This work was supported by Agence Nationale de la Recherche (Jeunes Chercheuses/Jeunes Chercheurs to EFN), Fondation Voir et Entendre and Fondation Bettencourt Schueller (Young Investigator Grants to EFN), Centre National de la Recherche Scientifique (CNRS, permanent position for EFN), and The National Eye Institute of the National Institutes of Health (R01-EY13295 to SCF). Additionally, the Institut de la Vision is funded by Institut National de la Sant&#233; et de la Recherche M&#233;dicale, Universit&#233; Pierre et Marie Curie-Paris 6, Centre National de la Recherche Scientifique and D&#233;partment de Paris.

This POS isolation experiment is time consuming and may require up to 12 hr to complete if POS are labeled before storage. The protocol has been adapted from a paper published by R.S. Molday and colleagues in 198731 and modified by S.C. Finnemann and colleagues in 199710.
Animals were handled according to the Association for Research in Vision and Ophthalmology (ARVO) Statement for the Use of Animals in Ophthalmic and Vision Research. Protocols were reviewed and approved by the Charles Darwin Ethics Committee from University Pierre and Marie Curie-Paris 06 and the Fordham University Institutional Animal Care and Use Committee.
1. General Set Up
<ol>
	<li>Obtain 80 fresh pig or cow eyes as fresh as soon after slaughtering as possible and keep them chilled in the dark. Provide instructions to the provider so the company proceeds the same way. This protocol is optimized for 80 eyes. To proceed with more eyes and get bigger stocks (e.g.,, from 160 eyes), double the solution quantities and perform 2 rounds of ultracentrifugation; pool samples later at the collection step (see step 2.2.2).</li>
	<li>Set up on the bench the red safelight lamp, absorbent pads, wipes (Materials table). Prepare 15 cm dishes and biohazard bags for waste collection (unused eye parts, vitreous&#8230;). Wear tight-fitting labcoat, gloves, sleeve protectors and goggles.</li>
	<li>Precautions:
	<ol>
		<li>Pre-chill all solutions then keep them cold during all steps. Keep eyes and gradients chilled on ice as much as possible.</li>
		<li>Keep eyes and derived tissues in the dark as much as possible until the collection step after the ultracentrifugation to avoid photobleaching of visual pigments and loss of the orange-pink color of the active form of the photopigments.</li>
	</ol>
	</li>
</ol>
2. Protocol Actions
<ol>
	<li>Prepare solutions and gradients:
	<ol>
		<li>Thaw taurine stock completely using a 37 &#176;C water bath.</li>
		<li>Prepare all solutions from stock solutions (Table 1, Stock solutions) and mix thoroughly the sucrose with other ingredients using a magnetic stirrer for each solution.
		<ol>
			<li>Prepare 15 ml of the homogenization solution to a final concentration of 20% sucrose, 20 mM tris acetate pH7.2, 2 mM MgCl2, 10 mM glucose and 5 mM taurine.</li>
			<li>Prepare the 25% sucrose solution to a final concentration of 25% sucrose (using 70% sucrose stock), 20 mM tris acetate pH 7.2, 10 mM glucose and 5 mM taurine.</li>
			<li>Prepare the 60% sucrose solution to a final concentration of 60% sucrose (using sucrose powder), 20 mM tris acetate pH7.2, 10 mM glucose and 5 mM taurine.</li>
			<li>Prepare the Wash 1 solution to a final concentration of 20 mM tris acetate pH 7.2 and 5 mM taurine.</li>
			<li>Prepare the Wash 2 solution to a final concentration of 10% sucrose, 20 mM tris acetate pH 7.2 and 5 mM taurine.</li>
			<li>Prepare the Wash 3 solution to a final concentration of 10% sucrose, 20 mM sodium phosphate pH 7.2 and 5 mM taurine.</li>
		</ol>
		</li>
		<li>Steady the gradient maker on a magnetic stirrer and insert a stir bar in the chamber closest to the exit where the 60% solution will be inserted. Use a cut-off P200 pipet tip placed at the exit of the tubing to achieve proper casting speed.</li>
		<li>Cast linear gradients delicately by diluting and stirring the 60% sucrose solution with the 25% one using 12 ml from each solution (i.e., total 6 tubes for 80 eyes) in pre-chilled ultracentrifuge tubes. Stir the gradually-diluting 60% sucrose solution well. Steady the speed of gradient flow, pouring the solution smoothly and not too fast. 
		NOTE: In order to get a continuous, linear gradient, keep the pipet tip opening right at the surface of the solution for the entire gradient formation.</li>
		<li>Let the gradients sit on ice for around 1 hr for stabilization. Keep the gradients chilled until loaded. Do not shake the tubes to prevent disruption of the gradient.</li>
	</ol>
	</li>
	<li>Tissue collection:
	<ol>
		<li>Collect tissues under dim red light. Take an eye into one hand and poke the front with edge of razor blade while holding the eye away (to avoid splashing; Figure 1). Use the razor blade to cut the anterior eyeball into 2 halves (cornea plus at least 5 mm into the sclera). Remove the lens and flip the eyecup inside out so that it can be held over the tip of one finger thus exposing the retina.</li>
