We would like to acknowledge the NIH for the following grant support: RO1EY032079 (VTR), R21EY029097-01 (VTR), 1F30EY033647-01 (KS), and 5T32GM008541-24 (KS). We would also like to acknowledge the Massachusetts Lions Eye Research Fund and the New England Corneal Transplant Fund.

The procedures involving animal subjects were approved by the Association for Research in Vision and Ophthalmology for the Use of Animals in Ophthalmic Care and Vision Research and the Boston University IACUC protocol (201800302).
1. Designing the 3D printed holders and cover bar
<ol>
	<li>Design the 3D printed holders and cover bar accounting for the average diameter of mouse globes and 3D print the design (Figure 1A, B).</li>
	<li>Keep the diameter of the inner wall of the holder slightly larger than the average diameter of the globe to account for the different sizes of individual mice. Keep the height of the holder at around half of the globe diameter, ensuring a tight fit of the globe when secured by the 3D printed cover bar.</li>
	<li>Size the holder cover bar to the length of the holder&#39;s outer diameter with a width that is 1/4 to 1/2 of the holder diameter. The cover bar is sized to allow for access to the globe when secured in the holder for hydration and the removal of the eye at the conclusion of the experiment.</li>
	<li>Print the holder and cover bar.</li>
</ol>
2. Sample collection
<ol>
	<li>Euthanize mice (male C57BL/6 mice aged 9-12 weeks and 27 weeks old were used for this study) using established protocols in compliance with institutional guidelines. For this protocol, perform euthanasia with carbon dioxide followed by decapitation.</li>
	<li>Remove the mouse head and place it immediately on ice to preserve the viability of the tissue. Enucleate the globes using dissection tools while preventing tissue damage.</li>
	<li>Proptose the globe using tweezers. Clip the optic nerve using dissection scissors just below where it is held by the tweezers. 
	NOTE: For further precautions, perform the following steps in a laminar flow hood.</li>
	<li>Incubate the globes in 2 mL of medium in a p35 cell culture dish including a calcium indicator and/or cell membrane stain for 1 h in a 37 &#176;C, 5% CO2 incubator with low light conditions. Ensure the globes are submerged in the staining medium for uniform staining.
	<ol>
		<li>For the experiments performed here, use the calcium indicator, Fluo4-AM (1:100)2, and cell membrane counter stain, deep red plasma membrane stain (1:10,000)2, with a final concentration of 1% (v/v) DMSO and 0.1% (w/v) pluronic acid in 2 mL of keratinocyte serum-free medium (KSFM) with the following growth supplements: 25 &#181;g/mL bovine pituitary extract, 0.02 nM epidermal growth factor, 0.3 mM CaCl2, and penicillin-streptomycin (100 units/mL and 100 &#181;g/mL, respectively). 
		&#8203;NOTE: The incubation conditions and times are variable depending on the calcium indicator, tissue type, and sample volume. When using pluronic acid, caution is advised as it renders tissue permeable. This protocol calls for 10% pluronic acid. Lower concentrations of pluronic acid have been determined experimentally to be ineffective, and higher concentrations risk damage to the tissue.</li>
	</ol>
	</li>
</ol>
3. Preparation of sample holders
<ol>
	<li>Adhere the holders to a clean glass-bottom coverslip with glue that has not been used previously. The glue used in this protocol comes from single-use containers to ensure sterility and a new, unopened container is used every time.</li>
	<li>Wash the holder in 70% ethanol. Place glue onto the holder and adhere the holder to the glass bottom coverslip. Ensure no glue is within the inner area of the holder as glue can fluoresce, complicating imaging.</li>
	<li>Wait until the glue solidifies. Confirm the holder is secure against the coverslip. 
	NOTE: P35 cell plates with glass-bottom coverslips were used for the experiments presented in this manuscript. Other glass-bottom slides and/or plates can be substituted based on the needs of the experiment.</li>
