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10 protocols using motorized stage

1

Fluorescent Live-Cell Microscopy Protocol

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Images were obtained using a Nikon Ti inverted microscope equipped with a Nikon motorized stage with an OkoLab gas incubator with a slide insert attachment, an Andor Zyla 4.2 Plus sCMOS camera, Lumencore SpectraX LED Illumination, Plan Apo lambda 100x/1.45 NA Oil Ph3 DM objective lens, and Nikon Elements 4.30 acquisition software. Images in the green and red channels were taken using Chroma 49002 and 49008 filter cubes, respectively.
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2

Live-cell imaging of cellular adhesion

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Cells were imaged on either an Olympus IX-81 or Nikon Ti-2 inverted microscope fitted with TIRF optics. The IX-81 microscope used a 60 × 1.49 NA objective (Olympus) and an Orca Flash 4.0 sCMOS camera (Hamamatsu). Cells were illuminated with solid-state lasers (Melles Griot) with simultaneous acquisition by a DV-2 image splitter (MAG Biosystems). The microscope was maintained at 37 °C with a WeatherStation chamber and temperature controller (Precision Control) and images were acquired using Metamorph software. The Nikon Ti2 microscope was equipped with a motorized stage (Nikon), automated Z focus control, LU-N4 integrated four-wavelength solid state laser setup, TIRF illuminator (Nikon), quad wavelength filter cube, NI-DAQ triggering acquisition (National Instruments), an Orca Flash 4.0 sCMOS camera (Hamamatsu), and triggerable filter wheel (Finger Lakes Intstrumentation) with 525/50 and 600/50 wavelength emission filters. Cells were seeded on autoclaved 25 mm #1.5 round coverslips coated with 1 mL matrigel (80 µg/ mL) or recombinant Vitronectin-N diluted in PBS (Thermo Fisher). Cells were maintained at 37 °C with a stage top incubator (OKO Lab) and images were acquired with Nikon Elements.
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3

Time-Lapse Imaging of Translocating Cells

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Time-lapse microscopy of translocating cells was performed as previously described (4 (link)). In brief, chamber slides were filled with soft agar medium (Todd-Hewitt broth–0.3% agar) and the medium was allowed to solidify. A coverslip inoculated with a tiny dot of cells at the center was inverted and placed onto the chamber filled with medium and mounted with nail polish. Imaging was performed at the interface of agar medium and coverslip. Phase-contrast microscopy and time-lapse imaging were performed using an inverted Nikon Eclipse Ti microscope system (Nikon, Tokyo, Japan) equipped with a motorized stage (Nikon), an Andor Zyla 5.5 scientific complementary metal oxide semiconductor (sCMOS) camera, a Perfect Focus system, and automated controls (NIS-Elements; Nikon). The microscope was located inside a Coy anaerobic chamber under the conditions described above. Using a Nikon 100× 1.40-numerical-aperture (NA) lens objective, surface translocation was monitored and recorded every minute for 7 to 10 days and every 15 ms for 2 to 3 min for recording fast movements.
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4

High-Resolution Fluorescence Microscopy Setup

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A Nikon inverted Ti‐E microscope (Nikon, Amsterdam, Netherlands) with a Nikon Perfect Focus System (PFS) hardware auto‐focus was used. All images were acquired using either a Photometrics CoolSnap HQ2 CCD camera (Photometrics, Tucson, AZ, USA) or a Photometrics Prime sCMOS camera (Photometrics, Tucson, AZ, USA). The microscope stage was enclosed in an incubator (Solent Scientific, Segensworth, UK) which was set to 37°C for all experiments. Illumination was provided by a LED lamp (CoolLED, Andover, UK). Epifluorescence was provided by a Lumencore Solar II light engine (Lumencore, Beaverton, OR, USA). Chroma filters (Chroma, Bellows Falls, USA) #41027 for the RFP channel, #49003 for the YFP channel and #49001 for the CFP channel were used. All experiments were done with a phase 100x Plan Apo (NA 1.4) objective (Nikon, Amsterdam, Netherlands). Metamorph (Molecular Device, Sunnyvale, CA, USA) controlled the camera, the motorized stage (Nikon, Amsterdam, Netherlands) and the microscope.
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5