		<li>Using the razor blade at an angle, gently scrape the retina, detaching easily and appearing as a pinkish layer, off the tapetum surface and cut at the optic nerve head (Figure 1). Collect all retinas in 2 x 50 ml tubes each containing 15 ml of homogenization solution on ice.</li>
		<li>Retina homogenization:
		<ol>
			<li>Shake the suspension vigorously by hand for 2 min in order to disrupt the different cell layers, break POS off the rest of the PR cell, fragment POS and homogenize the retina suspension.</li>
			<li>Filter 3x through a double-layer of clean gauze to remove large tissue fragments and collect the flow-through in clean 50 ml tubes (Figure 1). The retinal suspension being quite thick, to maximize the yield, gently press on the gauze to release remaining fragmented tissues after each filtration.</li>
		</ol>
		</li>
	</ol>
	</li>
	<li>Photoreceptor outer segment fragment (POS) isolation:
	<ol>
		<li>Gently lay the crude retina prep, around 6 - 7 ml per tube, over 6 x 30 ml ultracentrifuge tubes each containing 24 ml of fresh chilled continuous 25 - 60% sucrose gradient (Figure 1). Balance the opposing tubes as appropriate for the rotor to be used. Ultracentrifuge at 106,000 x g for 50 min at 4 &#176;C.</li>
		<li>Remove most of the solution above the orange-pink band in the upper third of gradient by aspiration (Figure 2A). Collect the orange-pink band with a cut-off P1000 tip into a beaker. Discard the rest after neutralizing using bleach (biological waste).</li>
		<li>Dilute with ~4 - 5 volumes of ice-cold Wash 1 solution. Separate into as many 30 ml tubes as needed. Centrifuge at 3,000 x g for 10 min at 4 &#176;C. Carefully discard the supernatant.</li>
		<li>Resuspend pellets in 10 ml Wash 2 solution and spin at 3,000 x g for 10 min as detailed above. Resuspend pellets in 15 ml Wash 3 and spin again at 3,000 x g for 10 min. Combine suspensions from several pellets to reduce the number of tubes needed before centrifugation in Wash 2 and Wash 3 solutions.</li>
	</ol>
	</li>
	<li>POS aliquoting without labeling:
	<ol>
		<li>Resuspend POS in 10 - 20 ml DMEM. Predilute 10 &#181;l in 490 &#181;l DMEM (1:50) and count elongated as well as whirled POS in a cell counting chamber (Figure 2B). Calculate yield and concentration in POS particles per mL. 
		NOTE: The yield varies, depending mostly on the age and strain of pigs/cows and size of the eyes, e.g., a good preparation ranges from 5 - 8 x 109 POS from 80 pig eyes.</li>
		<li>Decide on the final DMEM volume (typically 10 - 20 ml) and add sucrose to yield a final concentration of 2.5% sucrose.</li>
		<li>Prepare aliquots of the desired size, e.g., 5 x 107 POS per tube for a 2 ml resuspension volume for a 96-well experiment at 40 &#181;l/well. Spin 1 aliquot for 5 min at 2,300 x g at RT&#160;and evaluate pellet size. Prepare various aliquot sizes for different application volumes as POS should NOT be frozen and thawed twice.</li>
		<li>Freeze POS aliquots at -80 &#176;C until further use. 
		NOTE: Aliquots are stable for many months. In our hands, unlabeled or labeled POS can be stored for at least one year.</li>
	</ol>
	</li>
	<li>POS labeling and aliquoting: 
	NOTE: We typically use FITC to label POS for quantification of phagocytosis assays, but other dyes may be used as well depending on needs.
	<ol>
		<li>Resuspend 1 10 mg FITC vial at a 2.5 mg/ml concentration in 0.1 M Na carbonate buffer pH 9.5 by mixing 2.6 ml 0.1 M NaHCO3 pH 8.4 with 1.4 ml 0.1 M Na2CO3 pH 11.5 (Table 2, Stock solutions). Rotate for 1 hr at RT while protecting from light and spin for 5 min at maximum speed to pellet non-resuspended FITC solids.</li>
		<li>Resuspend the POS pellet in 10 ml of Wash 3 solution (or DMEM) and add 2 ml of FITC solution for 80 eyes. Store leftover FITC frozen at -80 &#176;C. Rotate for at least 1.5 hr at RT. Protect from light using aluminum foil.</li>
		<li>Wash labeled POS twice using Wash 3 solution as described in section 2.3.4, then once or twice in DMEM until almost no free FITC is seen in the supernatant fraction. Resuspend POS in DMEM and proceed as for unlabeled POS for counting and aliquoting (section 2.4).</li>
	</ol>
	</li>
	<li>Using POS in experiments:
	<ol>
		<li>Thaw POS at RT, and keep them in the dark as much as possible if they are fluorescently-labeled. Spin for 5 min at 2,300 x g at RT. Aspirate the supernatant.</li>
		<li>Immediately resuspend in appropriate volume of assay solution as dictated by the experiment. In case of different times of POS challenge, store resuspended POS at RT in the dark between time-points for several hours.</li>
	</ol>
	</li>
</ol>

The authors declare that they have no competing financial interest.

