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33 protocols using ti e widefield microscope

1

Imaging of Cellular Dynamics

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Fixed samples were imaged using a Perkin Elmer UltraView spinning disc confocal microscope, with a 60X/ 1.2NA water objective and a Z step size of 0.3 μm. For time lapse microscopy, cells were imaged with a confocal microscope (for experiments in Figs 3C–3E and 4A–4C) at 37°C with a 40X / 1.3 NA oil objective. Every 60, 30 or 5 seconds depending on experiment, a stack of 6 z-planes (step size of 0.5μm) was acquired sequentially in two or three channels using a 488nm, 561nm and 640nm laser depending on experiment. For mutant library rupture timing screen (Fig 3B) and Rab11 DN experiments (Fig 4D) cells were imaged at 37°C using a Nikon Ti-E wide-field microscope with a 20X air objective. Imaging was performed with excitation at 465 to 500 nm and 540 to 565 nm. Images were acquired every 90 or 120 seconds (depending on the exposure time) for 1 to 2 hours. In each screen experiment two mutants and one control (wild-type strain) were screened and images of 10 positions per strain acquired. For the Rab11 DN experiments 8 positions per condition were acquired with WT and IpgD as controls.
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2

Immunofluorescence Staining of Neuronal Differentiation

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A modified protocol from Hycult biotech (Version: 04-2010) was used for IF staining. On day 8 after LiF withdrawal embryoid bodies were dissociated and the cells were plated onto poly-D-lysine/laminin coated ibidi 35mm dishes (ibidi, Martinsried, Germany) and kept in N2 media till day 10. On day 10 cells were fixed in 2% paraformaldehyde in PBS for 15 min at RT, washed with PBS, permeabilized with cold methanol for 5 min at -20⁰C and washed again with PBS. The dishes were blocked in 2% BSA in PBS for 30 min and incubated with primary antibodies overnight at 4⁰C (rabbit anti-SOX2 antibody, Merck-Millipore AB5603 and mouse anti-ßTubulin III antibody, Abcam AB78078). Next day the dishes were incubated with secondary antibodies (Alexa488 anti-rabbit and Alexa 594 anti-mouse, both ThermoFisher Scientific) for 30 min at RT, washed and kept in PBS for imaging. Images were acquired with a Nikon Ti-E widefield microscope. For quantification of neuronal ß-tubulin III positive cells nuclei on 2 fields of view with >100 cells each were manually classified into ß-tubulin III positive and negative cells in Fiji.
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3

Fluorescent Mitochondrial Fusion Assay

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Mitochondria were imaged on microscope slides by mixing 3 μl fusion reaction with 3 μl of 3% low-melt agarose made in modified fusion buffer (20 mM PIPES-KOH, pH 6.8, 150 mM KOAc, 5 mM Mg(OAc)2, 0.4 M sorbitol) before overlaying with a coverslip. A Z-series of 0.2-μm steps was collected with a Nikon Ti-E wide-field microscope with a 100× NA 1.4 oil objective (Nikon), a solid -state light source (Spectra X; Lumencor), and a sCMOS camera (Zyla 5.5 megapixel). For each condition tested, mitochondrial fusion was assessed by counting ≥300 total mitochondria per condition from ≥4 images of each condition, and individual fusion events were scored by colocalization of the red and cyan fluorophores in three dimensions.
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4

Dual Gamete Formation Inhibition Assay

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The dual gamete-formation assay
was performed as described in Delves et al.37 (link) NF54 parasites were cultured in media supplemented with 10% human
serum and induced to form gametocytes. On day 14 post-induction, stage
V gametocytes were seeded into 384-well plates at 1% gametocytemia
and 4% hematocrit and exposed to drug for 48 h. To induce male exflagellation
and monitor female gametes, ookinete media containing 100 μM
xanthurenic acid (Sigma-Aldrich) and 0.5 μg/mL anti-Pfs25-cy3
antibody (MRA-315, BEI Resources) were added. Exflagellation was monitored
by phase contrast on a Nikon Ti-E widefield microscope. Plates were
incubated for an additional 24 h, and female gamete formation was
evaluated by the expression of Pfs25 on the TRITC channel. Exflagellation
centers and female gamete formation were quantified using the Icy
Bioimage Analysis Program (http://icy.bioimageanalysis.org/). The inhibition of gamete
formation by JIB-04 was calculated relative to positive (40 μM
gentian violet, MolPort) and negative (DMSO) controls.
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5

Multimodal Imaging and Electrical Stimulation Protocol

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Samples for all imaging experiments were imaged on a Nikon Ti-E spinning disc confocal microscope equipped with Nikon Elements software, Ti-E perfect focus system, Yokogawa CSU-X1 spinning disc head, Andor 888 Ultra EMCCD camera and Oko Labs enclosed environmental chamber set at 37 °C.
Samples for each type of imaging experiment except immunofluorescence experiments were also imaged on a Nikon Ti-E widefield microscope equipped with Nikon Elements software, Ti-E perfect focus system, Andor iXon3 EMCCD camera, Sutter Instruments LD-LS/30 xenon arc lamp, and Sutter Instruments Lambda 10-3 filter changer.
For electrical stimulation, an IonOptix Myopacer cell stimulator was equipped with a custom set of platinum wire electrodes. Stimulations were performed with 30 V bipolar waveform 10 ms pulses at 5 Hz for a duration of 1 minute, unless specified otherwise.
RNA extraction for next-generation sequencing was performed using a Promega Maxwell RSC Instrument.
Quantitative PCR was performed using a BIO-RAD CFX384 Real Time PCR Detection System instrument.
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6

