue sections or cell slides were fixed in cold methanol and acetone (1:1 mixture) for 2 hours, washed with PBS and permeabilized with 0.1% Triton X-100 in PBS for 15 minutes. This was followed by blocking using 10% donkey or goat FBS for 30 minutes at 37°C. The sections were incubated overnight at 4°C with primary antibodies against H3S10P (Cat: 3377T; CST; 1:200), PCNA (Cat: abs120180; Absin, Shanghai, China; 1:200), PKC (Cat: NB600-201; Novus, Littleton, CO, USA; 1:100) or P65 (Cat: NBP2-24541; Novus; 1:100). The slides were washed with PBS and then incubated with FITC-conjugated or PE-conjugated secondary antibodies (Abcam) for 2 hours at room temperature. The cell nuclei were counterstained with DAPI (Invitrogen) for 15 minutes at room temperature. The slides were then examined by laser scanning confocal microscopy (Nikon A1HD25; Nikon Corporation, Tokyo, Japan).
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Visualizing PHYB-GFP Dynamics in Seedlings

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Four-day-old light-grown 35Spro:PHYB-GFP seedlings were transferred to darkness at either 20°C or 28°C for the indicated times. Seedlings were fixed with 4% formaldehyde for 15 min under vacuum. Fluorescence images were obtained using a fluorescence microscope (Nikon A1 HD25; Nikon, Japan).
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ICAM1 Antibody Internalization in Thyroid Cancer

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PE conjugated ICAM1 antibody (Santa Cruz Biotechnology, sc-107) was incubated with thyroid cancer cells at 37 °C for 45min, then washed with cold PBS, fixed with 4% paraformaldehyde, and blocked by 1% BSA, and analyzed by confocal microscopy. For internalization experiments, cancer cells were incubated with PE conjugated ICAM1 antibody for different time points (0min, 30min, 60min, 120min, 240min), then processed and analyzed as described above. Cell nuclei were counterstained with Hoechst 33258 in PBS for 10 minutes at room temperature. The stained cells were visualized by using a fluorescence microscope (Nikon A1 HD25; Nikon, Japan).
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Counting Germ Cells in C. elegans Gonad

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The number of germ cells in the gonad was counted after staining with DAPI as previously described [32 (link),33 (link)]. About 40 synchronized L4 wild-type C. elegans were transferred to 200 μL of FAc solution (dissolved in sterile water) for 24 h, and at least 10 worms in each group were picked out and suspended in 1 μL of sterile water. After fixing with Carnoy’s fixative (60% ethanol, 30% chloroform, and 10% glacial acid), air drying, and staining with a drop of 2 μg/mL DAPI (MERCK, Darmstadt, Germany) solution (dissolved in M9 buffer), the number of germ cells in the gonad were counted under a confocal laser scanning microscope (Nikon A1HD25, Nikon, Tokyo, Japan).
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7

Immunohistochemical Analysis of Calbindin

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Sections (20 μm) were washed with PBS for 3×5 min. They were then permeabilized with a PBS and 0.3% Triton X-100 (Sigma-Aldrich) solution (PBST) for 2×20 min and blocked with a 10% NDS (Normal Donkey Serum, Jackson ImmunoResearch Labs) in PBST solution for 45 min. The sections were then incubated with a primary antibody for Calbindin (rabbit anti-Calbindin primary, 1:300, cat#: CB38a, Swant) diluted in PBST for 24 hours at 4 °C. The sections were then brought to room temperature (RT) and washed with PBS for 3×5 min. Secondary antibodies (Donkey anti-rabbit Alexa-647, 1:300, Jackson Labs, cat#: 711-605-152) diluted in PBST with a 1:1000 dilution of DAPI (Sigma-Aldrich) to stain nuclei was then applied to the sections for 1 hour at RT. Sections were then washed with PBS for 3×5 min, and the sections were coverslipped and sealed with Fluoromount-G (Electron Microscopy Sciences, cat#: 17984–25). Sections were imaged in 3 μm z-steps using an inverted confocal microscope (A1 HD25, Nikon Instruments Inc; excitation filters: 405/488/568/647nm).
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8

Senescence-Associated Heterochromatin and Paraspeckles

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H3K9me3 immunofluorescence analyses were carried out to analyse the heterochromatin foci formation of senescent cells. NONO and PSPC1 immunofluorescence staining analyses were carried out to analyse the paraspeckles formation. The control and experimental group cells were fixed and blocked in 3% BSA. Then primary antibody were added and incubated overnight at 4°C. The primary antibodies are as follows: H3K9me3 (ThemoFisher; 49−1008, 1:1000), PSPC1 (Santa Cruz; sc‐374181, 1:500), NONO (Abclonal; A5282, 1:500). The secondary corresponding fluorescence‐labelled antibody are as follow: CoraLite488‐conjugated Goat Anti‐Rabbit IgG(H+L) (Proteintech; SA00013‐2, 1:800) and CoraLite647‐conjugated AffiniPure F(ab')2 Fragment Goat Anti‐Rabbit/Mouse IgG (H+L) (Proteintech; SA00014‐9/10, 1:800). Pictures were taken by a laser scanning confocal microscope (ZEISS LSM900 and NIKON A1 HD25).
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9

Quantifying Protein Dynamics with FRAP

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FRAP was performed with confocal microscopy (NIKON A1 HD25) equipped with a 100X/1.45 NA oil objective (1,024 × 1,024 pixels) at room temperature. The concentration of the fluorescently labeled protein was adjusted to 1% by diluting the labeled protein into the unlabeled one. Defined regions were photobleached at a specific wavelength and the fluorescence intensities in these regions were collected every 3 s (for in vitro droplets) and normalized to the initial intensity before bleaching. Image intensity was measured by mean ROI and further analyzed by Prism (GraphPad).
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10

Subcellular Localization of TaPsb28 Protein

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The subcellular location of TaPsb28 was examined both in mesophyll protoplasts from Zea mays (inbred Line B73) and in transgenic Arabidopsis, as described by Hotto et al. [51 (link)]. Mesophyll protoplasts were isolated from ~5 g of leaf tissue obtained from the middle of the second fully expanded leaves of 2- to 3-week-old seedling leaves. The integrity of the extracted mesophyll protoplasts was guaranteed by microscopy observation. Subsequently, pYFPLT-TaPsb28 was transformed into protoplasts according to polyethylene glycol (PEG)-mediated transformation assays [52 (link)]. The transformed protoplasts were incubated at 25 °C for 12 h under dark conditions. The location of the fusion protein was examined for chloroplast autofluorescence and YFP fluorescence by a laser scanning confocal microscope (A1HD25, Nikon, Japan) at an excitation wavelength of 488 nm and instrumental magnification of ×40. For the subcellular location of TaPsb28 in transgenic Arabidopsis, the 2-week-old leaves from T2 generation plants were retrieved for observation directly following the procedure described above.
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