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13 protocols using orca flash 2.8 camera

1

Visualizing Xanthomonas citri Chromosome

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The initial cultures of X. citri wt and X. citri pMAJIIc-envC were prepared by cultivating bacteria in 5.0 mL of NB medium for approximately 16 h at 30 °C and 200 rpm. The cultures were then diluted to an OD 600 nm of 0.1 using fresh NB medium for a final volume of 5.0 mL and subsequently cultivated under the same conditions until an OD 600 nm of 0.3 was reached. At this point, arabinose was added to the medium to a final concentration of 0.05%, and the cultures were maintained at 30 °C and 200 rpm. After a minimum of 2 h of induction, 5 µL drops of cell cultures were placed on agarose-covered microscope slides for direct microscope observation [21 (link)]. For chromosome visualization, X. citri wt, ΔenvC and ΔenvC pMAJIIc-envC cells were cultivated under the same conditions described above and stained with DAPI using the protocol described in Ref [22 (link)]. Bacterial visualization was conducted using an Olympus BX61 microscope equipped with a monochromatic OrcaFlash2.8 camera (Hamamatsu, Japan) and TxRed and DAPI filters. Data collection and analysis were carried out using the CellSens Version 11 software (Olympus). Statistical analyses were conducted using GraphPad Prism version 6.
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2

Temperature Shift Assay of Xanthomonas

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Wild‐type Xcc, and the mutants Xcc amy::pPM2a‐zapA and Xcc parB::pAPU3 were cultivated as described in the growth curve section. Six flasks were prepared for each strain to be tested and when the cultures reached the OD600 nm of ~0.4, three flasks were subjected to a 6 h temperature shift at 20°C, 37°C, 40°C, 42°C, or 45°C, while the remaining three flasks were kept at 30°C to serve as internal experimental control. Right at the end of the shifts, three slides were prepared, one for each of the triplicates, for microscope analyses (20 μL of cell culture were dropped onto 1X PBS/1% agarose‐covered slides). Cells were visualized in the magnification of 100× using an Olympus BX‐61 microscope equipped with an orca‐flash2.8 camera (Hamamatsu, Higashi‐ku, Hamamatsu City, Japan). Images were captured and processed using the software CellSens Dimension ver. 11 (Olympus Latin America, INC., Miami, Florida, USA).
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3

Leptospira Microscopy and Motility

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Mid-log cultures of leptospires were observed by dark-field microscopy with or without 1% methylcellulose (Sigma), using ×20 to ×200 magnification with an Olympus BX-53 139 microscope connected to a Hamamatsu Orca Flash 2.8 camera. Images were taken with the CellSense Software (Olympus) and videos were recorded with the MicroManager 1.4 software (μManager). Images were post-treated and analyzed with the ImageJ software (ImageJ). Three images of each strain containing approximately 90 bacteria were used to measure cell length. Motility of Leptospira strains was also evaluated in triplicate onto 0.5% agar EMJH plates by inoculating 5 μl of mid-log phase cultures (OD450nm of approximately 0.3). Plates were incubated at 29°C for 10 days.
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4

Time-lapse Microscopy of ESC Colony Formation

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The temporal evolution of ESC colony formation and growth was assessed by means of time-lapse microscopy. Briefly, experiments started 1 h after cell seeding on patterned and control substrates. Cell populated samples were placed in an incubator (Okolab, Naples, Italy) mounted on the stage of an Olympus IX81 microscope. At least six regions per substrate were randomly acquired in bright field and in epifluorescent mode for 72 h at 2 frame/h rate. Images were collected with a 10× objective lens (numerical aperture 0.3) and were acquired with a digital ORCA- Flash 2.8 camera (Hamamatsu). In these experiments, ESCs were observed for 72 h after RA addition.
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5

Embryonic Mechanoreceptor Acquisition

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Pacinian and Meissner corpuscles acquire functionality several days before hatching and become capable of producing a rapidly adapting discharge in the innervating mechanoreceptor in response to touch as early as embryonic day 24 (E24) to E26, similar to corpuscles from adult animals (19 (link)–21 (link)). A patch of skin (~5 mm by 10 mm) from E24 to E26 duck embryo was peeled from the dorsal surface of the upper bill, and the epidermis was mechanically removed to expose Pacinian and Meissner corpuscles. Skin was incubated in collagenase P (2 mg/ml; Roche) in Krebs solution (117 mM NaCl, 3.5 mM KCl, 2.5 mM CaCl2, 1.2 mM MgCl2, 1.2 mM NaH2PO4, 25 mM NaHCO3, and 11 mM glucose, saturated with 95% O2 and 5% CO2 to pH 7.3–7.4 at 22°C) for 20 to 25 min, washed three times with Krebs, and imaged external side up on an Olympus BX51WI upright microscope equipped with an ORCA-Flash 2.8 camera (Hamamatsu).
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6

