This work was supported by NIEHS R01ES014470 (KMZ).

&#160;Prior to starting this protocol, collect neonatal mice at postnatal days 1-3 (P1-3) in a sterile container nested with original cage bedding for protection and warmth. It is important to work quickly and efficiently through this protocol to optimize microglial yield. Please see Table 1 for complete reagent list.
1.&#160;Preparation of instruments, Culture Media, and Dishes
<ol>
	<li>Prepare 10 ml/pup Microglia Complete Media (MCM; 1x Minimal Essential Medium Earle&#39;s [MEM] supplemented with: 1 mM L-glutamine, 1 mM sodium pyruvate, 0.6% v/v D-(+)-glucose, 100 &#956;g/ml&#160;Penicillin/Streptomycin (P/S), 4% v/v Fetal Bovine Serum (FBS), 6% v/v Horse Serum), and add to each T-75 flask (1 flask/pup); cap and place horizontally into an incubator (37 &#176;C, 5% CO2) to equilibrate for 1 hr. It is essential to equilibrate this media in flask(s) before starting the dissection.</li>
	<li>Prepare, aliquot, and warm in 37&#160;&#176;C water bath&#160;MCM for dissection&#160;(6 ml/pup) and in a separate conical tube MCM for cell resuspension (2 ml/pup).&#160;Prepare, aliquot, and&#160;chill on ice&#160;Mincing Media (MM; HBSS supplemented with: 100 &#956;g/ml&#160;P/S, 0.01 M HEPES; 3 ml/pup), and Dissecting Media (DM; MEM supplemented with 100 &#956;g/ml&#160;P/S; 2 ml/pup).</li>
	<li>Sterilize the following surgical tools by submersion in 70% ethanol for 10 min: scissor #1 (1; to decapitate), forcep #1 (2; to secure nose and remove cortices), scissor #2 (1; nonangled; to open scalp), forcep #2 (1; to remove scalp), forcep #3 (1; to remove skull), forcep #4 (2; to remove meninges), scissor #3 (1; to mince brain tissue). Allow to air dry on a sterile pad.</li>
	<li>Wipe down the horizontal-airflow workstation and dissection microscope with 70% ethanol.</li>
	<li>Dispense DM into 2 sterile, 100&#160;mm Petri dishes for capturing head (3 ml; 1 dish/3 pups) and dissection (1 ml; 1 dish/pup; chilled on ice prior to dissection). Dispense MM into 1 sterile, 100&#160;mm Petri dish for mincing brain tissue (1 ml; 1 dish/pup).</li>
</ol>
2.&#160;Brain Tissue Dissection
<ol>
	<li>Prior to euthanasia, gently sanitize neck and head of pup with 70% ethanol using a lab tissue. With scissor #1, quickly euthanize pup by removing the head; capture head in previously prepared Petri dish. Euthanize and complete the dissection of one pup before proceeding to the next animal.</li>
	<li>Transfer the head to the chilled dissection dish; under dissection microscope secure the head by pinching the nose using forcep #1 (alternatively, the head can be secured by piercing the forceps through the eye socket); open scalp using scissor #2 by creating a Y-cut: begin from base of head and at an angle toward the eyes. Use forcep #3 to gently remove scalp by peeling laterally, exposing the skull.</li>
	<li>Using forcep #3, gently remove connective tissue at base of head. When base of skull is exposed, carefully open skull by threading one arm of forcep in between the brain and skull (following the interhemispheric fissure); grip; gently pull the skull upwards to tear open.</li>
	<li>Disrupt connective tissue under ventral side of brain using forcep #1, and subsequently remove brain using the same tool. Lift the brain out of skull by using an upward force under the ventral side of the brain.</li>
	<li>Keep the brain in its anatomical position: dorsal side facing upwards to visualize the cortices under the dissection microscope; secure the brain in place by inserting tips of forceps in the intersection of the midbrain and the cortex; completely remove cortical meninges with forcep #4, then proceed to remove the ventral meninges. Once the meninges have been completely removed, separate the cortices from the remainder of the brain using forcep #4. It is essential to completely remove meningeal tissue to maximize microglia purity and yield.</li>
