This project is funded by UF Gatorade Award Start-up Package (X. T.), the UFHCC Pilot Award (X. T. and Dr. Dietmar Siemann), UF Opportunity Seed Fund (X. T.), and UFHCC University Scholars Program (H. Y. Wang). We sincerely appreciate the intellectual discussions with and the technical support from Dr. Jonathan Licht (UFHCC), Dr. Rolf Renne (UFHCC), Dr. Christopher Vulpe (UFHCC), Dr. Blanka Sharma (BME), Dr. Mark Sheplak (MAE &#38; ECE), Dr. Daniel Ferris (BME), Dr. Malisa Sarntinoranont (MAE), Dr. Ashok Kumar (MAE), Dr. Benjamin Keselowsky (BME), Dr. Brent Gila (RSC), Dr. Philip Feng (ECE), Dr. Gregory A. Hudalla (BME), Dr. Steven Ghivizzani (OSSM), Dr. Yenisel Cruz-Almeida (CDBS), Dr. Roger Fillingim (CD-BS), Dr. Robert Caudle (OMS), Dr. John Neubert (DN-OR), Dr. Justin Hiliard (Neurosurgery), Dr. Tian He (Harvard University), Dr. Youhua Tan (Hong Kong Polytechnic University), Dr. Jessie L-S Au (Institute of Quantitative Systems Pharmacology), Dr. David Hahn (University of Arizona), and Support Team of Nikon (Drs. Jose Serrano-Velez, Larry Kordon, and Jon Ekman). We are deeply grateful for the effective support from all members of Tang&#39;s, Yamaguchi&#39;s, Sharma&#39;s, Au&#39;s, Siemann&#39;s, and Guan&#39;s research laboratories and all staff members of the UF MAE Department.