</ol>
4. Wounding of the eye globes
<ol>
	<li>Remove the globes from the staining solution using sterile eye droppers, taking care to prevent tissue damage to the region of interest. Wash the globes for 5 min at room temperature using sterile phosphate-buffered saline to remove excess stain, and place the globes in the medium for transport to the microscope.</li>
	<li>Wound the globes using a sterile 25 G needle in the region of interest.
	<ol>
		<li>Using a sterile eye dropper, pick up and hold the globe from the back of the eye. This will keep the globe stable, prevent it from rolling, and allow consistent wounds to be made. Using this setup, the optic nerve will be inside the eye dropper nozzle, and the cornea will be facing outward.</li>
		<li>For a scratch wound, gently move a sterile 25 G needle across the exposed cornea. For a puncture wound, gently press the needle directly into the central cornea. Ensure the wound does not puncture the cornea. 
		&#8203;NOTE: Skip this step if a wound response or wounded environment is not required for the experiment. Previous studies have shown that both scratch wounds and puncture wounds to murine corneas made using this method are consistent in both diameter and depth10. Confirmation of the wound dimensions between independent globes was performed using a region of interest analysis.</li>
	</ol>
	</li>
</ol>
5. Sample placement on the holder
<ol>
	<li>Place the cornea or limbal region onto the coverslip in the inner area of the holder and stabilize using the 3D printed cover (Figure 1C-H).</li>
	<li>Confirm that the globe is positioned correctly and that the site of interest is in contact with the glass coverslip. Once the globe has been placed into the holder, do not try to remove the globe as this may cause tissue damage.</li>
	<li>Adhere the 3D printed cover to the holder using glue, ensuring stabilization. Ensure the cover bar adheres to the holder and not the globe. 
	&#8203;NOTE: The area to be imaged is placed down because the protocol is written for use on an inverted microscope. The protocol can be adapted for upright microscopes using holders with a smaller inner radius and the removal of the cover bar. This will result in less globe stabilization.</li>
</ol>
6. Sample imaging
<ol>
	<li>Turn on the microscope and environmental chamber and verify that the chamber is humidified. Set the environmental chamber to 35 &#176;C and 5% CO2 for the duration of the experiment. 
	NOTE: Microscopes with environmental chambers are preferable for this procedure to prevent dehydration and to keep the globe at optimal temperatures but are not required.</li>
	<li>Place the coverslip, holder, and stabilized globe on the microscope stage within the environmental chamber and image using live cell imaging techniques9.</li>
	<li>Pipette additional growth media onto the coverslip to prevent dehydration and maintain tissue viability. Ensure there is enough medium in the well to cover the globe in the holder. Depending on the duration of imaging, add fresh medium when needed throughout the experiment.</li>
	<li>Begin experiments using live cell imaging techniques and protocols. Use low power laser settings to preserve the tissue and prevent tissue damage in long-duration experiments. Use appropriate objectives for long working distances. The experiments in this manuscript were performed using a 20x objective. 
	NOTE: The laser power and gain, experimental duration, location, and plane of imaging are all variables depending on the experimental parameters. Imaging experiments on intact globes ranging from 1 h to 4 h in duration have been performed successfully in past publications10.</li>
	<li>Record and save data in the preferred file format. The software used by the microscope produces .czi files for data recording.</li>
	<li>Dispose of the globes as per the standard institutional protocols at the end of the protocol.</li>
</ol>