</ol>
3.&#160;Brain Tissue Mincing
<ol>
	<li>Transfer cortices to previously prepared mincing dish; continue to mincing step using sterile technique in Class II Biological Safety Cabinet.</li>
	<li>Mince brain tissue using scissor #3; transfer minced tissue to a 15&#160;ml&#160;conical tube; rinse scissors and mincing dish with 1 ml&#160;of MM each, collect and dispense rinses into the 15 ml&#160;conical tube containing the minced tissue. This rinse step will maximize the yield of microglia by ensuring that all residual tissue is transferred to conical tube. Leave tissue suspension undisturbed for 1-2 min, allowing minced tissue to settle at bottom of tube. Do not exceed 2 min&#160;as MM does not contain essential nutrients.</li>
	<li>Carefully remove and discard 2 ml&#160;of supernatant with generic 1,000 &#956;l&#160;micropipettor with a standard pipette tip, making certain not to disrupt the settled minced-tissue.</li>
	<li>Add 3 ml&#160;of MCM to the minced-tissue; triturate the tissue with full force using a generic 1,000 &#956;l&#160;micropipettor with a standard pipette tip. No discernable solid tissue should remain when trituration is complete. Add another 3 ml&#160;of MCM with the same pipette tip, collecting residual triturated sample from the pipette tip.</li>
</ol>
4.&#160;Growing Cortical Cells
<ol>
	<li>Centrifuge the minced tissue to pellet cells (215 x g; 5 min; RT; clinical centrifuge with swinging bucket rotor). Return pelleted cells to the biological safety cabinet, remove and discard the supernatant; gently resuspend the cell pellet (2 ml/tube; MCM); add the cell resuspension to the previously prepared T-75 flask; cap the flask and place it horizontally into a humidified, standard tissue culture incubator (37 &#176;C, 5% CO2). Allow the cells to incubate for 24 hr.</li>
	<li>After 24 hr, gently tap flask against palm of hand to disrupt tissue debris. Check cells before and after tapping to ensure complete removal of debris. Set flask vertical; remove and discard media; add fresh MCM to the bottom of the flask (12 ml; 37 &#176;C); cap and place back into the incubator, horizontally.</li>
	<li>Check cells daily for contamination and to monitor growth.</li>
	<li>At approximately 17-21 days in vitro (DIV), microglial cells will be ready for harvest from the mixed glial culture. To determine if cells are ready, examine cells under an inverted phase-contrast microscope. Microglia are ready for harvest when at ~40% confluency. They appear as small, bright, spherical cells, growing as a monolayer on top of other glia.</li>
</ol>
5.&#160;Isolation of Microglia from Mixed Glial Culture
<ol>
	<li>To isolate microglia, vigorously tap flask against laboratory bench. This agitation helps separate microglia from other glial cells due to the low-adherence properties of microglia.</li>
	<li>Seal T-75 flask caps with Parafilm and rotate the mixed glial cultures (200 rpm; 37 &#176;C; 5 hr) using a temperature-controlled, nonhumidified rotary shaker. Do not allow cells to shake for longer than 5 hr. Visually inspect that microglia have lifted off the flask surface after 5 hr, using an inverted phase-contrast microscope. Microglia are bright, spherical, free-floating cells. There will be a residual layer of astrocytes and oligodendrocytes adhering to the bottom of the flask.</li>
	<li>Collect supernatant media containing microglia into a sterile conical centrifuge tube; pellet microglia (215 x g; 5 min; swinging bucket rotor).</li>