Three steps or conditions are crucial for an optimized purification: quality of gradient casting and delicate gradient tubes manipulation, keeping tissues chilled and in the dark until the collection step, strength of shaking of retinal homogenates to obtain proper POS isolation from the rest of the PR cell. If some issues arise in seeing the orange band properly, they are most likely due to one of the three reasons above (see also the second paragraph of the Results section). Some modification of certai...

In the retina, vision is triggered by isomerization of photosensitive molecules called opsins, before being transformed into a signal that can be transmitted between neurons up to the visual areas in the brain. These molecules are embedded in stacks of membranous disks resembling pancakes that constitute the outer segment portions of photoreceptor cells (PRs). Being subjected to constant exposure to light and therefore considerable levels of oxidative stress, PRs continuously renew their outer segments to limit potential oxidative damage. Photoreceptor outer segments are in close contact with apical microvilli of the neighboring retinal pigment epithelial (RPE) cells. RPE cells constitute the outer part of the blood-retinal barrier and ensure numerous tasks that are crucial for photoreceptors health and function1, such as quenching light rays via melanin pigments, re-isomerization of the photoreactive opsin component retinal, providing nutrients and growth factors, participating in PR metabolite disposal.
In addition, RPE cells eliminate spent POS and recycle their components, a daily occupation that is regulated by the circadian rhythm in mammalian retina2,3. The clearance of shed POS is absolutely necessary for PR survival. When it is completely abrogated, POS debris accumulate and PRs degenerate causing rapid vision loss4,5. If the rhythmic profile is lost and replaced by a constant activity, PR and RPE defects accumulate with age6. Therefore, it is very important to characterize the molecular regulation of RPE phagocytosis in vitro in order to understand phenotypes linked to its dysfunction. Interestingly, the molecular machinery in RPE cells is very similar to the one used by macrophages to clear apoptotic cells and both are dependent on recognition of exposed phosphatidylserine on phagocytic debris7-9. Still, RPE cells and macrophages regulate phagocytosis differently, as macrophages opt for immediate elimination of apoptotic cells at encounter time while RPE cells rhythmically engulf POS only once a day despite their permanent contact with outer segments. This suggests specific regulation mechanisms that are not yet fully understood.
Many of the molecules implicated in the RPE phagocytic machinery have been identified or validated thanks to the use of isolated POS and cell culture phagocytosis assays. The alphavbeta5 integrin receptor located at the RPE apical cell surface, in coordination with its ligand MFG-E8, binds specifically to POS10-12, which are then internalized via the MerTK tyrosine kinase receptor13-15. The CD36 scavenger receptor has been shown to participate in POS intake and influence its speed16,17, and might serve as a sensor of oxidized phospholipids at the POS surface18. Internalization needs the recruitment of F-actin cytoskeleton-associated proteins such as annexin 219, myosin II20 and myosin VIIA21,22. Native or oxidized POS in vitro are also utilized to understand aging phenotypes of RPE cells in vivo linked to accumulation of poorly digested oxidized POS23-28. The generation of RPE cells derived from stem cells has initiated a new application for isolated POS that are used to prove functionality of cells before they are transplanted to animals or patients29,30,27.
First described by Molday and colleagues in 198731, the protocol for isolation of bovine POS combines an ultracentrifugation step of retinal homogenates on continuous sucrose gradients with observation of the characteristic orange appearance of unbleached retinal photopigment (carrying 11-cis retinal). In the past 10 years, due to precautions taken in order to minimize risk of mad cow disease, use of porcine eyes has become increasingly prominent. The protocol described here shows how to obtain large amounts of POS from porcine or bovine eyes that can be aliquoted and stored for extended periods of time. This eliminates the need to prepare POS from rodent eyes, which requires using a large number of animals per POS preparation and assay32,33,21,22. In addition, details about POS labeling before storage using fluorescent molecules are given, to quantify and visualize POS in a simplified and comparable manner for some applications compared to labeling POS after the phagocytosis assay32,10. Therefore, these large stocks allow for reproducibility and ease of use in many different types of experiments.

