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599 protocols using fm4 64

1

Confocal Microscopy Staining Protocols

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Confocal analyses were performed on either an Olympus FV3000 (Tokyo, Japan) or a Zeiss LSM 880 microscope (Oberkochen, Germany). For callose staining, roots were incubated in 150 mM K2HPO4 and 0.01% (w/v) aniline blue in the dark for 2 h. For ROS staining, roots were incubated with 10 μM H2DCFDA (Beyotime Biotech, Shanghai, China) in the dark for 30 min and then washed twice with deionized water. For PI or FM4-64 staining, roots were directly imaged in 10 μM PI or 4 μM FM4-64 (Thermo Fisher Scientific, Waltham, MA, USA). The excitation (ex)/emission (em) parameters for confocal analyses are as follows: GFP/YFP/H2CDFA ex: 488 nm, em: 500–550 nm; PI/FM4-64 ex: 561, em: 570–670 nm; aniline blue ex: 405 nm, em: 475–525 nm; esculin ex: 405 nm, em: 420–480 nm; and roGFP2-Orp1 ex: 405 and 488 nm in sequence, em: 505–535 nm and 425–475 nm (auto fluorescence recorded at ex: 405 nm for subtraction in calculating the ratio 405/488 nm)29 .
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2

Subcellular Localization of CNGC Proteins

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The coding sequences (CDSs) of three CNGC genes were amplified from mature anther cDNA and cloned into pGA3574 vectors fused with C-terminal GFP. All the cloning primers used in the experiments are listed in Supplementary Table S1. For the transfection of these constructs, rice protoplasts from leaf and stem tissue were isolated, as described previously [40 (link)]. The fluorescent tags used to determine the intracellular distribution of proteins were observed using a confocal laser scanning fluorescence microscopy (K1-Fluo; Nanoscope System, Daejeon, Republic of Korea) with 488/510 nm excitation/emission filter sets. To identify the subcellular localization in the cell membrane, the plasma and vacuolar membrane marker FM4-64 (Thermo Fisher Scientific, Waltham, MA, USA) was used; rice protoplasts were immersed in 0.1% FM4-64 solution for 10 min in the dark conditions and observed using the red fluorescence protein channel with 543/560 nm excitation/emission filter sets.
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Visualizing Transporter Localization in S. pombe

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For the evaluation of intracellular localization of the transporters, hmt-1-deleted S. pombe was transformed with pREP1-HMT-1-GFP or ABCB6-GFP. Cells were grown to mid-log phase (A600nm of 0.5–0.8) and stained with FM 4–64 as described in [58 (link)] with the following modifications. FM 4–64 (T3166 ThermoFischer Scientific Waltham, MA, USA) was dissolved in dimethyl-sulphoxide at a concentration of 1.64 mM. Cells were harvested and incubated with 1-μL FM 4–64 in 50-μL EMM medium at 30 °C for 20 min. An aliquot of 1-mL EMM was added and cells were centrifuged at 5000×g for 5 min at RT. The cell pellet was resuspended in 5-mL EMM, and the suspension was shaken at 30 °C for 90 min. The total volume was transferred to a centrifuge tube and spun for 5 min at 5000×g at RT. The cell pellet was resuspended in 1-mL sterile water, and centrifuged at 5000×g for 5 min at RT. Cells were resuspended in 25-μL EMM. An aliquot of 7 μL was spotted on ConA/polyK-coated (1:1 mixture of 2 mg/mL concanavalin A and 0.1% poly-l-lysine) glass slides covered with an 18 × 18 mm2 cover slip. Confocal images were obtained using a LSM 710 confocal laser scanning microscope (Carl Zeiss AG, Oberkochen, Germany) equipped with a Plan-Apochromat 63 ×/1.4 Oil DIC M27 objective. Noise reduction and deconvolution of the images were performed with Huygens Essential (Scientific Volume Imaging B.V.).
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Confocal Microscopy of Fluorescent Plant Tissues

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Confocal microscopy was performed using an UltraView VoX spinning disk confocal microscope (PerkinElmer) equipped with an EMCCD camera (C9100‐02; Hamamatsu) and Volocity software (Improvision). Citrine signal was examined with a 514‐nm excitation laser and 540/30 nm emission filter, and mRFP signal was examined with a 561‐nm excitation laser and 595/50 nm emission filter. Microscope settings were the same for all images acquired within the same experiment.
Developing seed was stained with FM4‐64 (cat# T13320, Thermo Fisher Scientific) by removing seeds from siliques and immersing in 10‐μM FM4‐64 in water. Seeds were vacuum infiltrated for 5 min, then left to stain for 10 min before imaging. Other tissues were stained with 10‐μM FM4‐64 for 5 min without applying a vacuum before imaging using a 561‐nm excitation laser and 650/75 nm emission filter.
Microscope images were processed with ImageJ (Schindelin et al., 2012 (link)), Photoshop (Adobe Photosystems) and Inkscape (inkscape.org). All images are single optical slices rather than flattened Z stacks.
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Quantifying Chromocenter and DNA Methylation