	<li>Resuspend the microglial pellet in warm Microglial Growth Medium (MGM; MEM supplemented with: 1 mM sodium pyruvate, 0.6% v/vglucose, 1 mM L-glutamine, 100 &#956;g/ml&#160;P/S, 5% v/v FBS; ~2 ml/flask), determine the cell concentration using a hemocytometer, and plate 1 x 105 cells/well in a 24-well plate format on plastic or sterile glass cover slips (500 &#956;l/well; MGM). Using this procedure the average microglia yield is 7.5 x 105 cells/pup cortex.</li>
	<li>24-hr&#160;post-plating, remove all of the media and refeed cells with fresh MGM (37 &#176;C) to remove floating cells and debris. This step is critical to cell survival and to maintain quiescent microglia. Cells may be utilized for experimentation immediately after refeeding.</li>
</ol>
6.&#160;Example Treatments
<ol>
	<li>Expose cells to 10 ng/ml&#160;of Pam3CSK4&#160;(Pam), 10 ng/ml&#160;lipopolysaccharide (LPS) or vehicle control; incubate for 2 or 24 hr&#160;in humidified incubator (37 &#176;C, 5% CO2).</li>
</ol>
7.&#160;Analyzing Microglia for Functionality Ex vivo via Immunofluorescent Imaging and Immunocytochemistry
<ol>
	<li>After treatment, harvest cell culture media in microfuge tubes (1.5 ml) and centrifuge using a tabletop microcentrifuge (2 min; 900 x g) to clear media. Transfer the supernatant to a clean microfuge tube; assay immediately, or store at -20 &#176;C until ready to use. Analyze TNF-&#945; concentration in cell culture supernatant via commercially available mouse TNF-&#945; ELISA kit.</li>
	<li>Wash cells with phosphate buffered saline (PBS), and fix cells with 4% (w/v) paraformaldehyde/4% (w/v) sucrose/PBS pH 7.4 (4% PFA; 15 min; RT). Following fixation, wash cells with PBS for 5 min&#160;with gentle shaking on an orbital shaker.
	<ol>
		<li>Immunofluorescence/Immunocytochemistry. After fixation and PBS wash, process microglia for immunocytochemistry. All steps carried out with gentle shaking. Permeabilize cells in PBS/0.1% triton X-100; block cells in PBS/10% normal goat serum for one hour. Incubate cells O/N&#160;at 4 &#176;C with rabbit anti-NF-&#954;B antibody (p65 subunit; 1/1,250) or rabbit anti-Iba-1 antibody (1/750) in blocking buffer. Visualize antigen:antibody complex following incubation with fluorescently conjugated goat anti-rabbit IgG secondary antibody (1 hr; 1/1,000). Remove unbound secondary antibody by washing with PBS/0.1% triton X-100 (3x 5 min).</li>
		<li>Counter stain cells with 4&#39;,6-Diamidino-2-Phenylindole/PBS (DAPI; 0.1 &#956;g/ml) to visualize the cell nucleus. All microglia derived from CX3CR1-GFP+/- mice express GFP. Utilize a 350 nm wavelength filter to visualize DAPI; a 488 nm wavelength filter to visualize GFP; and a 594 nm wavelength filter to visualize p65 and Iba-1 immunocomplexes.</li>
	</ol>
	</li>
	<li>Mount cover slips using aqueous mounting solution and visualize microglia using fluorescent microscopy.</li>
</ol>

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Res. 16, 238-254 (2009).</li><li>Jung, S., 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=Analysis+of+fractalkine+receptorCX(3)CR1+function+by+targeted+deletion+and+green+fluorescent+protein+reporter+gene+insertion.">Analysis of fractalkine receptorCX(3)CR1 function by targeted deletion and green fluorescent protein reporter gene insertion.</a> Mol. Cell. Biol. 20, 4106-4114 (2000).</li><li>Imai, T., 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=Identification+and+molecular+characterization+of+fractalkine+receptor+CX3CR1,+which+mediates+both+leukocyte+migration+and+adhesion.">Identification and molecular characterization of fractalkine receptor CX3CR1, which mediates both leukocyte migration and adhesion.</a> Cell. 91, 521-530 (1997).