1. Maintenance of CRISPR/Cas9-engineered B2B cells
<ol>
	<li>Culture B2B cells in a T25 flask with RPMI-1640 supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.</li>
	<li>Maintain the B2B cells in a humidified incubator at 37 &#176;C with 5% CO2.</li>
	<li>Subculture the B2B cells when the confluency reaches 70% to 80%.</li>
	<li>Store the B2B cell line in RPMI-1640 culture medium with 10% (v/v) DMSO in a -80 &#176;C freezer.</li>
	<li>Use the B2B cells with a passage number less than 10 in the experiments.</li>
</ol>
2. Cell culture
<ol>
	<li>Seed the cells onto a glass-bottom Petri dish.
	<ol>
		<li>Move the flask that contains B2B cells inside from the incubator to the biosafety cabinet.</li>
		<li>Remove the culture medium in the flask using an aspirating pipette with a vacuum pump connected.</li>
		<li>Wash the flask with 2 mL of phosphate-buffered saline (PBS).&#8239;</li>
		<li>Remove PBS using the aspirating pipette.</li>
		<li>Add 0.5 mL of 0.05% Trypsin solution to detach cells from the bottom of the flask substrate.</li>
		<li>Put the flask in the incubator for 5 min.</li>
		<li>Move the flask to the biosafety cabinet. Add 5 mL of new culture medium into the flask and pipette the solution up and down.</li>
		<li>Deposit 50 &#181;L of the medium with cells (300 cells/&#181;L) onto the glass-bottom Petri dish. Add 2 mL of culture medium into the Petri dish.</li>
		<li>Place the Petri dish into the incubator. Wait for 12 h for the cells to attach.</li>
	</ol>
	</li>
	<li>Culture the cells with magnetic microbeads.
	<ol>
		<li>Weigh 0.2 g of 7 &#181;m mean diameter carbonyl iron microbeads (hereafter called 7 &#181;m microbeads, see the Table of Materials).</li>
		<li>Use a pipette to suspend the microbeads in 1 mL of RPMI-1640 culture medium.</li>
		<li>Take the Petri dish with B2B cells to the biosafety cabinet.</li>
		<li>Add 200 &#181;L of the medium containing microbeads into the Petri dish. 
		NOTE: Add the medium quickly to avoid precipitation of the microbeads.</li>
		<li>Put the Petri dish back in the incubator until microbeads are internalized by the cells. Check the internalization every 6 h to determine the optimal time for internalization for different cell lines.</li>
		<li>To check the internalization, perform confocal fluorescence imaging to visualize the microbead, nuclear, and cell boundary. If the microbead is internalized by the cell, it will be within the cell boundary.</li>
	</ol>
	</li>
</ol>
3. Visualization of nucleus
<ol>
	<li>Warm 1.5 mL of the culture medium in the incubator for 15 min.</li>
	<li>Turn off the light of the biosafety cabinet. Take the Petri dish that contains the cell, warmed culture medium, nuclear stain, and Verapamil HCl into the biosafety cabinet. 
	NOTE: Nuclear staining components are sensitive to light. Avoid exposure to light during operation.</li>
	<li>Dilute 1000x nuclear stain by DMSO to 100x.</li>
	<li>Dilute 100 mM Verapamil HCl by DMSO to 10 mM.</li>
	<li>Add 15 &#181;L of 100x nuclear stain and 15 &#181;L of 10 mM Verapamil HCl to 1.5 mL of culture medium. Mix well by pipetting up and down.</li>
	<li>Remove the culture medium from the Petri dish. Add the culture medium containing nuclear staining into the Petri dish.</li>
	<li>Put the cells back in the incubator for over 2 h.</li>
</ol>
4. Preparation of the magnetic force application hardware
<ol>
	<li>3D print all parts using acrylonitrile butadiene styrene (ABS) and assemble them following the CAD design (Figure 1A). The CAD design is included in the Table of Materials.</li>
	<li>Use double-sided tape to attach the magnet to the magnet-moving device (Figure 1A).</li>
	<li>Set the magnet-moving device next to the microscope stage. Use the three knobs to adjust the spatial location of the magnet until it can move above the Petri dish between 13 mm and 120 mm. 
	NOTE: Ensure the upper limit of the distance between the magnet and Petri dish is as large as possible to avoid unwanted force application on the magnetic microbeads. 120 mm is the maximum value in this experimental setup. Ensure that the magnet does not interfere with microscope parts, including objectives and motorized stages.</li>
	<li>Set the magnet to the highest z-position (at 120 mm).</li>
</ol>
5. Force application and live-cell imaging
<ol>
	<li>Set up of the environment chamber for long-term imaging
	<ol>
		<li>Apply 75% ethanol solution to thoroughly sterilize and clean the environment chamber.</li>
		<li>Place the environment chamber onto the motorized stage of the inverted microscope.</li>
		<li>Open the CO2 tank and set the CO2 inflow rate to 160 mL/min.</li>
		<li>Adjust the temperature of the chamber to 44 &#176;C (Top), 42 &#176;C (Bath), and 40 &#176;C (Stage).</li>
		<li>Add 20 mL of purified water into the bath of the environment chamber to maintain 90% humidity.</li>
		<li>Take out the glass-bottom Petri dish that contains target cells from the tissue culture incubator and place it into the chamber.</li>
		<li>Apply the metal clamp of the environment chamber to fix the Petri dish position. 
		NOTE: The Petri dish must be clamped tightly in the chamber because the magnetic force may move the dish if it is not clamped.</li>
		<li>Close the lid of the chamber.&#8239;</li>
	</ol>
	</li>
	<li>Optimization of imaging parameters
	<ol>
		<li>Optimize the pinhole size: The pinhole blocks the out-of-focus photons. A larger pinhole size yields more out-of-focus photons but a brighter image. A smaller pinhole size yields a more focused and dimmer image. Make sure to optimize the pinhole size to get in-focus confocal images with the appropriate signal-to-noise ratio.</li>
		<li>Optimize the laser intensity: The laser intensity determines the intensity of excitation and thus emission light. The low laser intensity gives a low signal-to-noise ratio. Too high a laser intensity will cause photobleaching. Adjust the laser intensity accordingly.</li>
		<li>Optimize the step size and steps: Steps and step size determine how many images will take in a Z-stack. Smaller step sizes and more steps will increase the Z-stack resolution but will also increase photobleaching. In this experiment, 1 &#181;m step size was used for the cells with ~15 &#181;m cell height.</li>
		<li>Optimize the exposure time: The exposure time determines how long the cell will be exposed to the excitation laser. A low exposure time will decrease the signal-to-noise ratio. A high exposure time will cause photobleaching. An exposure time of 1 frame per 4 s was used in this experiment.</li>