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			<td height="43" style="height:43px;width:311px;">Name of Material/ Equipment</td>
			<td style="width:108px;">Company</td>
			<td style="width:103px;">Catalog Number</td>
			<td style="width:291px;">Comments/Description</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:311px;">Specific Material/Equipment</td>
			<td style="width:108px;"></td>
			<td style="width:103px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:311px;">2-chamber gradient maker</td>
			<td style="width:108px;"></td>
			<td style="width:103px;"></td>
			<td>gradient maker with 30-ml chambers</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:311px;">3-mm diameter silicone tubing</td>
			<td style="width:108px;"></td>
			<td style="width:103px;"></td>
			<td>tubing for gradient casting</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">small size magnetic stir bar</td>
			<td style="width:108px;"></td>
			<td style="width:103px;"></td>
			<td>stir bar fitting the gradient maker chamber</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:311px;">red safelight lamp</td>
			<td style="width:108px;"></td>
			<td style="width:103px;"></td>
			<td>inactinic lamp for dissection in the dark</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Ultra Clear 25x89 cm tubes</td>
			<td>Beckman</td>
			<td>344058</td>
			<td>ultracentrifugation tubes</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">PP Oak Ridge tubes</td>
			<td>Nalgene</td>
			<td>3119-0050</td>
			<td>30-mL centrifugation tubes&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Optima LE-80K&#160;</td>
			<td>Beckman Coulter&#160;</td>
			<td>365668</td>
			<td>ultracentrifuge</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">SW 32Ti swing rotor</td>
			<td>Beckman Coulter&#160;</td>
			<td>369694</td>
			<td>swing rotor for ultracentrifuge</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Avanti J-26 XP</td>
			<td>Beckman Coulter&#160;</td>
			<td>393124</td>
			<td>centrifuge</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">JA-25.50 rotor</td>
			<td>Beckman Coulter&#160;</td>
			<td>363058</td>
			<td>rotor for Avanti J-26 XP centrifuge</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">FITC Isomer I</td>
			<td>Life Technologies&#160;</td>
			<td>F-1906</td>
			<td>fluorescent dye</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:311px;">Other Material/Equipment</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td colspan="2" height="21" style="height:21px;">counting chamber (such as Neubauer or Malassez)</td>
			<td style="width:103px;"></td>
			<td style="width:291px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">dark ice buckets with lids</td>
			<td style="width:108px;"></td>
			<td style="width:103px;"></td>
			<td style="width:291px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">scales</td>
			<td style="width:108px;"></td>
			<td style="width:103px;"></td>
			<td style="width:291px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">magnetic stirrer and upholding pole</td>
			<td style="width:108px;"></td>
			<td style="width:103px;"></td>
			<td style="width:291px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">refrigated microcentrifuge</td>
			<td style="width:108px;"></td>
			<td style="width:103px;"></td>
			<td style="width:291px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">37 &#176;C water bath</td>
			<td style="width:108px;"></td>
			<td style="width:103px;"></td>
			<td style="width:291px;"></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">-80 &#176;C freezer</td>
			<td style="width:108px;"></td>
			<td style="width:103px;"></td>
			<td style="width:291px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:311px;">Consumables</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">labcoat</td>
			<td style="width:108px;"></td>
			<td style="width:103px;"></td>
			<td>Health and safety</td>
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			<td height="21" style="height:21px;">gloves</td>
			<td style="width:108px;"></td>
			<td style="width:103px;"></td>
			<td></td>
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		<tr height="21">
			<td height="21" style="height:21px;">sleeve protectors</td>
			<td style="width:108px;"></td>
			<td style="width:103px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">googles</td>
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			<td style="width:103px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">absorbent pads</td>
			<td style="width:108px;"></td>
			<td style="width:103px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">biohazard trash bags and bins</td>
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			<td style="width:103px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td colspan="2" height="21" style="height:21px;">Weck-Prep blades (60-mm/2.25-in wide razor blades)</td>
			<td style="width:103px;"></td>
			<td>Dissection</td>
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		<tr height="21">
			<td height="21" style="height:21px;">15-cm plastic dish</td>
			<td style="width:108px;"></td>
			<td style="width:103px;"></td>
			<td></td>
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		<tr height="21">
			<td height="21" style="height:21px;">sterile gauze sheets</td>
			<td style="width:108px;"></td>
			<td style="width:103px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">15- and 50-mL tubes</td>
			<td style="width:108px;"></td>
			<td style="width:103px;"></td>
			<td>Common consumables</td>
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			<td height="21" style="height:21px;">microtubes</td>
			<td style="width:108px;"></td>
			<td style="width:103px;"></td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">aluminum foil</td>
			<td style="width:108px;"></td>
			<td style="width:103px;"></td>
			<td></td>
		</tr>
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</table>

large-scale purification of porcine or bovine photoreceptor outer segments for phagocytosis assays on retinal pigment epithelial cells

Analysis of one of the vital functions of retinal pigment epithelial (RPE) cells, the phagocytosis of spent aged distal fragments of photoreceptor outer segments (POS) can be performed in vitro. Photoreceptor outer segments with stacks of membranous discs containing the phototransduction machinery are continuously renewed in the retina. Spent POS are eliminated daily by RPE cells. Rodent, porcine/bovine and human RPE cells recognize POS from various species in a similar manner. To facilitate performing large series of experiments with little variability, a large stock of POS can be isolated from porcine eyes and stored frozen in aliquots. This protocol takes advantage of the characteristic of photopigments that display an orange color when kept in the dark. Under dim red light, retinae are collected in a buffer from opened eyecups cut in halves. The retinal cell suspension is homogenized, filtered and loaded onto a continuous sucrose gradient. After centrifugation, POS are located in a discrete band in the upper part of the gradient that has a characteristic orange color. POS are then collected, spun, resuspended sequentially in wash buffers, counted and aliquoted. POS obtained this way can be used for phagocytosis assays and analysis of protein activation, localization or interaction at various times after POS challenge. Alternatively, POS can be labeled with fluorophores, e.g., FITC, before aliquoting for subsequent fluorescence quantification of POS binding or engulfment. Other possible applications include the use of modified POS or POS challenge combined with stress conditions to study the effect of oxidative stress or aging on RPE cells.