</li><li>Cardona, A. E., 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=Control+of+microglial+neurotoxicity+by+the+fractalkine+receptor.">Control of microglial neurotoxicity by the fractalkine receptor.</a> Nat. Neurosci. 9, 917-924 (2006).</li><li>Streit, W. J., Walter, S. A., Pennell, N. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reactive+microgliosis.">Reactive microgliosis.</a> Prog. Neurobiol. 57, 563-581 (1999).</li><li>Frank, M. G., Wieseler-Frank, J. L., Watkins, L. R., Maier, S. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+isolation+of+highly+enriched+and+quiescent+microglia+from+adult+rat+hippocampus:immunophenotypic+and+functional+characteristics.">Rapid isolation of highly enriched and quiescent microglia from adult rat hippocampus:immunophenotypic and functional characteristics.</a> J. Neurosci. Methods. 151, 121-130 (2006).</li></ol>

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

The present procedure offers an effective method for the isolation of cortical microglia from neonatal mice. This procedure has a two-fold benefit of 1) preserving microglia immunophenotype and functionality, as determined by fluorescent imaging, immunocytochemistry, and ELISA; and, 2) allowing microglia to mature in the presence of other glial cells (astrocytes and oligodentrocytes) prior to isolation, which may facilitate important cell-cell interactions during the glial culture maturation period. Importantly, isolated...

Microglial cells, the surveillance macrophages of the CNS parenchyma, comprise approximately 12% of the total cell population of the adult mammalian brain. Microglia are derived from yolk sac myeloid precursor cells&#160;and vary in cell density and morphology in different cytoarchitectural regions within the adult CNS1-5. In a healthy adult brain, microglia are small, ramified or polar cells with fine, dynamic processes. In contrast to peripheral macrophage morphology, microglia demonstrate a quiescent, low-profile phenotype in healthy brains that may appear as cellular inactivity; however, in vivo imaging studies demonstrate that microglial processes dynamically extend and retract to monitor their microenvironment in a manner reminiscent of &#34;sampling and surveying&#34;6,7.
Microglia are highly and differentially responsive to environmental and pathophysiological alterations in the brain, switching from a surveillant to an effector state&#8212;commonly regarded as their resting and activated states, respectively. This switch in activation can be mediated by engagement of membrane-bound pattern recognition receptors (PRRs), such as toll-like receptors (TLRs), which respond to pathogen-associated molecular patterns (PAMPs), namely bacterial- and viral-derived lipoproteins, nucleic acids, and carbohydrates8-11. In addition to PAMPs, PRRs have also been shown to induce microglial activation against sterile, nonpathogenic molecules known as danger/damage-associated molecular patterns (DAMPs), which represent a perturbation in CNS homeostasis, such as cellular damage12-16. Once engaged, PRRs initiate an intracellular signaling cascade that results in changes in microglial cell morphology and gene expression; specifically, activated microglia adapt an amoeboid-like phenotype, translocate the p65 NF-&#954;B subunit (p65) to the cell nucleus, and upregulate the production and secretion of proinflammatory cytokines, such as tumor necrosis factor-&#945; (TNF-&#945;), interleukin-1 &#946; (IL-1&#946;), along with reactive oxygen species (ROS)16-24. Although integral in the innate immune response of the CNS, these secreted molecules have also been found to increase neuronal oxidative stress, thereby inducing and exacerbating neurodegeneration in diseased states such as Parkinson&#39;s and Alzheimer&#39;s disease25-29.