Monitoring Endothelial to Hematopoietic Transition

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Endothelial to hematopoietic transition (EHT) was monitored by time-lapse microscopy using fluorescent optics. H1ESCs line expressing VE-Cadherin-Td tomato and CD43-GFP dual reporter were transduced with GATA2+ETV2 lentiviral constructs and cultured for 4 days until endothelial cluster were formed [13 (link)]. Time-lapse confocal imaging was performed over two days to capture blood formation. Time lapse movies were recorded using Nikon Eclipse Ti-E configured with an A1R confocal system, motorized stage (Nikon Instruments Inc. Melville, NY), and Tokai-Hit Stage Top Incubator (Tokai Hit CO., Ltd., Shizuoka-ken, Japan) at 37 °C and 5% CO2. Images were acquired using Nikon Elements (NIS – element C) imaging software for every 5 min with CFI Plan Fluor DLL 10× NA 0.5 WD 2.1MM objective (Nikon Instruments Inc. Melville, NY). The time-lapse serial images were converted to Quick-time movies (.mov) and analyzed using ImageJ software (NIMH, Bethesda, MD).
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6

Quantifying Cell-Bacteria Interactions

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All images were acquired using an inverted Nikon Ti2‐E widefield fluoresence microscope using a Plan Apo 20X objective (NA = 0.75). Fluorescence was excited with the SPECTRA X light engine® (Lumencore inc, Beaverton, OR, USA) and collected with a Nikon DS‐Qi2 CMOS controlled with NIS‐Elements AR (v5.21.02). Multiple stage coordinates were automatically generated and imaged using NIS‐Elements JOBs and a Nikon motorized stage.
For image analysis, cells (BV421) and bacteria (Green, FITC) were segmented based on a background threshold algorithm for each channel separately. The cell masks were dilated to account for the whole cell area. Interaction between cells and bacteria was quantified by generating masks where cell and bacteria overlap, and the area and intensity profiles (mean, median, std) within this region were measured. Described image analysis was written in Julia (v1.6.0).
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7

Microscopic Imaging of Stress-Induced Morphology

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Overnight cultures of the above strains were diluted to OD600 of 0.05 in 3 mL of M9 medium supplemented with 0.2% casamino acids, 0.2% maltose, and 25 μM IPTG. Cells were grown at 30°C until the OD600 reached 0.2, at which point the cells were spotted onto filter discs placed on LB agar medium supplemented with 100 μM IPTG, with or without 10 mM DTT. After 6 hours growth at 30°C, cells were suspended in liquid LB medium, fixed, and imaged using phase contrast microscopy. Scale bar, 5 μm. Where indicated, cells were fixed in 2.6% formaldehyde with 0.04% glutaraldehyde at room temperature for 1 h, followed by storage at 4°C for 24 hours. Prior to imaging, cells were immobilized on 2% agarose pads and covered with #1.5 coverslips.
Imaging was performed on a Nikon Ti inverted microscope equipped with a 100x Plan Apo 1.4 NA phase contrast objective, Andor Zyla 4.2 sCMOS camera, and Nikon motorized stage. Acquisition software was NIS Elements 4.30. The purchase of this microscope was funded in part by grant S10 RR027344–01. Microscopy was performed with the support of Microscopy Resources on the North Quad (MicRoN) at Harvard Medical School. The ImageJ plugin MicrobeJ41 was used segment cells and measure cell dimensions. Statistical significance was determined using a two-way ANOVA followed by Tukey’s Multiple Comparisons Test.
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8