The combination of the linear sucrose gradient and the ultracentrifugation allows the separation of the different components of the retinal suspension by density. Heavy larger retinal debris and RPE cells sink to or near the bottom of the gradient (Figure 2A). Lighter POS and lighter individual cells or cell debris from the retina migrate as separate bands to reach the top half of the gradient by the end of the centrifugation period. By keeping the eyes and the samples in the dark until after the centrif...

Watch this Scientific Journal Video about Large-Scale Purification of Porcine or Bovine Photoreceptor Outer Segments for Phagocytosis Assays on Retinal Pigment Epithelial Cells at JoVE.com

Large-Scale Purification of Porcine or Bovine Photoreceptor Outer Segments for Phagocytosis Assays on Retinal Pigment Epithelial Cells

This article describes the protocol for the purification of photoreceptor outer segment fragments (POS) via ultracentrifugation from porcine/bovine retinae using homogenization and sucrose gradient centrifugation. This protocol allows the preparation of large stocks of POS aliquots, labeled or unlabeled, that can then be stored at -80 &#176;C.

Analysis of one of the vital functions of retinal pigment epithelial (RPE) cells, the phagocytosis of spent aged distal fragments of photoreceptor outer ...

large-scale-purification-porcine-or-bovine-photoreceptor-outer

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Immunology and Infection

11.9K Views.  INSERM, U968. This article describes the protocol for the purification of photoreceptor outer segment fragments (POS) via ultracentrifugation from porcine/bovine retinae using homogenization and sucrose gradient centrifugation. This protocol allows the preparation of large stocks of POS aliquots, labeled or unlabeled, that can then be stored at -80 °C.

Video: Large-Scale Purification of Porcine or Bovine Photoreceptor Outer Segments for Phagocytosis Assays on Retinal Pigment Epithelial Cells

Application of a Mouse Ligated Peyer&#x2019;s Patch Intestinal Loop Assay to Evaluate Bacterial Uptake by M cells

The inside of our gut is inhabited with enormous number of commensal bacteria. The mucosal surface of the gastrointestinal tract is continuously exposed to them and occasionally to pathogens. The gut-associated lymphoid tissue (GALT) play a key role for induction of the mucosal immune response to these microbes1, 2. To initiate the mucosal immune response, the mucosal antigens must be transported from the gut lumen across the epithelial barrier into organized lymphoid follicles such as Peyer's patches. This antigen transcytosis is mediated by specialized epithelial M cells3, 4. M cells are atypical epithelial cells that actively phagocytose macromolecules and microbes. Unlike dendritic cells (DCs) and macrophages, which target antigens to lysosomes for degradation, M cells mainly transcytose the internalized antigens. This vigorous macromolecular transcytosis through M cells delivers antigen to the underlying organized lymphoid follicles and is believed to be essential for initiating antigen-specific mucosal immune responses. However, the molecular mechanisms promoting this antigen uptake by M cells are largely unknown. We have previously reported that glycoprotein 2 (Gp2), specifically expressed on the apical plasma membrane of M cells among enterocytes, serves as a transcytotic receptor for a subset of commensal and pathogenic enterobacteria, including Escherichia coli and Salmonella enterica serovar Typhimurium (S. Typhimurium), by recognizing FimH, a component of type I pili on the bacterial outer membrane 5. Here, we present a method for the application of a mouse Peyer's patch intestinal loop assay to evaluate bacterial uptake by M cells. This method is an improved version of the mouse intestinal loop assay previously described 6, 7. The improved points are as follows: 1. Isoflurane was used as an anesthetic agent. 2. Approximately 1 cm ligated intestinal loop including Peyer's patch was set up. 3. Bacteria taken up by M cells were fluorescently labeled by fluorescence labeling reagent or by overexpressing fluorescent protein such as green fluorescent protein (GFP). 4. M cells in the follicle-associated epithelium covering Peyer's patch were detected by whole-mount immunostainig with anti Gp2 antibody. 5. Fluorescent bacterial transcytosis by M cells were observed by confocal microscopic analysis. The mouse Peyer's patch intestinal loop assay could supply the answer what kind of commensal or pathogenic bacteria transcytosed by M cells, and may lead us to understand the molecular mechanism of how to stimulate mucosal immune system through M cells.

Application of a Mouse Ligated Peyer&amp;#8217;s Patch Intestinal Loop Assay to Evaluate Bacterial Uptake by M cells

M cells in a specialized follicle-associated epithelium covering Peyer&#x2019;s patches play an important role for the mucosal immunosurveillance in gut-associated lymphoid tissue. Here we described the evaluation method for bacterial transcytosis by M cells in vivo. This method provides a method to understand M-cell function in the immune system.

The inside of our gut is inhabited with enormous number of commensal bacteria. The mucosal surface of the gastrointestinal tract is continuously exposed ...