However, the mechanisms of microglial activation in pathological states are not completely understood. Therefore, isolation of microglia is a powerful investigative tool into these biological processes, as many in vivo features of microglial activation can be recapitulated in culture. Several methods are available for isolating microglia, including isolation via a Percoll gradient following enzymatic digestion of CNS tissue30,31. However, enzymatic digestion can alter the immunophenotype of the cells by reducing cell-surface antigen expression32, and results in lower cell yield per animal than the method described herein. Specifically, we report an average microglia yield per pup cortex of 7.5 x 105 cells, while previously reported isolation methods from whole CNS via a Percoll gradient yield 3-5 x 105 cells30,33,34. The present procedure circumvents the use of digestion enzymes by isolating microglia based on their low-adherence properties, thereby preserving the microglial immunophenotype and functionality.
In the present study, we describe the isolation of microglial cells from mixed glial cultures derived from neonatal heterozygous CX3CR1-GFP (CX3CR1-GFP+/-), and C57BL/6 murine cortices via mechanical agitation on a rotary shaker, an extension of previously published method24,35. We utilize the former mouse strain for easy visualization of microglia, as these mice express GFP under the control of the endogenous Cx3Cr1 locus -&#160;a monocyte-specific promoter36-38. This method produces highly pure microglial cultures with a preserved immunophenotype ex vivo as demonstrated by morphological changes, nuclear translocation of p65, and secretion of TNF-&#945; when challenged with bacterial lipopolysaccharide (LPS) or Pam3CSK4, TLR4 and TLR1/2 agonists, respectively.

<table border="0" cellpadding="0" cellspacing="0" width="680">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="160">
			<td height="160" style="height:160px;width:233px;">Glucose</td>
			<td style="width:149px;">Sigma</td>
			<td style="width:155px;">G8270</td>
			<td style="width:143px;">Make 20% Stock Solution with MilliQ water; filter sterilize; store at 4 &#176;C; shelf life: 3-6 months. Used to make MCM and MGM.</td>
		</tr>
		<tr height="60">
			<td height="60" style="height:60px;width:233px;">Sodium pyruvate 100 mM (100x)</td>
			<td style="width:149px;">Hyclone</td>
			<td style="width:155px;">SH30239.01</td>
			<td style="width:143px;">Store at 4 &#176;C. Used to make MCM and MGM.</td>
		</tr>
		<tr height="80">
			<td height="80" style="height:80px;width:233px;">Penicillin/Streptomycin 10,000 units/ml (100x)</td>
			<td style="width:149px;">Gibco</td>
			<td style="width:155px;">15140-122</td>
			<td style="width:143px;">Store at -20 &#176;C. Used to make MCM, MGM, MM, and DM.</td>
		</tr>
		<tr height="60">
			<td height="60" style="height:60px;width:233px;">L-glutamine 200 mM (100x)</td>
			<td style="width:149px;">Gibco</td>
			<td style="width:155px;">25030-081</td>
			<td style="width:143px;">Store at -20 &#176;C. Used to make MCM and MGM.</td>
		</tr>
		<tr height="80">
			<td height="80" style="height:80px;width:233px;">Fetal Bovine Serum (Defined)</td>
			<td style="width:149px;">Hyclone</td>
			<td style="width:155px;">SH30070.03</td>
			<td style="width:143px;">Filter sterilize; store at -20 &#176;C. Used to make MCM and MGM.</td>
		</tr>
		<tr height="120">
			<td height="120" style="height:120px;width:233px;">Minimum Essential Medium Earle&#39;s (MEM)</td>
			<td style="width:149px;">Cellgro</td>
			<td style="width:155px;">15-010-CV</td>
			<td style="width:143px;">Without L-glutamine. Contains Earle&#39;s salts. Used to make MCM, MGM, and DM.</td>
		</tr>
		<tr height="80">
			<td height="80" style="height:80px;width:233px;">Horse Serum</td>
			<td style="width:149px;">Gibco</td>
			<td style="width:155px;">16050</td>