<ol>
	<li>Kneer, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High+fat+diet+induces+pre-type+2+diabetes+with+regional+changes+in+corneal+sensory+nerves+and+altered+P2X7+expression+and+localization.">High fat diet induces pre-type 2 diabetes with regional changes in corneal sensory nerves and altered P2X7 expression and localization.</a> Experimental Eye Research. 175, 44-55 (2018).</li><li>Lee, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sustained+Ca2++mobilizations:+A+quantitative+approach+to+predict+their+importance+in+cell-cell+communication+and+wound+healing.">Sustained Ca2+ mobilizations: A quantitative approach to predict their importance in cell-cell communication and wound healing.</a> PLoS One. 14 (4), 0213422 (2019).</li><li>Stepp, M. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Wounding+the+cornea+to+learn+how+it+heals.">Wounding the cornea to learn how it heals.</a> Experimental Eye Research. 121, 178-193 (2014).</li><li>Klepeis, V. S., Cornell-Bell, A., Trinkaus-Randal, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Growth+factors+but+not+gap+junctions+play+a+role+in+injury-induced+Ca2++waves+in+epithelial+cells.">Growth factors but not gap junctions play a role in injury-induced Ca2+ waves in epithelial cells.</a> Journal of Cell Science. 114 (23), 4185-4195 (2001).</li><li>Lee, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hypoxia-induced+changes+in+Ca(2+)+mobilization+and+protein+phosphorylation+implicated+in+impaired+wound+healing.">Hypoxia-induced changes in Ca(2+) mobilization and protein phosphorylation implicated in impaired wound healing.</a> American Journal of Physiology. Cell Physiology. 306 (10), 972-985 (2014).</li><li>Boucher, I., Rich, C., Lee, A., Marcincin, A., Trinkaus-Randall, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+P2Y2+receptor+mediates+the+epithelial+injury+response+and+cell+migration.">The P2Y2 receptor mediates the epithelial injury response and cell migration.</a> American Journal of Physiology. Cell Physiology. 299 (2), 411-421 (2010).</li><li>Awal, M. R., Wirak, G. S., Gabel, C. V., Connor, C. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Collapse+of+global+neuronal+states+in+Caenorhabditis+elegans+under+isoflurane+anesthesia.">Collapse of global neuronal states in Caenorhabditis elegans under isoflurane anesthesia.</a> Anesthesiology. 133 (1), 133-144 (2020).</li><li>Burnett, K., Edsinger, E., Albrecht, D. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+and+gentle+hydrogel+encapsulation+of+living+organisms+enables+long-term+microscopy+over+multiple+hours.">Rapid and gentle hydrogel encapsulation of living organisms enables long-term microscopy over multiple hours.</a> Communications Biology. 1, 73 (2018).</li><li>Rhodes, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pannexin1:+Role+as+a+sensor+to+injury+is+attenuated+in+pretype+2+corneal+diabetic+epithelium.">Pannexin1: Role as a sensor to injury is attenuated in pretype 2 corneal diabetic epithelium.</a> Analytical Cellular Pathology. 2021, 4793338 (2021).</li><li>Segars, K. L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Age+dependent+changes+in+corneal+epithelial+cell+signaling.">Age dependent changes in corneal epithelial cell signaling.</a> Frontiers in Cell and Developmental Biology. 10, 886721 (2022).</li><li>Xu, P., Londregan, A., Rich, C., Trinkaus-Randall, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Changes+in+epithelial+and+stromal+corneal+stiffness+occur+with+age+and+obesity.">Changes in epithelial and stromal corneal stiffness occur with age and obesity.</a> Bioengineering. 7 (1), 14 (2020).</li><li>Minns, M. S., Teicher, G., Rich, C. B., Trinkaus-Randall, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Purinoreceptor+P2X7+regulation+of+Ca(2+)+mobilization+and+cytoskeletal+rearrangement+is+required+for+corneal+reepithelialization+after+injury.">Purinoreceptor P2X7 regulation of Ca(2+) mobilization and cytoskeletal rearrangement is required for corneal reepithelialization after injury.</a> The American Journal of Pathology. 186 (2), 285-296 (2016).</li><li>Tadvalkar, G., Pal-Ghosh, S., Pajoohesh-Ganji, A., Stepp, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+impact+of+euthanasia+and+enucleation+on+mouse+corneal+epithelial+axon+density+and+nerve+terminal+morphology.">The impact of euthanasia and enucleation on mouse corneal epithelial axon density and nerve terminal morphology.</a> The Ocular Surface. 18 (4), 821-828 (2020).</li></ol>