		<li>Optimization of imaging parameters: Change one of the four parameters iteratively and keep the other parameters consistent. Each time, measure the YAP N/C ratio of each image and compare the YAP N/C ratio change to determine the photobleaching level. Repeat the optimization process until achieving a balance between the signal-to-noise ratio, imaging speed, and photobleaching.</li>
		<li>Define the imaging configurations using the optimized imaging parameters for faster imaging settings during the experiments. 
		NOTE: Configurations used in this study are described in section 5.3 of imaging parameters. To optimize imaging parameters of configurations in section 5.3, use the same method as in step 5.2.5.</li>
	</ol>
	</li>
	<li>Small force application and confocal imaging 
	NOTE: Nikon Ti2-E microscope was used for imaging in this study, and detailed steps for image acquisition are given below.
	<ol>
		<li>Open the inverted microscope. Open the software application Elements.</li>
		<li>Define configuration magnetic_find. Check only FITC channel. Set PMT HV = 70, Offset = 0, Laser intensity = 10. Set the scanning speed to 1 frame per 2 s by clicking the 1/2 button. Set pinhole size to 1.2 AU by clicking the 1.2 A.U. button. This configuration will be used in step 5.3.5.</li>
		<li>Define configuration magnetic_YAP_Nucleus. Check FITC channel. Set PMT HV = 70, Offset = 0, Laser intensity = 10. Set the scanning speed to 1 frame per 4 s by clicking the 1/2 button. Set pinhole size to 1.2 AU by clicking the 1.2 A.U. button. To image the nucleus boundary and nuclear stain intensity, check Cy5 channel. Set PMT HV = 70, Offset = 0, Laser intensity = 10. The pinhole size is optimized for 3D YAP imaging. Do not click the 1.2 A.U. button again after checking the Cy5 channel. This configuration will be used in step 5.3.7.</li>
		<li>Turn on DIA through Elements if necessary. Open SpinView, use a bright-field, and adjust the focus of the object to get a clear in-focus image of cells. Use a 10x objective to find appropriate multiple single cells in three conditions: with a single microbead inside, with multiple microbeads inside, and without any microbead inside. Switch to 40x objective. Name this position with the appropriate position number.</li>
		<li>Open Elements. Click on magnetic_find. Click the Remove Interlock button.</li>
		<li>Click Scan and adjust the Z-position of the focal plane. Click the Top and Bottom buttons to set the lower and upper limit for the Z-stack of the selected cells. Stop scanning by clicking Scan again.</li>
		<li>Switch to magnetic_YAP_Nucleus configuration. Set file name as before_small_force.nd2. Click on the Run button with the recorded Z-stack.</li>
		<li>Switch to the right light path and turn on DIA. Open SpinView and click on the Recording button. Meanwhile, spin the knob of the magnet-moving device to move the magnet down to 46 mm above the Petri dish bottom. Save bright-field image sequence or video. Check the video to confirm microbeads show displacement induced by magnetic force.</li>
		<li>Repeat steps 5.3.5-5.3.7; set the file name to after_small_force.nd2.</li>
		<li>Switch to the right light path and turn on DIA. Next, open SpinView and click on the Recording button. Meanwhile, spin the knob of the magnet-moving device to move the magnet up to 120 mm above the Petri dish bottom. Save bright-field image sequence or video.</li>
		<li>Repeat steps 5.3.5-5.3.7 and set the file name to before_large_force.nd2.</li>
	</ol>
	</li>
	<li>Large force application and confocal imaging
	<ol>
		<li>Remove the lid of the environment chamber to allow the magnet to reach 13 mm above the Petri dish bottom.</li>
		<li>Switch to the right light path and turn on DIA. Open SpinView and click on the Recording button. Meanwhile, spin the knob of the magnet-moving device to move the magnet down to 13 mm above the Petri dish bottom. Save bright-field image sequence or video. Check the video to confirm microbeads show displacement induced by magnetic force.</li>
		<li>Repeat steps 5.3.5-5.3.7 and set the file name to after_large_force.nd2.</li>
		<li>Switch to the right light path and turn on DIA. Next, open SpinView and click on the Recording button. Meanwhile, spin the knob of the magnet-moving device to move the magnet up to 120 mm above the Petri dish bottom. Save bright-field image sequence or video.</li>
		<li>Repeat steps 5.3.5-5.3.7; set the file name to retract_large_force.nd2.</li>
		<li>Close the lid of the environment chamber.</li>
	</ol>
	</li>
	<li>Repeat steps 5.2 and 5.3 for multiple fields of view to obtain more data if needed.</li>
</ol>
6. Image processing and data analysis
<ol>
	<li>Quantification of YAP N/C ratio
	<ol>
		<li>Open Fiji ImageJ. Open the .nd2 images taken in step 5.</li>
		<li>Click on Analyze &#62; Set Measurements. Check Area, Integrated Density, Mean Grey Value, and Shape Descriptors.</li>
		<li>Use the Cy5 channel to identify the nucleus. Click on Freehand Selections to use the free-selection tool to outline the nucleus. Also, check the automatic nuclear mask macro in ImageJ (see the Table of Materials).</li>
		<li>Click Analyze &#62; Measure in the FITC channel. The measured value of the Mean is the average nuclear YAP intensity DN.</li>
		<li>Use the Cy5 channel to identify the nucleus. Use the FITC channel to identify the cell. Click Freehand Selections to use the free-selection tool to select a region of interest within the cytoplasm and avoid the magnetic microbead. This region of interest must not include the nucleus.</li>
		<li>Click Analyze &#62; Measure in the FITC channel. The measured value of the Mean is the average cytoplasmic YAP intensity DC.</li>
		<li>Calculate the YAP N/C ratio = DN / DC.</li>
	</ol>
	</li>
	<li>Quantification of nuclear shape and normalized nuclear stain intensity
	<ol>
		<li>Open Fiji ImageJ. Open the .nd2 images taken in step 5.</li>
		<li>Click on Analyze &#62; Set Measurements. Check Area, Integrated Density, Mean Grey Value, and Shape Descriptors.</li>
		<li>Use the Cy5 channel to identify the nucleus. Click on Freehand Selections to use the free-selection tool to outline the nucleus.</li>
		<li>Click on Analyze &#62; Measure in Cy5 channel. The measured value of the Mean is the nuclear stain intensity. The measured value of Circ. is nuclear circularity.</li>
		<li>To compare the nuclear stain intensity at different force state, all nuclear stain intensity is divided by the nuclear stain intensity in &#34;before_small_force.nd2&#34; to generate the normalized nuclear stain intensity.</li>
	</ol>
	</li>
</ol>