Single Molecule Imaging Microscopy

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Single molecule imaging experiments were performed at room temperature (23 °C) using an inverted Nikon Ti2 microscope using a 100 x oil immersion Nikon TIRF objective (1.49 NA). The x-axis and y-axis positions were controlled using a Nikon motorized stage, joystick, and Nikon’s NIS element software. Fluorescently labeled proteins were excited with one of three diode lasers: a 488 nm, a 561 nm, or 642 nm (OBIS laser diode, Coherent Inc, Santa Clara, CA). The lasers were controlled with a Vortran laser launch and acousto-optic tuneable filters (AOTF) control. Excitation and emission light was transmitted through a multi-bandpass quad filter cube (C-TIRF ULTRA HI S/N QUAD 405/488/561/642; Semrock) containing a dichroic mirror. The laser power measured through the objective for single particle visualized was 1–3 mW. Fluorescence emission was captured on an iXon Life 897 EMCCD camera (Andor Technology Ltd., UK) after passing through one of the following 25 mm a Nikon Ti2 emission filters mounted in a Nikon emission filter wheel: ET525/50M, ET600/50M, and ET700/75M (Semrock).
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9

Widefield Epifluorescence Imaging of Intracellular Bacteria

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Images of internalized and extracellular bacteria were acquired using a widefield epifluorescent Nikon Ti2-E inverted microscope with Nikon SR Plan Apo IR 60xAC WI, NA = 1.27. Fluorescence was excited with the SPECTRA X light engine® (Lumencore Inc, Beaverton, OR, USA) and collected with DAPI (Exc. 379-405 nm, Em. 414-480 nm), FITC (Exc. 457-487 nm, Em. 503-538 nm), TRITC (Exc. 543-566 nm, Em. 582-636 nm) and Cy5 (Exc. 590-645 nm, Em. 659-73 6nm) filter cubes, all from Semrock. Images were acquired using Nikon DS-Qi2 CMOS controlled with NIS-Elements (v. 5.21.02). Multiple stage positions were collected using a Nikon motorized stage. For each data set, 3x3 20X magnification images were first collected, including z-stacks, allowing them to cover a wide area of the sample. From these images, multiple areas of interest were imaged at 60X and deconvolved using NIS-Elements (v 5.21.02) to remove out-of-focus light. After analysis of the deconvolved images, representative images were selected. Image gamma, brightness, and contrast were adjusted using NIS-Elements Viewer.
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10

Microscopic Imaging of Stress-Induced Morphology

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Overnight cultures of the above strains were diluted to OD600 of 0.05 in 3 mL of M9 medium supplemented with 0.2% casamino acids, 0.2% maltose, and 25 μM IPTG. Cells were grown at 30°C until the OD600 reached 0.2, at which point the cells were spotted onto filter discs placed on LB agar medium supplemented with 100 μM IPTG, with or without 10 mM DTT. After 6 hours growth at 30°C, cells were suspended in liquid LB medium, fixed, and imaged using phase contrast microscopy. Scale bar, 5 μm. Where indicated, cells were fixed in 2.6% formaldehyde with 0.04% glutaraldehyde at room temperature for 1 h, followed by storage at 4°C for 24 hours. Prior to imaging, cells were immobilized on 2% agarose pads and covered with #1.5 coverslips.
Imaging was performed on a Nikon Ti inverted microscope equipped with a 100x Plan Apo 1.4 NA phase contrast objective, Andor Zyla 4.2 sCMOS camera, and Nikon motorized stage. Acquisition software was NIS Elements 4.30. The purchase of this microscope was funded in part by grant S10 RR027344–01. Microscopy was performed with the support of Microscopy Resources on the North Quad (MicRoN) at Harvard Medical School. The ImageJ plugin MicrobeJ41 was used segment cells and measure cell dimensions. Statistical significance was determined using a two-way ANOVA followed by Tukey’s Multiple Comparisons Test.
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