We have no conflicts of interest to disclose.

This protocol describes a&#160;live cell imaging technique that uses a 3D printed holder to stabilize and immobilize intact animal eyes. It is designed to circumvent several significant disadvantages recognized with previous live cell imaging protocols of ex vivo corneal tissue. This protocol offers many advantages for the live cell imaging of intact globes. It significantly reduces unnecessary tissue damage that could interfere with the wound healing response to experimentally induced scratch wounds. This inclu...

Cornea 
The cornea is a clear, avascular structure covering the anterior surface of the eye that refracts light to enable vision and protects the interior of the eye from damage. As the cornea is exposed to the environment, it is susceptible to damage from both mechanical causes (scratching) and from infection. A corneal injury in an otherwise healthy patient typically heals within 1-3 days. However, in patients with underlying conditions including limbal stem cell deficiency and type II diabetes, the corneal wound healing process can be greatly prolonged1. As the cornea is highly innervated, these non-healing corneal ulcers and recurrent corneal erosions are very painful and greatly diminish the quality of life of patients experiencing them1.
Cell signaling 
When an otherwise healthy cornea is injured, calcium signaling events in the cells adjacent to the wound precede and prompt cellular migration into the wound bed, where they close the injury without the risk of scarring2,3. These signaling events have been well-characterized in corneal epithelial cell culture models using live cell imaging2. Preliminary experiments demonstrate significantly more calcium signaling after injury in non-diabetic cells compared to diabetic cells. However, characterization of the cell signaling events in ex vivo globes has proved to be a technical challenge.
Live cell imaging 
Previous studies have successfully recorded calcium signaling events from in vitro cell culture models of corneal wound healing4,5,6. Developing a methodology to produce high-quality images of these signaling events in ex vivo tissue is of great interest because it would permit the study of these events in a more complex and true-to-life system. Previous approaches have involved dissection of the cornea followed by immobilization in a UV-induced PEG gel7,8,9. Immobilization is an essential yet challenging step when working with live tissue, as it must remain viable and hydrated throughout the course of the experiment. Furthermore, immobilization must not damage the tissue. While the PEG solution immobilized the tissue, the resolution and quality of the images produced were not consistent. Therefore, 3D printed holders were developed to immobilize intact globes to produce higher-quality images with less risk of tissue damage.
The approach 
A unique 3D printed holder was developed to immobilize intact ex vivo globes for live cell imaging. This holder prevents damage from two major sources: it allows for imaging of an enucleated globe without the need to dissect the cornea, and it eliminates exposure to UV light. Without these sources of damage, the images obtained more accurately represented the response to the scratch injuries made experimentally. Furthermore, the 3D printed holder was calibrated to the precise dimensions of the murine eye. This provided a much better fit than immobilization in PEG solution, leading to a higher-quality image at lower-powered objectives due to decreased tissue movement. A cover bar attached to the top of the holder ensures that the globe remains immobile throughout the duration of the experiment and that there is no displacement of the globe when growth media is applied to maintain hydration and viability. The ability to print the holder to precise dimensions also allows us to generate an optimal fit for murine eyes of different sizes due to the age or disease status. This technology can be applied more broadly to develop holders for the eyes of different species based on their dimensions.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1.75 blue polylactic acid (PLA) plastic</td>
			<td>Creality (Shenzen, China)</td>
			<td>N/A</td>
			<td>Material for holder</td>
		</tr>
		<tr>
			<td>35 mm Dish, No. 1.5 Coverslip, 14 mm glass diameter, Poly-D-Lysine Coated</td>
			<td>MatTek Corporation (Ashland, MA)</td>
			<td>P35GC-1.5-14-C</td>
			<td>Well for imaging.&#160;</td>
		</tr>
		<tr>
			<td>Autodesk Fusion 360 software</td>
			<td>Autodesk (San Rafael, CA).</td>
			<td>N/A</td>
			<td>Software used for printing the holders.</td>
		</tr>
		<tr>
			<td>BD 25 G 7/8 sterile needles single use 100 needles/box</td>
			<td>Thermo Fisher Scientific (Waltham, MA)</td>
			<td>305124</td>
			<td>For experimentally-induced wounds to the globes</td>
		</tr>
		<tr>
			<td>CellMask DeepRed</td>
			<td>Invitrogen (Carlsbad, CA)</td>
			<td>C10046</td>
			<td>Cell membrane counterstain. Calcium indicator. 1:10,000 concentration with a final concentration of 1%(v/v) DMSO and 0.1% (w/v) pluronic acid</td>
		</tr>
		<tr>
			<td>Complete Home Super Glue</td>
			<td>Walgreens (Deerfield, IL)</td>
			<td>N/A</td>
			<td>For attaching the holder to the imaging well</td>
		</tr>
		<tr>
			<td>Ender 3 Pro 3D printer&#160;</td>
			<td>Creality (Shenzen, China)</td>
			<td>N/A</td>
			<td>For printing the holder</td>
		</tr>
		<tr>
			<td>FIJI/ImageJ</td>
			<td>ImageJ (Bethesda, MD)</td>
			<td>License Number: GPL2</td>
			<td>Softwareused for confirming consistency of wound depth and diameter between independent globes using Region of Interest analysis</td>
		</tr>
		<tr>
			<td>Fluo-4</td>
			<td>Invitrogen (Carlsbad, CA)</td>
			<td>F14201</td>
			<td>Calcium indicator. 1:100 concentration with a final concentration of 1%(v/v) DMSO and 0.1% (w/v) pluronic acid</td>
		</tr>
		<tr>
			<td>Keratinocyte Serum-Free Medium</td>
			<td>Gibco (Waltham, MA)</td>
			<td>17005042</td>
			<td>25 mg/mL bovine pituitary extract, 0.02 nM EGF, 0.3 mM CaCl2, and penicillin-streptomycin (100 units/mL, 100 &#181;g/mL, respectively) added to medium</td>
		</tr>
		<tr>
			<td>Phophate-Buffered Saline (PBS)</td>
			<td>Corning, Medlabtech (Manassas, VA)</td>
			<td>21-040-CV</td>
			<td>Used to wash excess stain off of corneas before imaging</td>
		</tr>
		<tr>
			<td>Zeiss Confocal 880 Microscope with AiryScan</td>
			<td>Zeiss (Thornwood, NY)</td>
			<td>N/A</td>
			<td>20x magnification objective was used</td>
		</tr>
	</tbody>
</table>