Ras Anchor Dynamics in Membrane Blebs

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BHK cells co-expressing GFP-tagged Ras anchors and the empty vector pC1 or RFP-tagged Ras anchors were grown to ∼85% confluency and washed with 2× Hepes buffer. The cells were then incubated in Hepes buffer containing 2 mM (N-ethyl maleimide [NEM]) for ∼90 min to induce blebbing (83 (link)). GPMVs containing GFP- and RFP-tagged Ras anchors (or GFP-tagged Ras anchors with pC1) were then incubated in Hepes buffers containing various percentages of deionized water (hypotonic conditions) or concentrations of NaCl (hypertonic conditions) for 5 min.
GFP fluorescence was visualized using a Nikon TiE wide-field microscope using a 60× oil-emersion PLAN-Apo/1.4 numerical aperture lens (25 (link),26 (link)). The fluorescence lifetime of GFP was measured using a Lambert FLIM unit attached to the wide-field microscope. GFP was excited using a sinusoidally stimulated and modulating 3-W 497-nm light-emitting diode at 40 Hz. At least 20 vesicles were imaged and the fluorescence lifetime values were pooled and averaged. Statistical significance was evaluated using one-way ANOVA, with * indicating P < 0.05.
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7

Inhibition of Plasmodium Ookinete Development

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All mouse procedures were performed in accordance with the UK Animals (Scientific Procedures) Act (PPL 70/7185) and approved by the Imperial College Animal Welfare and Ethical Review Body (AWERB). The ability of test compounds to inhibit P. berghei early mosquito stage development was tested in the Ookinete Development Assay37 (link) with a few exceptions. Anaesthetised 6- to 8-week-old female Tucks Ordinary (TO) mice infected with P. berghei strain CTRPpGFP38 (link) were rapidly exsanguinated by cardiac puncture and 500 µl of blood diluted in 25 ml of ookinete medium supplemented with 20% foetal bovine serum. Immediately the blood/medium mixture was dispensed by multichannel pipette into 384 well plates containing pre-plated test compounds. 10 µM cycloheximide and DMSO were used as the positive and negative controls, respectively. Plates were stored in the dark in a humidified incubator at 18 °C for 24 h. Ookinete production was imaged by fluorescence microscopy of GFP expression under the ookinete-specific CTRP promoter using a Nikon Ti-E widefield microscope and ×10 objective. Ookinete production was quantified using ICY and percentage inhibition calculated as above with reference to positive and negative controls.
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8

Visualizing Pancreatic Endocrine Cells

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Pancreatic sections were stained with anti-CD3 (CD3-12, Thermo Fisher), anti-BSRP-A (polyclonal sheep IgG, R&D), and DAPI. Images were obtained using Nikon Ti-E widefield microscope at x20 magnification. BSRP-A was used to identify endocrine cells [50 (link),51 (link)]. Nikon NIS-Elements scope/software was used to obtain the images. Background autofluorescence was removed using a previously published method in Fiji [52 (link)].
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9

Imaging Neuronal Dynamics with S-mCherry

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Primary cortical neurons were isolated from E15 mouse embryos dissociated in 0.05% trypsin-EDTA (Thermo Scientific) at 37 °C for 12 min. 320,000 cells/ml were plated on poly-D-lysine (0.125 mg/ml, Sigma Aldrich) and lamin (5 µg/ml, Corning) coated 96-well glass plates and grown at 37 °C and 5% CO2 in Neurobasal medium (Thermo Fisher) supplemented with 2% B27 and 1% Glutamax (Thermo Scientific). Four DIV neurons were transfected with 0.2 µl Lipofectamine 2000 (Thermo Scientific) and 100 ng DNA following manufacturer’s recommendations. A ratio of 4:1 was used for the GFP and S-mCherry vectors. Thirsty-six hours after transfection, Leptomycin B (10 mg/L) was added to the culture medium immediately before image acquisition. Cells were imaged using a Nikon TiE widefield microscope equipped with temperature- and CO2-controlled environmental chamber. Movies were acquired with a ×20 lens at a rate of 1 frame every 1 or 2 min for 1 h. For rescue experiments, neurons were fixed immediately after acquisition and stained with V5 antibody to detect V5-PFN1 expression.
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10

PFN1 Modulation and Axon Outgrowth

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Motor neurons were co-transfected as outlined above with green fluorescent protein (GFP) and V5-tagged PFN1 constructs in a 1:2 ratio. KPT-276 (50 nM) or equal volumes of DMSO were added to the culture medium 1 day after transfection and maintained throughout the experiment for a total of 3 days. Cells were fixed and stained to detect V5-PFN1 expression 4 days after transfection. Cells were imaged as individual focal planes using a ×10 lens. GFP was used to identify transfected cells and highlight the whole cell structure. For live imaging of axon outgrowth, KPT-276 (50 nM) or equal volumes of DMSO were added to the culture medium 1 day after transfection and maintained throughout the experiment for a total of ~18–24 h. Cells were imaged at 3 DIV using a Nikon TiE widefield microscope equipped with temperature- and CO2-controlled environmental chamber. Movies were acquired with a ×20 lens at a rate of 1 frame every 10 min for 1 h.
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