Isolation of Myeloid Dendritic Cells and Epithelial Cells from Human Thymus

In this protocol we provide a method to isolate dendritic cells (DC) and epithelial cells (TEC) from the human thymus. DC and TEC are the major antigen presenting cell (APC) types found in a normal thymus and it is well established that they play distinct roles during thymic selection. These cells are localized in distinct microenvironments in the thymus and each APC type makes up only a minor population of cells. To further understand the biology of these cell types, characterization of these cell populations is highly desirable but due to their low frequency, isolation of any of these cell types requires an efficient and reproducible procedure. This protocol details a method to obtain cells suitable for characterization of diverse cellular properties. Thymic tissue is mechanically disrupted and after different steps of enzymatic digestion, the resulting cell suspension is enriched using a Percoll density centrifugation step. For isolation of myeloid DC (CD11c+), cells from the low-density fraction (LDF) are immunoselected by magnetic cell sorting. Enrichment of TEC populations (mTEC, cTEC) is achieved by depletion of hematopoietic (CD45hi) cells from the low-density Percoll cell fraction allowing their subsequent isolation via fluorescence activated cell sorting (FACS) using specific cell markers. The isolated cells can be used for different downstream applications.

This protocol details a method to isolate antigen presenting cells from human thymus via different steps of enzymatic digestion of the tissue followed by density centrifugation of the single cell suspension and finally magnetic and/or FACS sorting of the cell populations of interest.

In this protocol we provide a method to isolate dendritic cells (DC) and epithelial cells (TEC) from the human thymus. DC and TEC are the major antigen ...

High Yield Purification of Plasmodium falciparum Merozoites For Use in Opsonizing Antibody Assays

Plasmodium falciparum merozoite antigens are under development as potential malaria vaccines. One aspect of immunity against malaria is the removal of free merozoites from the blood by phagocytic cells. However assessing the functional efficacy of merozoite specific opsonizing antibodies is challenging due to the short half-life of merozoites and the variability of primary phagocytic cells. Described in detail herein is a method for generating viable merozoites using the E64 protease inhibitor, and an assay of merozoite opsonin-dependent phagocytosis using the pro-monocytic cell line THP-1. E64 prevents schizont rupture while allowing the development of merozoites which are released by filtration of treated schizonts. &#160;Ethidium bromide labelled merozoites are opsonized with human plasma samples and added to THP-1 cells. Phagocytosis is assessed by a standardized high throughput protocol. Viable merozoites are a valuable resource for assessing numerous aspects of P. falciparum biology, including assessment of immune function. Antibody levels measured by this assay are associated with clinical immunity to malaria in naturally exposed individuals. The assay may also be of use for assessing vaccine induced antibodies. &#160;

High Yield Purification of Plasmodium falciparum Merozoites For Use in Opsonizing Antibody Assays

Measuring antibody function is key to understanding immunity to Plasmodium falciparum malaria. This method describes the purification of viable merozoites, and measurement of opsonization-dependent phagocytosis by flow cytometry.

Plasmodium falciparum merozoite antigens are under development as potential malaria vaccines. One aspect of immunity against malaria is the removal of ...

Isolation, Identification, and Purification of Murine Thymic Epithelial Cells

The thymus is a vital organ for T lymphocyte development. Of thymic stromal cells, thymic epithelial cells (TECs) are particularly crucial at multiple stages of T cell development: T cell commitment, positive selection and negative selection. However, the function of TECs in the thymus remains incompletely understood. In the article, we provide a method to isolate TEC subsets from fresh mouse thymus using a combination of mechanical disruption and enzymatic digestion. The method allows thymic stromal cells and thymocytes to be efficiently released from cell-cell and cell-extracellular matrix connections and to form a single-cell suspension. Using the isolated cells, multiparameter flow cytometry can be applied to identification and characterization of TECs and dendritic cells. Because TECs are a rare cell population in the thymus, we also describe an effective way to enrich and purify TECs by depleting thymocytes, the most abundant cell type in the thymus. Following the enrichment, cell sorting time can be decreased so that loss of cell viability can be minimized during purification of TECs. Purified cells are suitable for various downstream analyses like Real Time-PCR, Western blot and gene expression profiling. The protocol will promote research of TEC function and as well as the development of in vitro T cell reconstitution.

Here we describe an efficient method for isolation, identification, and purification of mouse thymic epithelial cells (TECs). The protocol can be utilized for studies of thymus function for normal T cell development, thymus dysfunction, and T cell reconstitution.

The thymus is a vital organ for T lymphocyte development. Of thymic stromal cells, thymic epithelial cells (TECs) are particularly crucial at multiple ...