live-cell imaging of intact ex vivo globes using a novel 3d printed holder

Corneal epithelial wound healing is a migratory process initiated by the activation of purinergic receptors expressed on epithelial cells. This activation results in calcium mobilization events that propagate from cell to cell, which are essential for initiating cellular motility into the wound bed, promoting efficient wound healing. The Trinkaus-Randall lab has developed a methodology for imaging the corneal wound healing response in ex vivo murine globes in real time. This approach involves enucleating an intact globe from a mouse that has been euthanized per established protocols and immediately incubating the globe with a calcium indicator dye. A counterstain that stains other features of the cell can be applied at this stage to assist with imaging and show cellular landmarks. The protocol worked well with several different live cell dyes used for counterstaining, including SiR actin to stain actin and deep red plasma membrane stain to stain the cell membrane. To examine the response to a wound, the corneal epithelium is injured using a 25 G needle, and the globes are placed in a 3D printed holder. The dimensions of the 3D printed holder are calibrated to ensure immobilization of the globe throughout the duration of the experiment and can be modified to accommodate eyes of different sizes. Live cell imaging of the wound response is performed continuously at various depths throughout the tissue over time using confocal microscopy. This protocol allows us to generate high-resolution, publication-quality images using a 20x air objective on a confocal microscope. Other objectives can also be used for this protocol. It represents a significant improvement in the quality of live cell imaging in ex vivo murine globes and permits the identification of nerves and epithelium.

This protocol has been used to consistently produce publication-quality data and images10. The images obtained represent a significant improvement when compared to previous approaches (Figure 2). Using the 3D printed holder, images can be captured throughout the layers of the cornea, and calcium mobilization in different z-planes can be observed (Figure 3). This approach has been used to compare cell-cell signaling between apical and basa...

Watch this Scientific Journal Video about Live-Cell Imaging of Intact Ex Vivo Globes Using a Novel 3D Printed Holder at JoVE.com

Live-Cell Imaging of Intact Ex Vivo Globes Using a Novel 3D Printed Holder

The present work describes a novel experimental protocol that utilizes a 3D printed holder to enable high-resolution live cell imaging of enucleated globes. Through this protocol, the cellular calcium signaling activity in wounded corneal epithelium from ex vivo globes can be observed in real time.

Live-Cell Imaging of Intact Ex Vivo Globes Using a Novel 3D Printed Holder

Corneal epithelial wound healing is a migratory process initiated by the activation of purinergic receptors expressed on epithelial cells. This activation ...

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Biochemistry

2.5K Views.  Boston University. The present work describes a novel experimental protocol that utilizes a 3D printed holder to enable high-resolution live cell imaging of enucleated globes. Through this protocol, the cellular calcium signaling activity in wounded corneal epithelium from ex vivo globes can be observed in real time. 

Video: Live-Cell Imaging of Intact Ex Vivo Globes Using a Novel 3D Printed Holder

Single-molecule Super-resolution Imaging of Phosphatidylinositol 4,5-bisphosphate in the Plasma Membrane with Novel Fluorescent Probes

Phosphoinositides in the cell membrane are signaling lipids with multiple cellular functions. Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) is a determinant phosphoinositide of the plasma membrane (PM), and it is required to modulate ion channels, actin dynamics, exocytosis, endocytosis, intracellular signaling, and many other cellular processes. However, the spatial organization of PI(4,5)P2 in the PM is controversial, and its nanoscale distribution is poorly understood due to the technical limitations of research approaches. Here by utilizing single molecule localization microscopy and the Pleckstrin Homology (PH) domain based dual color fluorescent probes, we describe a novel method to visualize the nanoscale distribution of PI(4,5)P2 in the PM in fixed membrane sheets as well as live cells.

PI(4,5)P2 regulates various cellular functions, but its nanoscale organization in the cell plasma membrane is poorly understood. By labeling PI(4,5)P2 with a dual-color fluorescent probe fused to the Pleckstrin Homology domain, we describe a novel approach to study the PI(4,5)P2 spatial distribution in the plasma membrane at the nanometer scale.

Phosphoinositides in the cell membrane are signaling lipids with multiple cellular functions. Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) is a ...

Identification of Small Molecule-binding Proteins in a Native Cellular Environment by Live-cell Photoaffinity Labeling

Identifying the molecular target(s) of small molecules is a challenging but necessary step towards understanding their mechanism of action. While several target identification methods have been developed and used to successfully elucidate the binding proteins of a variety of small molecules, these techniques have drawbacks that make them unsuitable for detecting certain types of small molecule-target interactions. In particular, non-covalent interactions that depend on native cellular conditions, such as those of membrane proteins whose structures may be perturbed upon cell lysis, are often not amenable to affinity-based target identification methods. Here, we demonstrate a method wherein a probe containing a photolabile group is used to covalently crosslink to the small molecule binding protein within the environment of the live cell, allowing the detection and isolation of the target protein without the need for maintenance of the interaction after cell lysis. This technique is a valuable tool for studying biologically interesting small molecules with unknown mechanisms, both in the context of basic biology as well as drug discovery.