There are no conflicts of interest to declare.

Internalization of magnetic microbeads (section 2.2) is critical because extracellular microbeads cannot apply force directly to the nucleus. Force application and imaging (section 5.3)&#160;are&#160;critical steps in this experiment, and the force needed to deform the nucleus and induce meaningful biological consequences might be sample-dependent. The force magnitude in this experiment (0.8 nN and 1.4 nN) can be further increased to trigger nuclear mechano-sensing in less sensitive cells.
To ...

This study aims to develop and apply a new technique to elucidate nucleus mechanobiology by combining the magnetic actuators that apply mechanical force directly on the cell nucleus and the confocal fluorescence microscopy that simultaneously images the structural and functional subcellular changes. Cells sense extracellular biophysical signals including tissue stiffness1,2,3,4, interstitial fluid pressure and shear stress5,6,7, surface topology/geometry8,9,10,11,12, and tension/compression stress13,14,15,16. Biophysical signals are converted into biochemical signals and trigger potential downstream changes of gene expression and cell behaviors-a process known as mechanotransduction17,18,19,20,21,22,23,24,25,26,27. To study mechanotransduction processes, a myriad of techniques have been developed to apply mechanical force on the cells, such as atomic force microscopy28, cell stretching device29, bio-MEMS (micro-electromechanical systems) force sensor15,30,31, shear rheology32, and Stereo Vision System33. A recent review summarizes the approaches to apply extracellular mechanical cues and interfere with mechanosensing34. To date, most of these methods apply force on the cell plasma membrane, and cells directly receive these extracellular biophysical signals via membrane receptors such as integrin, cadherin, ion channels, and G-Protein-coupled receptors. Subsequently, they transmit the signal to the intracellular cytoskeleton and nucleus. For example, using yes-associated protein (YAP) translocation as an indicator of mechano-sensing, cells are shown to sense the mechanical signals of substrate stiffness and extracellular tension from the cell membrane and transmit them through the cytoskeleton into the nucleus to induce YAP cytoplasm-to-nucleus translocation28,35.
Recent evidence suggests that the cell nucleus itself is an independent mechano-sensor8,36,37. This is proven by experiments performed on the isolated nucleus harvested from cells, where it was revealed that nuclei adaptively change their stiffness in response to the mechanical force directly applied on them36. During many physiological conditions, nuclei in both tumor and healthy cells sense extracellular biophysical signals and change their mechanical properties and assemblies38,39,40. For example, upon extravasation, the nuclear stiffness of tumor cells decreases and maintains softness for over 24 h38. During migration through confined interstitial space, the nuclei of tumor cells frequently lose and recover their structural integrity39. However, the way in which the nucleus senses the biophysical signal is unknown, although several nuclear-envelope proteins and families of proteins have been found to be involved, such as Lamin A/C and linker of nucleoskeleton and cytoskeleton (LINC) complex38,41. Hence, new non-invasive methods that can directly apply force to the nucleus will decouple the effect of force transmission from the cell-plasma membrane and cytoskeleton, and will help elucidate the previously inaccessible molecular mechanisms of nuclear mechano-sensing.
Research that employed optical tweezers to manipulate organelles42 and microbeads injected into cells43 showed the technological capability of directly applying force on the nucleus. However, the optical-tweezer technique has several limitations: (1) low throughput-optical tweezers often only manipulate one cell or microbead at a time; and (2) potential photodamage and temperature artifact-deformation of nuclear requires tens of pN36, and the corresponding necessary laser power is about 10 mW per pN44,45. Such laser intensity is sufficient to trigger photodamage in the cells and perturb cell functions during the experiment46.
Magnetic force applied through microbeads within living cells shows the potential to directly apply force on the nucleus and overcomes the limitations of optical tweezers. Once microbeads are delivered into the cytoplasm, a magnetic field can exert a magnetic force on multiple microbeads simultaneously in a high-throughput manner. The magnetic field does not influence cell functions47,&#160;but generates force from pN to nN, which is enough to induce nuclear deformation36,48,49.&#160;To date, manipulation of magnetic microbeads has been applied on cell plasma membrane48, inside the cytoplasm50, on F-actin51, inside the nucleus47, and on the isolated nucleus36. However, magnetic manipulation of microbeads has never been used to apply direct mechanical force on the nuclear envelope to study mechanotransduction in the nucleus.
In this paper, a simple technique is developed to non-invasively deliver magnetic microbeads into the cytoplasm and use these microbeads to apply mechanical force on the nucleus (Figure 1). Here, CRISPR/Cas9-engineered human normal B2B cell lines that endogenously express mNeonGreen21-10/11-tagged YAP are used to validate the method. YAP is a mechano-sensitive protein, and the translocation of YAP is regulated by nuclear mechano-sensing14,28. The CRISPR/Cas9-regulated knock-in approach was chosen to tag endogenous YAP with a fluorescent protein (FP) mNeonGreen21-10/11. Although CRISPR editing is known to have incomplete efficiency and off-target effect, the protocols in previous publications integrated fluorescence sorting to select for correct open reading frame insertion52,53,54. With this additional layer of selection, no off-target tagging event was observed in 20+ cell lines previously generated52,53,54,55. This is a split fluorescent protein construct, but in principle, any expressible fluorescent tag could be usable. This labeling approach is superior to transgene or antibody methods. First, unlike the transgene expression, the tagged protein maintains single-copy gene dosage and expresses in the physiological context of the native gene regulatory network, limiting deviations in protein concentration, localization, and interaction. The tagging method used in this study achieves over an order-of-magnitude higher throughput and efficiency than full FP tagging. It also avoids challenges associated with immunofluorescence due to fixation artifacts and the limited availability of high-quality, high-specificity antibodies. Second, the approach used in this paper does minimum perturbation to the cell physiology and enables the real-time revelation of all endogenous YAPs authentically. In contrast, other common transgene methods often lead to overexpression of YAP. The resulting artificial distribution can potentially cause cytotoxicity and affect mechano-sensing of cells56,57,58.
This study presents a protocol to directly apply force on the nucleus through magnetic microbeads delivered into the cytoplasm and to conduct simultaneous live-cell fluorescent imaging. In summary, the protocols presented here demonstrate how to (1) deliver magnetic microbeads into the cell while outside the nucleus, (2) manipulate the microbeads to apply magnetic force on the nucleus, (3) perform confocal fluorescent imaging of the cells during manipulation, and (4) quantitatively analyze the YAP nuclear/cytoplasm (N/C) ratio throughout the force application process. The results suggest that (1) through endocytosis, magnetic microbeads can be non-invasively delivered into the cytoplasm of B2B cells within 7 h (Figure 2 and Figure 3); and (2) quantified magnetic force directly applied on the nucleus (Figure 4, Figure 5, and Figure 6) alone can trigger diverse changes of YAP N/C ratio in CRISPR/Cas9-engineered B2B cells (Figure 7 and Figure 8).