Macrophage Cholesterol Depletion and Its Effect on the Phagocytosis of Cryptococcus neoformans

Cryptococcosis is a life-threatening infection caused by pathogenic fungi of the genus Cryptococcus. Infection occurs upon inhalation of spores, which are able to replicate in the deep lung. Phagocytosis of Cryptococcus by macrophages is one of the ways that the disease is able to spread into the central nervous system to cause lethal meningoencephalitis. Therefore, study of the association between Cryptococcus and macrophages is important to understanding the progression of the infection. The present study describes a step-by-step protocol to study macrophage infectivity by C. neoformansin vitro. Using this protocol, the role of host sterols on host-pathogen interactions is studied. Different concentrations of methyl--cyclodextrin (MCD) were used to deplete cholesterol from murine reticulum sarcoma macrophage-like cell line J774A.1. Cholesterol depletion was confirmed and quantified using both a commercially available cholesterol quantification kit and thin layer chromatography. Cholesterol depleted cells were activated using Lipopolysacharide (LPS) and Interferon gamma (IFN&#947;) and infected with antibody-opsonized Cryptococcus neoformans wild-type H99 cells at an effector-to-target ratio of 1:1. Infected cells were monitored after 2 hr of incubation with C. neoformans and their phagocytic index was calculated. Cholesterol depletion resulted in a significant reduction in the phagocytic index. The presented protocols offer a convenient method to mimic the initiation of the infection process in a laboratory environment and study the role of host lipid composition on infectivity.

Macrophage Cholesterol Depletion and Its Effect on the Phagocytosis of Cryptococcus neoformans

In this article, a protocol for infection of macrophages with Cryptococcus neoformans is described. Also, a method for sterol depletion from the macrophages is explained. These protocols provide a guide to study fungal infections in vitro and examine the role of sterols in such infections.

Cryptococcosis is a life-threatening infection caused by pathogenic fungi of the genus Cryptococcus. Infection occurs upon inhalation of spores, which are ...

Generation of Lymphocytic Microparticles and Detection of their Proapoptotic Effect on Airway Epithelial Cells

Interest in the biological roles of cell membrane&#8211;derived vesicles in cell&#8211;cell communication has increased in recent years. Microparticles (MPs) are one such type of vesicles, ranging in diameter from 0.1 &#956;m to 1 &#956;m, and typically shed from the plasma membrane of eukaryotic cells undergoing activation or apoptosis. Here we describe the generation of T lymphocyte&#8211;derived microparticles (LMPs) from apoptotic CEM T cells stimulated with actinomycin D. LMPs are isolated through a multistep differential centrifugation process and characterized using flow cytometry. This protocol also presents an in situ cell death detection method for demonstrating the proapoptotic effect of LMPs on bronchial epithelial cells derived from mouse primary respiratory bronchial tissue explants. Methods described herein provide a reproducible procedure for isolating abundant quantities of LMPs from apoptotic lymphocytes in vitro. LMPs derived in this manner can be used to evaluate the characteristics of various disease models, and for pharmacology and toxicology testing. Given that the airway epithelium offers a protective physical and functional barrier between the external environment and underlying tissue, use of bronchial tissue explants rather than immortalized epithelial cell lines provides an effective model for investigations requiring airway tract tissue.

Cell membrane&#8211;shed microparticles (MPs) are active biological vesicles that can be isolated and their pathophysiological effects investigated in various models. Here we describe a method for generating MPs derived from T lymphocytes (LMPs) and for demonstrating their proapoptotic effect on airway epithelial cells.

Interest in the biological roles of cell membrane&#8211;derived vesicles in cell&#8211;cell communication has increased in recent years. Microparticles ...

Legionella pneumophila Outer Membrane Vesicles: Isolation and Analysis of Their Pro-inflammatory Potential on Macrophages

Bacteria are able to secrete a variety of molecules via various secretory systems. Besides the secretion of molecules into the extracellular space or directly into another cell, Gram-negative bacteria can also form outer membrane vesicles (OMVs). These membrane vesicles can deliver their cargo over long distances, and the cargo is protected from degradation by proteases and nucleases. 
Legionella pneumophila (L. pneumophila) is an intracellular, Gram-negative pathogen that causes a severe form of pneumonia. In humans, it infects alveolar macrophages, where it blocks lysosomal degradation and forms a specialized replication vacuole. Moreover, L. pneumophila produces OMVs under various growth conditions. To understand the role of OMVs in the infection process of human macrophages, we set up a protocol to purify bacterial membrane vesicles from liquid culture. The method is based on differential ultracentrifugation. The enriched OMVs were subsequently analyzed with regard to their protein and lipopolysaccharide (LPS) amount and were then used for the treatment of a human monocytic cell line or murine bone marrow-derived macrophages. The pro-inflammatory responses of those cells were analyzed by enzyme-linked immunosorbent assay. Furthermore, alterations in a subsequent infection were analyzed. To this end, the bacterial replication of L. pneumophila in macrophages was studied by colony-forming unit assays. 
Here, we describe a detailed protocol for the purification of L. pneumophila OMVs from liquid culture by ultracentrifugation and for the downstream analysis of their pro-inflammatory potential on macrophages.

Legionella pneumophila Outer Membrane Vesicles: Isolation and Analysis of Their Pro-inflammatory Potential on Macrophages

Here, we describe the purification of Legionella pneumophila (L. pneumophila) outer membrane vesicles (OMVs) from liquid cultures. These purified vesicles are then used for the treatment of macrophages to analyze their pro-inflammatory potential.

