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57 protocols using zyla 4

1

Zebrafish Lens Cataract Imaging

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Zebrafish lenses were assessed for cataract at 4 days post fertilisation. Larvae were anaesthetised in tricaine methanesulfonate (300 mg/L, MS222 (Glentham Life Sciences), pH 7.0) and whole mounted in 0.5% w/v agarose and imaged using differential interference contrast illumination, under ×40 magnification, using an inverted microscope (Nikon Eclipse Ti-E) equipped with an s-CMOS camera, Zyla 4.2 plus s-CMOS camera (Zyla 4.2, Andor) and NIS-Elements AR acquisition software (Nikon).
Lens images from all experiments were collated, blinded and viewed with ImageJ [29 (link)] for cataract assessment by two independent researchers. Any divergent calls were resolved by a third researcher to obtain a result. Images were assessed for structural and organisational defects using a rubric of images. P values were calculated using a Fisher’s Exact test and experimental replicates were performed to confirm results. A post hoc power analysis (G*Power 3.1.9.4 [30 ]) from the aqp0a positive control experiments was used to determine that a sample size of >93 total embryos was required to achieve 80% power to detect an effect of size of 0.29, which is equivalent to the cataract rate of 16% observed with this morpholino in our laboratory.
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2

Evanescent-field Fluorescence Microscopy Setup

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Fluorescence
microscopy was performed at a custom inverted microscope described
in detail in a previous publication.31 (link) Light
from a solid-state laser (561 nm, DPSS-System, MPB) was intensity-adjusted
using a half-wave plate and a polarizing beam splitter (WPH05M-561
and PBS101, THORLABS). The beam passed through a refractive beam-shaping
device (piShaper 6_6_VIS, AdlOptica) to create a flat illumination
profile. To achieve evanescent-field illumination, the beam excentrically
entered the oil immersion objective lens (100× NA 1.49 UAPON,
Olympus). Fluorescence emission was collected by the same objective
and filtered through suitable band-pass filters (605/64, AHF Analsentechnik)
before detection on a CMOS camera (Zyla 4.2, Andor). During acquisitions,
the temperature was stabilized at 23 °C (H101-CRYO-BL, Okolab),
and z-positioning of the sample was stabilized via
a piezo stage (Z-INSERT100, Piezoconcept and CRISP, ASI). The camera
was operated with the open source acquisition software μManager32 (link) and images were acquired with 2 × 2 pixel2 binning and field of view cropping to the central 700 ×
700 (prebinned) pixels to achieve an effective pixel width of 130
nm and a field of view matching the circular flat illumination profile
ca. 130 μm in diameter.
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3

Measuring Thapsigargin-Induced Calcium Entry

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Cells were incubated with 5 μM fura-FFP18/AM for 2 h at 37 °C as described previously [45 (link)]. Coverslips with cultured cells were mounted on a perfusion chamber and placed on the stage of an epifluorescence inverted microscope (Nikon Eclipse Ti2, Amsterdam, The Netherlands) with an image acquisition and analysis system for videomicroscopy (NIS-Elements Imaging Software, Nikon). Cells were continuously superfused with HBS supplemented with 0.1% (w/v) BSA at room temperature and were examined at 40× magnification (Nikon CFI S FLUOR 40× Oil, Amsterdam, The Netherlands). Cells were alternatively excited with light from a xenon lamp passed through a high-speed monochromator Optoscan ELE 450 (Cairn Research; Faversham, UK) at 335 and 364 nm, and fluorescence emission, at 490 and 502 nm, respectively, was detected using a cooled digital sCMOS camera Zyla 4.2 (Andor; Belfast, UK) and recorded using NIS-Elements AR software (Nikon, Tokyo, Japan). Fluorescence ratio (F335/F364) was calculated pixel by pixel, and the data were presented as ΔF335/F364. TG-evoked Ca2+ entry was measured as the integral of the rise in fura-FFP18 fluorescence ratio for 3 min after the addition of extracellular Ca2+ taking a sample every second (AUC). To compare the rate of increase in fura-FFP18 fluorescence between different treatments, traces were fitted to the equation mentioned in Section 4.3.
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4