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>0.05 % Trypsin</td>
			<td>Corning</td>
			<td>25-051-CI</td>
			<td></td>
		</tr>
		<tr>
			<td>25 cm2 flask</td>
			<td>Corning</td>
			<td>156340</td>
			<td></td>
		</tr>
		<tr>
			<td>7-&#181;m mean diameter carbonyl iron microbeads</td>
			<td>N/A</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>A1R confocal system</td>
			<td>Nikon</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Carbonyl Iron Powder CM</td>
			<td>BASF</td>
			<td>30042253</td>
			<td>Magnetic microbead</td>
		</tr>
		<tr>
			<td>Culture medium (RPMI-1640)</td>
			<td>Gibco</td>
			<td>11875093</td>
			<td></td>
		</tr>
		<tr>
			<td>Desktop Computer</td>
			<td>Dell</td>
			<td></td>
			<td>with Windows 10 operating system</td>
		</tr>
		<tr>
			<td>Environmental chamber TIZB</td>
			<td>Tokai Hit</td>
			<td>TIZB</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal bovine serum (FBS)</td>
			<td>Gibco</td>
			<td>26140</td>
			<td></td>
		</tr>
		<tr>
			<td>Fiji ImageJ</td>
			<td>National Institutes of Health and the Laboratory for Optical and Computational Instrumentation</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Glass-bottom petri dish</td>
			<td>MatTek</td>
			<td>P35G-1.5-14-C</td>
			<td></td>
		</tr>
		<tr>
			<td>Magnet</td>
			<td>K&#38;J Magnetics, Inc.</td>
			<td>D99-N52</td>
			<td></td>
		</tr>
		<tr>
			<td>Monochrome&#160;Camera</td>
			<td>FLIR</td>
			<td>BFS-U3-70S7M-C</td>
			<td></td>
		</tr>
		<tr>
			<td>NIS-Elements software platform</td>
			<td>Nikon</td>
			<td></td>
			<td>software platform</td>
		</tr>
		<tr>
			<td>Nucleus mask ImageJ macro</td>
			<td></td>
			<td></td>
			<td>https://github.com/KOLIUG/Nuclear mask</td>
		</tr>
		<tr>
			<td>NucSpot Live 650</td>
			<td>Biotium</td>
			<td>#40082</td>
			<td>Nuclear stain</td>
		</tr>
		<tr>
			<td>Penicillin-streptomycin</td>
			<td>Gibco</td>
			<td>15140122</td>
			<td></td>
		</tr>
		<tr>
			<td>Phosphate buffered saline (PBS)</td>
			<td>Gibco</td>
			<td>10010023</td>
			<td></td>
		</tr>
		<tr>
			<td>Ti2-E inverted microscope</td>
			<td>Nikon</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>XYZ mover (CAD files)</td>
			<td></td>
			<td></td>
			<td>https://github.com/KOLIUG/XYZ-mover</td>
		</tr>
	</tbody>
</table>

combining 3d magnetic force actuator and multi-functional fluorescence imaging to study nucleus mechanobiology

A fundamental question in mechanobiology is how living cells sense extracellular mechanical stimuli in the context of cell physiology and pathology. The cellular mechano-sensation of extracellular mechanical stimuli is believed to be through the membrane receptors, the associated protein complex, and the cytoskeleton. Recent advances in mechanobiology demonstrate that the cell nucleus in cytoplasm itself can independently sense mechanical stimuli simultaneously. However, a mechanistic understanding of how the cell nucleus senses, transduces, and responds to mechanical stimuli is lacking, mainly because of the technical challenges in accessing and quantifying the nucleus mechanics by conventional tools. This paper describes the design, fabrication, and implementation of a new magnetic force actuator that applies precise and non-invasive 3D mechanical stimuli to directly deform the cell nucleus. Using CRISPR/Cas9-engineered cells, this study demonstrates that this tool, combined with high-resolution confocal fluorescent imaging, enables the revelation of the real-time dynamics of a mechano-sensitive yes-associated protein (YAP) in single cells as a function of nucleus deformation. This simple method has the potential to bridge the current technology gap in the mechanobiology community and provide answers to the knowledge gap that exists in the relation between nucleus mechanotransduction and cell function.

Design of a magnet-moving device and application of magnetic force 
To apply force on the nucleus through the magnetic microbeads, a magnet-moving device was designed and built to control the spatial position of the magnet. The magnet-moving device contains a central frame, three knobs, and rails to move the attached magnet in x, y, and z directions independently at the spatial resolution of 1.59 mm per cycle (Figure 1A). Once the magnet is moved close to the 7 &#181;m ...

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Combining 3D Magnetic Force Actuator and Multi-Functional Fluorescence Imaging to Study Nucleus Mechanobiology

This study presents a new protocol to directly apply mechanical force on the cell nucleus through magnetic microbeads delivered into the cytoplasm and to conduct simultaneous live-cell fluorescent imaging.

A fundamental question in mechanobiology is how living cells sense extracellular mechanical stimuli in the context of cell physiology and pathology. The ...

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2.2K Views.  University of Florida. This study presents a new protocol to directly apply mechanical force on the cell nucleus through magnetic microbeads delivered into the cytoplasm and to conduct simultaneous live-cell fluorescent imaging.