We describe here a method for identification of small molecule-binding proteins using photoaffinity labeling. The advantage of this technique is that binding and covalent labeling of the target proteins occurs within the live cellular environment, removing the risk of disrupting native protein structure and binding conditions upon cell lysis.

Identifying the molecular target(s) of small molecules is a challenging but necessary step towards understanding their mechanism of action. While several ...

Brain Membrane Fractionation: An Ex Vivo Approach to Assess Subsynaptic Protein Localization

Assessing the synaptic protein composition and function constitutes an important challenge in neuroscience. However, it is not easy to evaluate neurotransmission that occurs within synapses because it is highly regulated by dynamic protein-protein interactions and phosphorylation events. Accordingly, when any method is used to study synaptic transmission, a major goal is to preserve these transient physiological modifications. Here, we present a brain membrane fractionation protocol that represents a robust procedure to isolate proteins belonging to different synaptic compartments. In other words, the protocol describes a biochemical methodology to carry out protein enrichment from presynaptic, postsynaptic, and extrasynaptic compartments. First, synaptosomes, or synaptic terminals, are obtained from neurons that contain all synaptic compartments by means of a discontinuous sucrose gradient. Of note, the quality of this initial synaptic membrane preparation is critical. Subsequently, the isolation of the different subsynaptic compartments is achieved with light solubilization using mild detergents at differential pH conditions. This allows for separation by gradient and isopycnic centrifugations. Finally, protein enrichment at the different subsynaptic compartments (i.e., pre-, post- and extrasynaptic membrane fractions) is validated by means of immunoblot analysis using well-characterized synaptic protein markers (i.e., SNAP-25, PSD-95, and synaptophysin, respectively), thus enabling a direct assessment of the synaptic distribution of any particular neuronal protein.

Brain Membrane Fractionation: An Ex Vivo Approach to Assess Subsynaptic Protein Localization

Here, we present a brain membrane fractionation protocol that represents a robust procedure to isolate proteins belonging to different synaptic compartments.

Assessing the synaptic protein composition and function constitutes an important challenge in neuroscience. However, it is not easy to evaluate ...

Glycoproteomics of the Extracellular Matrix: A Method for Intact Glycopeptide Analysis Using Mass Spectrometry

Fibrosis is a hallmark of many cardiovascular diseases and is associated with the exacerbated secretion and deposition of the extracellular matrix (ECM). Using proteomics, we have previously identified more than 150 ECM and ECM-associated proteins in cardiovascular tissues. Notably, many ECM proteins are glycosylated. This post-translational modification affects protein folding, solubility, binding, and degradation. We have developed a sequential extraction and enrichment method for ECM proteins that is compatible with the subsequent liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis of intact glycopeptides. The strategy is based on sequential incubations with NaCl, SDS for tissue decellularization, and guanidine hydrochloride for the solubilization of ECM proteins. Recent advances in LC-MS/MS include fragmentation methods, such as combinations of higher-energy collision dissociation (HCD) and electron transfer dissociation (ETD), which allow for the direct compositional analysis of glycopeptides of ECM proteins. In the present paper, we describe a method to prepare the ECM from tissue samples. The method not only allows for protein profiling but also the assessment and characterization of glycosylation by MS analysis.

This paper describes a methodology to prepare cardiovascular tissue samples for MS analysis that allows for (1) the analysis of ECM protein composition, (2) the identification of glycosylation sites, and (3) the compositional characterization of glycan forms. This methodology can be applied, with minor modifications, to the study of the ECM in other tissues.

Fibrosis is a hallmark of many cardiovascular diseases and is associated with the exacerbated secretion and deposition of the extracellular matrix (ECM). ...