Visualizing Callose Deposition During Microsporogenesis

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In the analysis of callose deposition during microsporogenesis, stamens in various flowering stages were mounted in the aniline blue solution (see the ‘Methods’ section on ‘Preparation of transgenic plants’) and squashed to release pollen from the anthers. Fluorescent images of tdTomato and aniline blue were photographed using an Olympus IX73 inverted microscope (Tokyo, Japan) equipped with an sCMOS camera (Zyla 4.2; Andor, Belfast, UK) using RFP and CFP filters, respectively. To obtain a super-resolution image, we used the deconvolution software Huygens Ver. 17.04. (Scientific Volume Imaging, Hilversum, the Netherlands) from an image acquired using the photon-counting mode of a confocal laser scanning microscope (Leica TCS SP8, Wetzlar, Germany). Pollen from SC-cal RHT carrying the pGCS1:GCS1-Clover or pACA3:Lyn24-mNeonGreen reporter gene were mounted in 5% sucrose and observed by the TCS SP8.
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5

Fluorescence In Situ Hybridization of BAC Clones

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Bacterial artificial chromosome (BAC) clones 261B8, 116B8, and 206E12 cover 8-, 26-, and 35-Mb (neocentromere region in #1320 cells) regions on the Z chromosome, respectively, and were used as FISH probes. Each BAC clone was labeled by a nick-translation method with DNase I (Roche), DNA polymerase I (Boehringer Mannheim), and Cy3-3-dUTP (NEL578; PerkinElmer) or FITC-12-dUTP (NEL412001EA; PerkinElmer). For double-color FISH analysis, DT40 cells were fixed with 3% PFA for 10 min after cytospinning to a slide glass (Matsunami). Fixed cells were treated with PBS:methanol:acetic acid (8:3:1) for 15 min and incubated in methanol:acetic acid (3:1) for 15 min. Samples were denatured with labeled probes at 73°C for 1 h. After overnight incubation at 39°C, cells were washed with 2× SSC twice, with formamide; 2× SSC (1:1) twice; and 2× SSC twice at 37°C by each wash for 5 min, respectively. After DAPI staining, cells were washed with PBS twice and mounted with Vectashield mounting reagent (Vector Laboratories). FISH images were captured by sCMOS camera (Zyla 4.2; Andor) mounted on ECLIPSE Ti microscope (Nikon) with an objective lens (Plan Apo lambda 100×/1.45 NA; Nikon) and CSU-W1 confocal scanner unit (Yokogawa) controlled by NIS elements (Nikon). The distance between two signals was measured by Imaris software (Bitplane).
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6

Multimodal Fluorescence Imaging Setup

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The detection system
was set up on
an epi-fluorescence microscope (Nikon Eclipse Ti2). A multilaser engine
(Toptica Photonics, Munich, Germany) was used for selective fluorescence
excitation of CFP, GFP, RFP, and Cy5 at 405, 488, 561, and 640 nm,
respectively. The samples were illuminated in TIR configuration (Nikon
Ti-LAPP) using a 60× oil immersion objective (NA = 1.49, APON
60XO TIRF). After appropriate filtering using standard filter sets,
the fluorescence was imaged onto a sCMOS camera (Zyla 4.2, Andor,
Northern Ireland). The samples were mounted on an x-y-stage (CMR-STG-MHIX2-motorized table, Märzhäuser,
Germany), and scanning of the larger areas was supported by a laser-guided
automated Perfect Focus System (Nikon PFS).
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7