Video: Combining 3D Magnetic Force Actuator and Multi-Functional Fluorescence Imaging to Study Nucleus Mechanobiology

Testing Visual Sensitivity to the Speed and Direction of Motion in Lizards

Testing visual sensitivity in any species provides basic information regarding behaviour, evolution, and ecology. However, testing specific features of the visual system provide more empirical evidence for functional applications. Investigation into the sensory system provides information about the sensory capacity, learning and memory ability, and establishes known baseline behaviour in which to gauge deviations (Burghardt, 1977). However, unlike mammalian or avian systems, testing for learning and memory in a reptile species is difficult. Furthermore, using an operant paradigm as a psychophysical measure of sensory ability is likewise as difficult. Historically, reptilian species have responded poorly to conditioning trials because of issues related to motivation, physiology, metabolism, and basic biological characteristics. Here, I demonstrate an operant paradigm used a novel model lizard species, the Jacky dragon (Amphibolurus muricatus) and describe how to test peripheral sensitivity to salient speed and motion characteristics. This method uses an innovative approach to assessing learning and sensory capacity in lizards. I employ the use of random-dot kinematograms (RDKs) to measure sensitivity to speed, and manipulate the level of signal strength by changing the proportion of dots moving in a coherent direction. RDKs do not represent a biologically meaningful stimulus, engages the visual system, and is a classic psychophysical tool used to measure sensitivity in humans and other animals. Here, RDKs are displayed to lizards using three video playback systems. Lizards are to select the direction (left or right) in which they perceive dots to be moving. Selection of the appropriate direction is reinforced by biologically important prey stimuli, simulated by computer-animated invertebrates.

Testing visual sensitivity in lizards using an operant conditioning paradigm that employs video playback of random-dot kinematograms and computer-generated invertebrates.

Testing visual sensitivity in any species provides basic information regarding behaviour, evolution, and ecology. However, testing specific features of ...

Isolation and Purification of Drosophila Peripheral Neurons by Magnetic Bead Sorting

The Drosophila peripheral nervous system (PNS) is a powerful model for investigating the complex processes of neuronal development and dendrite morphogenesis at the functional and molecular levels. To aid in these analyses, we have developed a strategy for the isolation of a subclass of PNS neurons called dendritic arborization (da) neurons that have been widely used for studying dendrite morphogenesis1,2. These neurons are very difficult to isolate as a pure population, due in part to their extremely low occurrence and their difficult-to-reach location below the tough chitinous larval cuticle. Our newly developed method overcomes these challenges, and is based on a fast and specific cell enrichment using antibody-coated magnetic beads. For our magnetic bead sorting studies, we have used age-matched third instar larvae expressing a mouse CD8 tagged GFP fusion protein (UAS-mCD8-GFP)3 under the control of either the class IV dendritic arborization (da) neuron-specific pickpocket (ppk)-GAL4 driver4 or the control of the pan-da neuron-specific GAL421-7 driver5. Although this protocol has been optimized for isolating PNS cells which are attached to the inner wall of the larval cuticle, by varying a few parameters, the same protocol could be used to isolate many different cell types attached to the cuticle at larval or pupal stages of development (e.g. epithelia, muscle, oenocytes etc.), or other cell types from larval organs depending upon the GAL4-specific driver expression pattern. The RNA isolated by this method is of high quality and can be readily used for downstream genomic analyses such as microarray gene expression profiling studies. This approach offers a powerful new tool to perform studies on isolated Drosophila dendritic arborization (da) neurons thereby providing novel insights into the molecular mechanisms underlying dendrite morphogenesis.

Isolation and Purification of Drosophila Peripheral Neurons by Magnetic Bead Sorting

In this video-article we present a method for the isolation and purification of Drosophila peripheral neurons using a fast magnetic bead assisted cell sorting strategy. RNA obtained from the isolated cells can be readily used for downstream applications including microarray analyses.

The Drosophila peripheral nervous system (PNS) is a powerful model for investigating the complex processes of neuronal development and dendrite ...

Time-lapse Imaging of Mitosis After siRNA Transfection

Changes in cellular organization and chromosome dynamics that occur during mitosis are tightly coordinated to ensure accurate inheritance of genomic and cellular content. Hallmark events of mitosis, such as chromosome movement, can be readily tracked on an individual cell basis using time-lapse fluorescence microscopy of mammalian cell lines expressing specific GFP-tagged proteins. In combination with RNAi-based depletion, this can be a powerful method for pinpointing the stage(s) of mitosis where defects occur after levels of a particular protein have been lowered. In this protocol, we present a basic method for assessing the effect of depleting a potential mitotic regulatory protein on the timing of mitosis. Cells are transfected with siRNA, placed in a stage-top incubation chamber, and imaged using an automated fluorescence microscope. We describe how to use software to set up a time-lapse experiment, how to process the image sequences to make either still-image montages or movies, and how to quantify and analyze the timing of mitotic stages using a cell-line expressing mCherry-tagged histone H2B. Finally, we discuss important considerations for designing a time-lapse experiment. This strategy is complementary to other approaches and offers the advantages of 1) sensitivity to changes in kinetics that might not be observed when looking at cells as a population and 2) analysis of mitosis without the need to synchronize the cell cycle using drug treatments. The visual information from such imaging experiments not only allows the sub-stages of mitosis to be assessed, but can also provide unexpected insight that would not be apparent from cell cycle analysis by FACS.

Here we describe a basic protocol to image and quantify the mitotic timing of live mammalian tissue culture cells after siRNA transfection.

Changes in cellular organization and chromosome dynamics that occur during mitosis are tightly coordinated to ensure accurate inheritance of genomic and ...