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Dissected shoot apical meristems from greenhouse plants or naked meristems from in vitro-grown NPA-treated seedlings were imaged with a water-dipping lens (×25, numerical aperture = 0.8) using an upright SP8 confocal microscope to generate a stack of optical sections with an interval of 0.15 μm between slices. The membranes were stained with FM4-64 [also called N-(3-triethylammoniumpropyl)-4-(6-(4-(diethylamino) phenyl) hexatrienyl) pyridinium dibromide, ThermoFisher]. Images are presented using the Fire lookup table (ImageJ). Image analysis for chromocenter and CG-methylated regions detection was performed using the 3D object counter option in Fiji software (https://fiji.sc/wiki/index.php/Fiji). The nuclear average signal density was calculated following along the line of the protocol, described in ref. 31 (link). In this case, the mean signal values were normalized to the maximal projected area of the corresponding nuclei and then correlated with their aspect ratio. Statistical analysis was performed using either Microsoft Excel or R software. The two-tailed Student's test was performed to compare the means of independent biological sample groups.
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Antimicrobial Susceptibility Assay with Microscopy

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Overnight stationary-phase bacterial cultures were diluted in LB broth and mixed with antimicrobials to a final antimicrobial concentration of 5× MIC. Where an MIC could not be measured (i.e., where bacterial growth continued along the whole length of the Etest), the upper limit of the Etest was arbitrarily used in place of the MIC. The bacteria were incubated with and without antimicrobials in static incubators in ultrathin 96-well plates for 2 h at 37°C. The plates were aspirated, and the remaining adherent bacteria were fixed with 4% paraformaldehyde (Alfa Aesar, J61899.AK) for 10 min. The wells were washed once with 50 μl of Dulbecco phosphate-buffered saline (DPBS) (Thermo Fisher, 10010023) before staining. Fixed cells were stained with 50 μl per well FM4-64 (2 μg/ml, Thermo Fisher, T13320), SYTOX green (0.25 μM, Thermo Fisher, S7020), and 4′,6-diamidino-2-phenylindole dihydrochloride (DAPI; 2 μg/ml, Sigma, D9542) diluted in Hanks balanced salt solution (HBSS) buffer (Thermo Fisher, 14175095). Staining was performed at ambient temperature for 20 min in the dark followed by a wash with 50 μl PBS. Finally, 50 μl of PBS was added to wells, and the plates were imaged within 24 h.
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7

Membrane Staining of E. coli Using FM4-64

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For membrane staining using FM4-64 (Thermo), cultures of E. coli MG1655 carrying pBAD18-Kn derived plasmids were inoculated to a starting OD600 of 0.02 in 25 mL LB and incubated at 37 °C for 1.5 h. When the exponential phase was reached (OD600 of 0.15–0.2), gene expression was induced by the addition of 0.2% l-arabinose followed by a further 1 h incubation. FM4-64 was added to a final concentration of 1 µM and samples were incubated at 37 °C for 20 min. Three µL of stained cells were placed on a microscope slide layered with a pad of M9 media56 solidified by the addition of 1.5% agarose. Imaging was performed as described in the following section.
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8

Subcellular Localization of OsANTH Genes

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The coding sequences (CDSs) of four OsANTH genes were amplified from mature anther cDNA and cloned into pGreen vectors fused with C-terminal green fluorescence protein (GFP). All the cloning primers used in the experiments are listed in Supplementary Table 2. The constructs were transfected into Agrobacterium tumefaciens strain GV3101 and used for Nicotiana benthamiana infiltration. Two to three days after infiltration, GFP fluorescence was observed with a confocal laser scanning microscope (Zeiss LSM 510; Zeiss, Oberkochen, Germany) using 488/505–530 nm excitation/emission filter sets. Fluorescence images were digitized using the Zeiss LSM image browser. To identify the subcellular localization in the cell membrane, the tobacco leaves were stained with FM4–64 (Thermo Fisher Scientific, Waltham, MA, United States). Tobacco leaf discs were immersed in 0.1% FM4–64 solution for more than 15 min under dark conditions and observed in a red fluorescence protein (RFP) channel using 558 nm excitation/emission filter sets. Brefeldin A (BFA) treatment was performed for approximately an hour after the tobacco leaf was immersed in 10 μM BFA.
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Evaluating CA's Protective Effect on Neuromast Hair Cells

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To evaluate the protective effect of CA on neuromast hair cells within the posterior lateral line, the hydrophilic dye, FM4-64 (N-(3-Triethylammoniumpropyl)-4-(6-(4-(Diethylamino) Phenyl) Hexatrienyl) Pyridinium Dibromide) (Thermo Scientific, Rockford, IL, USA), was carried out to determine the need for living cells. The 7-dpf transgenic zebrafish larvae were treated with neomycin for 0.5 h with or without CA (5 μM, 2 h) pretreatment. After the exposure period, the larvae were incubated in an embryo medium containing 50 μM FM4-64 dye for 10 min and then wash twice with a fresh embryo medium. Anesthetized with 0.4% tricaine and embedded in 0.5% low melt agarose on a glass slide, they were determined and photographed with an inverted fluorescence microscope (Olympus CKX53, Tokyo, Japan).
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10

Vesicle Budding Quantification by Flow Cytometry

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Vesicle budding reactions were scaled up 6× for flow cytometry analyses. After a 7,000-g, 10-min centrifugation of a 600-µl cell-free reaction, 540 µl supernatant was collected from the top. The lipid dye FM4-64 (Thermo Fisher Scientific) was added to the supernatant at 5 µg/ml immediately before the flow cytometry analyses. 100,000 particles were collected for each sample. FSC-A and FSC-H were used to gate for single particles (singlets), which were used for further analysis. Gating of each fluorescent channel was determined by comparing a control sample without any fluorescent labeling and a control that was labeled in a single channel. Data were collected on a BD LSR Fortessa (BD) and analyzed by FlowJo software. Instrument and software were provided by the LKS flow core facility at the University of California, Berkeley.
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