GUV Morphology and Lamellarity Imaging

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Fluorescence images of GUV samples were collected using a 100× oil immersion objective mounted on an Olympus IX73 inverted epifluorescence microscope coupled with a sCMOS camera (Zyla 4.2; Andor Technology, Belfast, UK). Samples were illuminated using a green LED at 10% (pE300white; CoolLED, Andover, UK) and tetramethylrhodamine filter. The acquired microscopy images were used to examine GUV’s morphology. Measurements for each experimental condition were carried out in 15 different areas of the chamber and repeated in at least three independent experiments. A total of at least 100 vesicles were screened for each condition. Lamellarity of vesicles was measured in 15 different areas of the chamber by using a semiautomated algorithm implemented in ImageJ (36 ). Fluorescence images reported in this study show typical GUV morphology and lamellarity for each experimental condition.
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8

Live-Cell Imaging of Axonal Transport

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For live imaging, cells were maintained in Hibernate E medium without phenol red (Brain-Bits). Images were acquired using a microscope (model Ti-E; Nikon) equipped with a spinning-disk confocal-head (model CSUW1, Yokogawa), and images were captured with an sCMOS camera (Zyla, Andor). KIF3AB and KIF3AC images were acquired with an Andor Dragonfly built on a Ti2 (Nikon) with a CFI Apo 60× 1.49 objective (Nikon) and captured with an sCMOS camera (Zyla 4.2+, Andor). The entire imaging stage and objectives were maintained at 37°C in a warmed enclosure (full lexan incubation ensemble; OkoLab). A Plan-Apo 100× 1.49 NA objective (Nikon) was used with 2 × 2 binning to acquire image streams. During image acquisition, z-axis movement was controlled by the Perfect Focus system on the Ti-E microscope (Nikon). Recordings were acquired at two frames per second. For further details, see Kaech et al.82 Axons were identified with anti-neurofascin antibody (NeuroMab, Cat #: 75–027) conjugated to CF405 (Mix-n-Stain CF405S Antibody Labeling Kit; Biotum, Cat#: 92231) in the imaging medium. Cells expressing constructs with HaloTag were treated with 50 nM Janelia Farm 549 dye18 (link) for 10 minutes and washed with conditioned medium for 10 minutes prior to imaging.
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9

Calcium Transience Imaging of hiPSC-CMs

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hiPSC-CM monolayers were loaded with 5 μM Calbryte-590 in RPMI + B27 medium at 37°C for 45 minutes. Loading media was washed and replaced with Tyrode’s salt solution. Calcium transience videos were acquired at 50 frames per second using a sCMOS camera (Zyla 4.2, Andor Technology) connected to an inverted fluorescence microscope (IX-81, Olympus) with cells placed in a live-cell chamber (STX Temp & CO2 Stage Top Incubator, Tokai Hit). Calcium signal analysis was performed using custom Python script as previously described (65 (link)).
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10

Cytoplasmic ATP Imaging in Living Cells

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Imaging of cytoplasmic ATP levels in living cells was performed as previously described13 (link), 40 (link). Briefly, cells expressing ATeam1.03 were plated on collagen-coated 35-mm glass-bottom dishes (MatTek, Ashland, MA). The following day, the cells were washed once with the customized media and the cells were subjected to ATP imaging. Observations of cells that were maintained at 5% CO2 and 37 °C using a stage-top incubator (Tokai Hit, Shizuoka, Japan) were performed using a Nikon ECLIPSE Ti-E microscope with an oil-immersion type CFI Plan Apo VC 60x lens (Nikon Instruments Inc, Tokyo, Japan). The filters, 438/24-nm BrightLine single-band bandpass filter (FF01–438/24–25), 458-nm edge BrightLine single-edge dichroic mirror (FF458-Di02), and two emission filters (FF01–483/32 and FF01–542/27) used for dual-emission ratio imaging of ATeam1.03 were obtained from Semrock Inc. (Rochester, NY). Fluorescence emission from the ATeam1.03 was imaged by altering the emission filters with a filter changer and a scientific CMOS camera (Zyla 4.2, Andor Technology), and the imaging analysis was performed using MetaMorph (Molecular Devices). The YFP/CFP emission ratio was calculated by dividing the YFP intensity by the CFP intensity of each cell.
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