Sample Preparation for Single Virion Atomic Force Microscopy and Super-resolution Fluorescence Imaging

Immobilization of virions to glass surfaces is a critical step in single virion imaging. Here we present a technique&#160;adopted from single molecule imaging assays which allows adhesion of single virions to glass surfaces with specificity. This preparation is based on grafting the surface of the glass with a mixture of PLL-g-PEG and PLL-g-PEG-Biotin, adding a layer of avidin, and finally creating virion anchors through attachment of biotinylated virus specific antibodies. We have applied this technique across a range of experiments including atomic force microscopy (AFM) and super-resolution fluorescence imaging. This sample preparation method results in a control adhesion of the virions to the surface.

The attachment of virions to a surface is a requirement for single virion imaging by Super-resolution fluorescence imaging or atomic force microscopy (AFM). Here we demonstrate a sample preparation method for controlled adhesion of virions to glass surfaces suitable for use in AFM and super-resolution fluorescence imaging.

Immobilization of virions to glass surfaces is a critical step in single virion imaging. Here we present a technique&#160;adopted from single molecule ...

Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions

The paper describes the combination of optical tweezers and single molecule fluorescence detection for the study of protein-DNA interaction. The method offers the opportunity of investigating interactions occurring in solution (thus avoiding problems due to closeby surfaces as in other single molecule methods), controlling the DNA extension and tracking interaction dynamics as a function of both mechanical parameters and DNA sequence. The methods for establishing successful optical trapping and nanometer localization of single molecules are illustrated. We illustrate the experimental conditions allowing the study of interaction of lactose repressor (lacI), labeled with Atto532, with a DNA molecule containing specific target sequences (operators) for LacI binding. The method allows the observation of specific interactions at the operators, as well as one-dimensional diffusion of the protein during the process of target search. The method is broadly applicable to the study of protein-DNA interactions but also to molecular motors, where control of the tension applied to the partner track polymer (for example actin or microtubules) is desirable.

Here we describe the instrumentation and methods for detecting single fluorescently-labeled protein molecules interacting with a single DNA molecule suspended between two optically trapped microspheres.

The paper describes the combination of optical tweezers and single molecule fluorescence detection for the study of protein-DNA interaction. The method ...

High-throughput Image Analysis of Tumor Spheroids: A User-friendly Software Application to Measure the Size of Spheroids Automatically and Accurately

The increasing number of applications of three-dimensional (3D) tumor spheroids as an in vitro model for drug discovery requires their adaptation to large-scale screening formats in every step of a drug screen, including large-scale image analysis. Currently there is no ready-to-use and free image analysis software to meet this large-scale format. Most existing methods involve manually drawing the length and width of the imaged 3D spheroids, which is a tedious and time-consuming process. This study presents a high-throughput image analysis software application &#8211; SpheroidSizer, which measures the major and minor axial length of the imaged 3D tumor spheroids automatically and accurately; calculates the volume of each individual 3D tumor spheroid; then outputs the results in two different forms in spreadsheets for easy manipulations in the subsequent data analysis. The main advantage of this software is its powerful image analysis application that is adapted for large numbers of images. It provides high-throughput computation and quality-control workflow. The estimated time to process 1,000 images is about 15 min&#160;on a minimally configured laptop, or around 1 min&#160;on a multi-core performance workstation. The graphical user interface (GUI) is also designed for easy quality control, and users can manually override the computer results. The key method used in this software is adapted from the active contour algorithm, also known as Snakes, which is especially suitable for images with uneven illumination and noisy background that often plagues automated imaging processing in high-throughput screens. The complimentary &#8220;Manual Initialize&#8221; and &#8220;Hand Draw&#8221; tools provide the flexibility to SpheroidSizer in dealing with various types of spheroids and diverse quality images. This high-throughput image analysis software remarkably reduces labor and speeds up the analysis process. Implementing this software is beneficial for 3D tumor spheroids to become a routine in vitro model for drug screens in industry and academia.

We present a high-throughput image analysis software application to measure the size of three-dimensional tumor spheroids imaged with bright-field microscopy. This application provides a fast and effective way to examine the effects of therapeutic drugs on spheroids, which is beneficial for researchers who wish to use spheroids in drug screens.

The increasing number of applications of three-dimensional (3D) tumor spheroids as an in vitro model for drug discovery requires their adaptation to ...

A Method for Selecting Structure-switching Aptamers Applied to a Colorimetric Gold Nanoparticle Assay

Small molecules provide rich targets for biosensing applications due to their physiological implications as biomarkers of various aspects of human health and performance. Nucleic acid aptamers have been increasingly applied as recognition elements on biosensor platforms, but selecting aptamers toward small molecule targets requires special design considerations. This work describes modification and critical steps of a method designed to select structure-switching aptamers to small molecule targets. Binding sequences from a DNA library hybridized to complementary DNA capture probes on magnetic beads are separated from nonbinders via a target-induced change in conformation. This method is advantageous because sequences binding the support matrix (beads) will not be further amplified, and it does not require immobilization of the target molecule. However, the melting temperature of the capture probe and library is kept at or slightly above RT, such that sequences that dehybridize based on thermodynamics will also be present in the supernatant solution. This effectively limits the partitioning efficiency (ability to separate target binding sequences from nonbinders), and therefore many selection rounds will be required to remove background sequences. The reported method differs from previous structure-switching aptamer selections due to implementation of negative selection steps, simplified enrichment monitoring, and extension of the length of the capture probe following selection enrichment to provide enhanced stringency. The selected structure-switching aptamers are advantageous in a gold nanoparticle assay platform that reports the presence of a target molecule by the conformational change of the aptamer. The gold nanoparticle assay was applied because it provides a simple, rapid colorimetric readout that is beneficial in a clinical or deployed environment. Design and optimization considerations are presented for the assay as proof-of-principle work in buffer to provide a foundation for further extension of the work toward small molecule biosensing in physiological fluids.