Bacteria are able to secrete a variety of molecules via various secretory systems. Besides the secretion of molecules into the extracellular space or ...

Phagocytosis Assay for Apoptotic Cells in Drosophila Embryos

The molecular mechanisms underlying the phagocytosis of apoptotic cells need to be elucidated in more detail because of its role in immune and inflammatory intractable diseases. We herein developed an experimental method to investigate phagocytosis quantitatively using the fruit fly Drosophila, in which the gene network controlling engulfment reactions is evolutionally conserved from mammals. In order to accurately detect and count engulfing and un-engulfing phagocytes using whole animals, Drosophila embryos were homogenized to obtain dispersed cells including phagocytes and apoptotic cells. The use of dispersed embryonic cells enables us to measure in vivo phagocytosis levels as if we performed an in vitro phagocytosis assay in which it is possible to observe all phagocytes and apoptotic cells in whole embryos and precisely quantify the level of phagocytosis. We confirmed that this method reproduces those of previous studies that identified the genes required for the phagocytosis of apoptotic cells. This method allows the engulfment of dead cells to be analyzed, and when combined with the powerful genetics of Drosophila, will reveal the complex phagocytic reactions comprised of the migration, recognition, engulfment, and degradation of apoptotic cells by phagocytes.

Phagocytosis Assay for Apoptotic Cells in Drosophila Embryos

We herein describe a phagocytosis assay using the dispersed embryonic cells of Drosophila. It enables us to easily and precisely quantify in vivo phagocytosis levels, and to identify new molecules required for the phagocytosis of apoptotic cells.

The molecular mechanisms underlying the phagocytosis of apoptotic cells need to be elucidated in more detail because of its role in immune and ...

Laminar Flow-based Assays to Investigate Leukocyte Recruitment on Cultured Vascular Cells and Adherent Platelets

The recruitment of leukocytes upon injury or inflammation to sites of injury or tissue damage has been investigated during recent decades and has resulted in the concept of the leukocyte adhesion cascade. However, the exact molecular mechanisms involved in leukocyte recruitment have not yet been fully identified. Since leukocyte recruitment remains an important subject in the field of infection, inflammation, and (auto-) immune research, we present a straightforward laminar flow-based assay to study underlying mechanisms of the adhesion, de-adhesion, and transmigration of leukocytes under venous and arterial flow regimes. The in vitro assay can be used to study the molecular mechanisms that underlie the interactions between leukocytes and their cellular partners in different models of vascular inflammation. This protocol describes a laminar flow-based assay using a parallel-flow chamber and an inverted phase contrast microscope connected to a camera to study the interactions of leukocytes and endothelial cells or platelets, which can be visualized and recorded then analyzed offline. Endothelial cells, platelets, or leukocytes can be pretreated with inhibitors or antibodies to determine the role of specific molecules during this process. Shear conditions, i.e. arterial or venous shear stress, can be easily adapted by the viscosity and flow rate of the perfused fluids and the height of the channel.

Leukocytes avidly interact with vascular cells and platelets after vessel wall injury or during inflammation. Here, we describe a straightforward laminar flow-based assay to characterize the molecular mechanisms that underlie the interactions between leukocytes and their cellular partners.

The recruitment of leukocytes upon injury or inflammation to sites of injury or tissue damage has been investigated during recent decades and has resulted ...

Isolation of Salivary Epithelial Cells from Human Salivary Glands for In Vitro Growth as Salispheres or Monolayers

The salivary glands are a site of significant interest for researchers interested in multiple aspects of human disease. One goal of researchers is to restore function of glands damaged by radiation therapies or due to pathologies associated with Sj&#246;gren's syndrome. A second goal of researchers is to define the mechanisms by which viruses replicate within glandular tissue where they can then gain access to salivary fluids important for horizontal transmission. These goals highlight the need for a robust and accessible in vitro salivary gland model that can be utilized by researchers interested in the above mentioned as well as related research areas. Here we discuss a simple protocol to isolate epithelial cells from human salivary glands and propagate them in vitro. Our protocol can be further optimized to meet the needs of individual studies. Briefly, salivary tissue is mechanically and enzymatically separated to isolate single cells or small clusters of cells. Selection for epithelial cells occurs by plating onto a basement membrane matrix in the presence of media optimized to promote epithelial cell growth. These resulting cultures can be maintained as three-dimensional clusters, termed "salispheres", or grown as a monolayer on treated plastic tissue culture dishes. This protocol results in the outgrowth of a heterogenous population of mainly epithelial cells that can be propagated for 5-8 passages (15-20 population doublings) before undergoing cellular senescence.

We present a method for isolating and cultivating primary human salivary gland-derived epithelial cells. These cells exhibit gene expression patterns consistent with them being of salivary epithelial origin and can be grown as salispheres on basement membrane matrices derived from Engelbreth-Holm-Swarm tumor cells or as monolayers on treated culture dishes.

The salivary glands are a site of significant interest for researchers interested in multiple aspects of human disease. One goal of researchers is to ...