Evaluating Membrane Integrity of S. aureus with Live/Dead Assay

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The assay was performed using Staphylococcus aureus (ATCC 29213), an MSSA strain. Bacterial cells were cultivated in solid TSA broth (tryptone soya) at 36 °C and stirred at 200 rpm. S. aureus (106 cells) was exposed to LCC at its MIC value (12.5 µg/mL) in DMSO for 15 min in a 1.5 mL microcentrifuge tube in a total volume of 100 μL of TSA medium. Next, 900 μL of the TSA medium was added to the tube to dilute the compound and stop the reaction [59 (link)]. Cells were stained with the Live/Dead BacLight Kit (Thermo-Scientific® L7012, Carlsbad, CA, USA), which is composed of two nucleic acid dyes: SYTO9, which stains all cells, and propidium iodide, which penetrates cells with damaged membranes [60 (link)]. The stained cells were immobilized on agarose-covered slides as described by Martins [61 (link)]. Untreated S. aureus cells with intact membranes were used as negative controls, and S. aureus cells exposed to nisin (Sigma-Aldrich® N5764, St. Louis, MO, USA) were used as positive controls for membrane damage [62 (link)]. Microscopic analyses were carried out using an Olympus BX-61 microscope, equipped with a monochromatic OrcaFlash-2.8 camera (Hamamatsu, Japan), and the software CellSens Dimension Version 11 (Olympus).
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7

Bacterial Induction and Microscopic Visualization

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Bacteria were cultivated in 5.0 mL of NB medium for approximately 16 hours at 30°C and 200 rpm. The cultures were adjusted to the OD 600 nm of 0.1 with NB medium for a final volume of 5.0 mL and subsequently cultivated in the same conditions until the OD 600 nm of 0.3. At this point, arabinose was added to the medium to a final concentration of 0.05% and the culture was kept at 30°C and 200 rpm. After a minimum of two hours of induction, drops of 5 μL of cell culture were placed on microscope slides covered with a slide cover slip as described by Martins et al. [23 (link)]. Bacteria were immediately visualized using an Olympus BX61 microscope equipped with a monochromatic OrcaFlash2.8 camera (Hamamatsu, Japan) and TxRed filter. Data collection and analysis were performed with the software CellSens Version 11 (Olympus).
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8

Tracking Cell-Induced Pillar Displacements

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Cells were spreading on pillar arrays coated with fibronectin (10 μg/ml, Roche). Time lapse imaging of pillars was performed with bright-field microscopy using an Orca-flash 2.8 camera (Hamamatsu) attached to an inverted microscope (Olympus IX81) maintained at 37°C running MicroManager software (Edelstein et al., 2010 (link)). Images were recorded at 1 Hz using a ×100 objective (1.4 NA oil immersion, Olympus). Videos were processed with ImageJ (National Institutes of Health) using the Nano Tracking plugin to track the position of pillars. The time-series positions of all pillars in contact with the cell were fed into a MatLab program (MathWorks) to generate displacement maps as explained previously (Wolfenson et al., 2016 (link); Saxena et al., 2017a (link)).
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9

Intravital and Ex Vivo Imaging Protocols

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Intravital images were acquired using a 10X (water, NA = 0.3) objective on an upright Nikon Eclipse LV100 microscope coupled with a Hamamatsu ORCA-Flash 2.8 camera. Ex vivo tissues and fixed immunohistochemicistry tissues were imaged using 4X (dry, NA = 0.1), 10X (dry, NA = 0.3), and 20X (oil, NA = 1.4) objectives on an inverted Olympus IX70 microscope coupled with a Photometrics CoolSNAP EZ camera.
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10

Time-lapse Imaging of Embryo Development

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For live-imaging, embryos were cultured in a 35 mm dish by the New culture method at 37 °C. Time-lapse images were recorded with Nikon TIRF/Spinning Disk microscope (Nikon Ti inverted fluorescent Microscope with CSU-22 spinning disc confocal) supported by Prime 95B Scientific CMOS camera (Photometrix), Nikon Widefield Epifluorescence inverted microscope (Nikon Ti inverted fluorescent Microscope with CSU-W1 large field of view) supported by ANDOR iXon camera and Nikon Eclipse TE2000-E supported by Hamamatsu ORCA-Flash 2.8 camera. The acquisition time was every 3 min using Nikon Elements Advance Research software V4.00.07. All time-lapse images were recorded every 3 min.
Immunostained chick embryos were imaged by Leica TCS SPE confocal microscope and Crest LFOV Spinning Disk with Nikon Ti2-E. Fixed ISH samples were imaged by Leica MZ16F microscope with Leica DFC300 Fx camera and Leica FireCam V.3.4.1 software.
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