A protocol is provided to select structure-switching aptamers for small molecule targets based on a tunable stringency magnetic bead selection method. Aptamers selected with structure-switching properties are beneficial for assays that require a conformational change to signal the presence of a target, such as the described gold nanoparticle assay.

Small molecules provide rich targets for biosensing applications due to their physiological implications as biomarkers of various aspects of human health ...

Design and Development of Aptamer&#8211;Gold Nanoparticle Based Colorimetric Assays for In-the-field Applications

The design and development of an aptamer&#8211;gold nanoparticle (AuNP) colorimetric assay for the detection of small molecules for in-the-field applications was examined. Target selective AuNP based color assays have been developed in controlled proof-of-concept laboratory settings. However, these schemes have not been exerted to a point of failure to determine their practical use beyond laboratory settings. This work describes a generic approach to design, develop, and troubleshoot an aptamer-AuNP colorimetric assay for small molecule analytes and using the assay for in-the-field settings. The assay is advantageous because adsorbed aptamers passivate the nanoparticle surfaces and provide a means to reduce and eliminate false positive responses to non-target analytes. Transitioning this system to practical uses required defining not only the shelf-life of the aptamer-AuNP assay, but establishing methods and procedures for extending the long-term storage capabilities. Also, one of the recognized concerns with colorimetric readout is the burden placed on analysts to accurately identify often subtle changes in color. To lessen the responsibility on analysts in the field, a color analysis protocol was designed to perform the color identification duties without the need for performing this task on laboratory grade equipment. The method for creating and testing the data analysis protocol is described. However to understand and influence the design of adsorbed aptamer assays, the interactions associated with the aptamer, target, and AuNPs require further study. The knowledge gained could lead to tailoring aptamers for improved functionality.

The design and development of an aptamer&#8211;gold nanoparticle colorimetric assay for the detection of small molecules for in-the-field applications was examined. Additionally, a smart-device colorimetric application (app) was validated and long-term storage of the assay was established for use in the field.

The design and development of an aptamer&#8211;gold nanoparticle (AuNP) colorimetric assay for the detection of small molecules for in-the-field ...

Functional Imaging of Viral Transcription Factories Using 3D Fluorescence Microscopy

It is well known that spatial and temporal regulation of genes is an integral part of governing proper gene expression. Consequently, it is invaluable to understand where and when transcription is taking place within nuclear space and to visualize the relationship between episomes infected within the same cell's nucleus. Here, both immunofluorescence (IFA) and RNA-FISH have been combinedto identify actively transcribing Kaposi's sarcoma-associated herpesvirus (KSHV) episomes. By staining KSHV latency-associated nuclear antigen (LANA), it is possible to locate where viral episomes exist within the nucleus. In addition, by designing RNA-FISH probes to target the intron region of a viral gene, which is expressed only during productive infection, nascent RNA transcripts can be located. Using this combination of molecular probes, it is possible to visualize the assembly of large viral transcription factories and analyze the spatial regulation of viral gene expression during KSHV reactivation. By including anti-RNA polymerase II antibody staining, one can also visualize the association between RNA polymerase II (RNAPII) aggregation and KSHV transcription during reactivation.

Viral transcriptional factories are discrete structures that are enriched with cellular RNA polymerase II to increase viral gene transcription during reactivation. Here, a method to locate sites of actively transcribing viral chromatin in 3D nuclear space by a combination of immunofluorescence staining and in situ RNA hybridization is described.

It is well known that spatial and temporal regulation of genes is an integral part of governing proper gene expression. Consequently, it is invaluable to ...

Time-Resolved Fluorescence Imaging and Analysis of Cancer Cell Invasion in the 3D Spheroid Model

The invasion of cancer cells from the primary tumor into the adjacent healthy tissues is an early step in metastasis. Invasive cancer cells pose a major clinical challenge because no efficient method exist for their elimination once their dissemination is underway. A better understanding of the mechanisms regulating cancer cell invasion may lead to the development of novel potent therapies. Due to their physiological resemblance to tumors, spheroids embedded in collagen I have been extensively utilized by researchers to study the mechanisms governing cancer cell invasion into the extracellular matrix (ECM). However, this assay is limited by (1) a lack of control over the embedding of spheroids into the ECM; (2) high cost of collagen I and glass bottom dishes, (3) unreliable immunofluorescent labeling, due to the inefficient penetration of antibodies and fluorescent dyes and (4) time-consuming image processing and quantification of the data. To address these challenges, we optimized the three-dimensional (3D) spheroid protocol to image fluorescently labeled cancer cells embedded in collagen I, either using time-lapse videos or longitudinal imaging, and analyze cancer cell invasion. First, we describe the fabrication of a spheroid imaging device (SID) to embed spheroids reliably and in a minimal collagen I volume, reducing the assay cost. Next, we delineate the steps for robust fluorescence labeling of live and fixed spheroids. Finally, we offer an easy-to-use Fiji macro for image processing and data quantification. Altogether, this simple methodology provides a reliable and affordable platform to monitor cancer cell invasion in collagen I. Furthermore, this protocol can be easily modified to fit the users&#8217; needs.

Presented here is a protocol for the fabrication of a spheroid imaging device. This device enables dynamic or longitudinal fluorescence imaging of cancer cell spheroids. The protocol also offers a simple image processing procedure for the analysis of cancer cell invasion.

The invasion of cancer cells from the primary tumor into the adjacent healthy tissues is an early step in metastasis. Invasive cancer cells pose a major ...