Fluorescence Live-cell Imaging of the Complete Vegetative Cell Cycle of the Slow-growing Social Bacterium Myxococcus xanthus

Fluorescence live-cell imaging of bacterial cells is a key method in the analysis of the spatial and temporal dynamics of proteins and chromosomes underlying central cell cycle events. However, imaging of these molecules in slow-growing bacteria represents a challenge due to photobleaching of fluorophores and phototoxicity during image acquisition. Here, we describe a simple protocol to circumvent these limitations in the case of Myxococcus xanthus (which has a generation time of 4 - 6 h). To this end, M. xanthus cells are grown on a thick nutrient-containing agar pad in a temperature-controlled humid environment. Under these conditions, we determine the doubling time of individual cells by following the growth of single cells. Moreover, key cellular processes such as chromosome segregation and cell division can be imaged by fluorescence live-cell imaging of cells containing relevant fluorescently labeled marker proteins such as ParB-YFP, FtsZ-GFP, and mCherry-PomX over multiple cell cycles. Subsequently, the acquired images are processed to generate montages and/or movies.

Fluorescence Live-cell Imaging of the Complete Vegetative Cell Cycle of the Slow-growing Social Bacterium Myxococcus xanthus

Bacterial cells are spatially highly organized. To follow this organization over time in slow growing Myxococcus xanthus cells, a set-up for fluorescence live-cell imaging with high spatiotemporal resolution over several generations was developed. Using this method, spatiotemporal dynamics of important proteins for chromosome segregation and cell division could be determined.

Fluorescence live-cell imaging of bacterial cells is a key method in the analysis of the spatial and temporal dynamics of proteins and chromosomes ...

Calibration-free In Vitro Quantification of Protein Homo-oligomerization Using Commercial Instrumentation and Free, Open Source Brightness Analysis Software

Number and brightness is a calibration-free fluorescence fluctuation spectroscopy (FFS) technique for detecting protein homo-oligomerization. It can be employed using a conventional confocal microscope equipped with digital detectors. A protocol for the use of the technique in vitro is shown by means of a use case where number and brightness can be seen to accurately quantify the oligomeric state of mVenus-labelled FKBP12F36V before and after the addition of the dimerizing drug AP20187. The importance of using the correct microscope acquisition parameters and the correct data preprocessing and analysis methods are discussed. In particular, the importance of the choice of photobleaching correction is stressed. This inexpensive method can be employed to study protein-protein interactions in many biological contexts.

Calibration-free In Vitro Quantification of Protein Homo-oligomerization Using Commercial Instrumentation and Free, Open Source Brightness Analysis Software

This protocol describes a calibration-free approach for quantifying protein homo-oligomerization in vitro based on fluorescence fluctuation spectroscopy using commercial light scanning microscopy. The correct acquisition settings and analysis methods are shown.

Number and brightness is a calibration-free fluorescence fluctuation spectroscopy (FFS) technique for detecting protein homo-oligomerization. It can be ...

Identification of Novel CK2 Kinase Substrates Using a Versatile Biochemical Approach

The study of kinase-substrate relationships is essential to gain a complete understanding of the functions of these enzymes and their downstream targets in both physiological and pathological states. CK2 is an evolutionarily conserved serine/threonine kinase with a growing list of hundreds of substrates involved in multiple cellular processes. Due to its pleiotropic properties, identifying and characterizing a comprehensive set of CK2 substrates has been particularly challenging and remains a hurdle in the study of this important enzyme. To address this challenge, we have devised a versatile experimental strategy that enables the targeted enrichment and identification of putative CK2 substrates. This protocol takes advantage of the unique dual co-substrate specificity of CK2 allowing for specific thiophosphorylation of its substrates in a cell or tissue lysate. These substrate proteins are subsequently alkylated, immunoprecipitated, and identified by liquid chromatography/tandem mass spectrometry (LC-MS/MS). We have previously used this approach to successfully identify CK2 substrates from Drosophila ovaries and here we extend the application of this protocol to human glioblastoma cells, illustrating the adaptability of this method to investigate the biological roles of this kinase in various model organisms and experimental systems.

The objective of this protocol is to label, enrich, and identify substrates of protein kinase CK2 from a complex biological sample such as a cell lysate or tissue homogenate. This method leverages unique aspects of CK2 biology for this purpose.

The study of kinase-substrate relationships is essential to gain a complete understanding of the functions of these enzymes and their downstream targets ...

In Vivo Calcium Imaging in C. elegans Body Wall Muscles

The model organism C. elegans provides an excellent system to perform in vivo calcium imaging. Its transparent body and genetic manipulability allow for the targeted expression of genetically encoded calcium sensors. This protocol outlines the use of these sensors for the in vivo imaging of calcium dynamics in targeted cells, specifically the body wall muscles of the worms. By utilizing the co-expression of presynaptic channelrhodopsin, stimulation of acetylcholine release from excitatory motor neurons can be induced using blue light pulses, resulting in muscle depolarization and reproducible changes in cytoplasmic calcium levels. Two worm immobilization techniques are discussed with varying levels of difficulty. Comparison of these techniques demonstrates that both approaches preserve the physiology of the neuromuscular junction and allow for the reproducible quantification of calcium transients. By pairing optogenetics and functional calcium imaging, changes in postsynaptic calcium handling and homeostasis can be evaluated in a variety of mutant backgrounds. Data presented validates both immobilization techniques and specifically examines the roles of the C. elegans sarco(endo)plasmic reticular calcium ATPase and the calcium-activated BK potassium channel in the body wall muscle calcium regulation.

In Vivo Calcium Imaging in C. elegans Body Wall Muscles

This method provides a way to couple optogenetics and genetically encoded calcium sensors to image baseline cytosolic calcium levels and changes in evoked calcium transients in the body wall muscles of the model organism C. elegans.

The model organism C. elegans provides an excellent system to perform in vivo calcium imaging. Its transparent body and genetic manipulability allow for ...

An All-in-one Sample Holder for Macromolecular X-ray Crystallography with Minimal Background Scattering

Macromolecular X-ray crystallography (MX) is the most prominent method to obtain high-resolution three-dimensional knowledge of biological macromolecules. A prerequisite for the method is that highly ordered crystalline specimen need to be grown from the macromolecule to be studied, which then need to be prepared for the diffraction experiment. This preparation procedure typically involves removal of the crystal from the solution, in which it was grown, soaking of the crystal in ligand solution or cryo-protectant solution and then immobilizing the crystal on a mount suitable for the experiment. A serious problem for this procedure is that macromolecular crystals are often mechanically unstable and rather fragile. Consequently, the handling of such fragile crystals can easily become a bottleneck in a structure determination attempt. Any mechanical force applied to such delicate crystals may disturb the regular packing of the molecules and may lead to a loss of diffraction power of the crystals. Here, we present a novel all-in-one sample holder, which has been developed in order to minimize the handling steps of crystals and hence to maximize the success rate of the structure determination experiment. The sample holder supports the setup of crystal drops by replacing the commonly used microscope cover slips. Further, it allows in-place crystal manipulation such as ligand soaking, cryo-protection and complex formation without any opening of the crystallization cavity and without crystal handling. Finally, the sample holder has been designed in order to enable the collection of in situ X-ray diffraction data at both, ambient and cryogenic temperature. By using this sample holder, the chances to damage the crystal on its way from crystallization to diffraction data collection are considerably reduced since direct crystal handling is no longer required.

A novel sample holder for macromolecular X-ray crystallography along with a suitable handling protocol is presented. The system allows crystal growth, crystal soaking and in situ diffraction data collection at both, ambient and cryogenic temperature without the need of any crystal manipulation or mounting.

Macromolecular X-ray crystallography (MX) is the most prominent method to obtain high-resolution three-dimensional knowledge of biological macromolecules. ...

Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using &#967;CRAC

The interaction between RNA-binding proteins (RBPs) and their RNA substrates exhibits fluidity and complexity. Within its lifespan, a single RNA can be bound by many different RBPs that will regulate its production, stability, activity, and degradation. As such, much has been done to understand the dynamics that exist between these two types of molecules. A particularly important breakthrough came with the emergence of &#8216;cross-linking and immunoprecipitation&#8217; (CLIP). This technique allowed stringent investigation into which RNAs are bound by a particular RBP. In short, the protein of interest is UV cross-linked to its RNA substrates in vivo, purified under highly stringent conditions, and then the RNAs covalently cross-linked to the protein are converted into cDNA libraries and sequenced. Since its conception, many derivative techniques have been developed in order to make CLIP amenable to particular fields of study. However, cross-linking using ultraviolet light is notoriously inefficient. This results in extended exposure times that make the temporal study of RBP-RNA interactions impossible. To overcome this issue, we recently designed and built much-improved UV irradiation and cell harvesting devices. Using these new tools, we developed a protocol for time-resolved analyses of RBP-RNA interactions in living cells at high temporal resolution: Kinetic CRoss-linking and Analysis of cDNAs (&#967;CRAC). We recently used this technique to study the role of yeast RBPs in nutrient stress adaptation. This manuscript provides a detailed overview of the &#967;CRAC method and presents recent results obtained with the Nrd1 RBP.

Kinetic cross-linking and analysis of cDNA is a method that allows investigation of the dynamics of protein-RNA interactions in living cells at high temporal resolution. Here the protocol is described in detail, including the growth of yeast cells, UV cross-linking, harvesting, protein purification, and next generation sequencing library preparation steps.

The interaction between RNA-binding proteins (RBPs) and their RNA substrates exhibits fluidity and complexity. Within its lifespan, a single RNA can be ...