			<td style="width:143px;">Filter sterilize; store at -20 &#176;C. Used to make MCM and MGM.</td>
		</tr>
		<tr height="80">
			<td height="80" style="height:80px;width:233px;">Hanks&#39; Balanced Salt Solution (HBSS)</td>
			<td style="width:149px;">Cellgro</td>
			<td style="width:155px;">21-021-CV</td>
			<td style="width:143px;">Without calcium and magnesium. Store at 4 &#176;C. Used to make MM.</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:233px;">HEPES 1 M</td>
			<td style="width:149px;">Gibco</td>
			<td style="width:155px;">15630-031</td>
			<td style="width:143px;">Store at 4 &#176;C. Used to make MM.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:233px;">T-75 Flask</td>
			<td style="width:149px;">Corning</td>
			<td style="width:155px;">430641</td>
			<td style="width:143px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:233px;">4&#39;,6-Diamidino-2-Phenylindole, dilactate (DAPI)</td>
			<td style="width:149px;">Invitrogen</td>
			<td style="width:155px;">D3571</td>
			<td style="width:143px;">Used to stain cell nucleus.</td>
		</tr>
		<tr height="60">
			<td height="60" style="height:60px;width:233px;">Rabbit anti-Iba1</td>
			<td style="width:149px;">Wako</td>
			<td style="width:155px;">019-19741</td>
			<td style="width:143px;">Used at 1/750 dilution for ICC staining of Iba1.&#160;</td>
		</tr>
		<tr height="60">
			<td height="60" style="height:60px;width:233px;">Rabbit anti-NF&#954;B (p65)</td>
			<td style="width:149px;">Abcam</td>
			<td style="width:155px;">7970</td>
			<td style="width:143px;">Used at 1/1250 dilution for ICC staining for p65.</td>
		</tr>
		<tr height="100">
			<td height="100" style="height:100px;width:233px;">Alexafluor 594 Goat anti-Rabbit IgG (H+L)</td>
			<td style="width:149px;">Invitrogen</td>
			<td style="width:155px;">A11012</td>
			<td style="width:143px;">Used at 1/1000 dilution for visualization of antigen:antibody complex in ICC.</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:233px;">10 ml Disposable Serological Pipet</td>
			<td style="width:149px;">Fisher Scientific</td>
			<td style="width:155px;">13-678-11E</td>
			<td style="width:143px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:233px;">50 ml Disposable Centrifuge Tube</td>
			<td style="width:149px;">Fisher Scientific</td>
			<td style="width:155px;">05-539-8</td>
			<td style="width:143px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:233px;">15 ml Disposible Centrifuge Tube</td>
			<td style="width:149px;">Fisher Scientific</td>
			<td style="width:155px;">05-539-12</td>
			<td style="width:143px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:233px;">Sterile Polystyrene Petri Dish</td>
			<td style="width:149px;">Fisher Scientific</td>
			<td style="width:155px;">875713</td>
			<td style="width:143px;">100 mm x 15 mm</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:233px;">Scissor: Straight Metzembaum (scissor #1)</td>
			<td style="width:149px;">Roboz Surgical</td>
			<td style="width:155px;">RS-6010</td>
			<td style="width:143px;">1; 5 inch; used for removing head</td>
		</tr>
		<tr height="80">
			<td height="80" style="height:80px;width:233px;">Scissor: Vannas 
			(scissor #2)</td>
			<td style="width:149px;">Fine Science Tools</td>
			<td style="width:155px;">15000-08</td>
			<td style="width:143px;">1; non-angled; 2.5mm cutting edge; used to open scalp</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:233px;">Scissor: Student Vannas (scissor #3)</td>
			<td style="width:149px;">Fine Science Tools</td>
			<td style="width:155px;">91501-09</td>
			<td style="width:143px;">1; curved; used to mince brain tissue</td>
		</tr>
		<tr height="60">
			<td height="60" style="height:60px;width:233px;">Forcep: Dumont #7 
			(forcep #1)</td>
			<td style="width:149px;">Fine Science Tools</td>
			<td style="width:155px;">91197-00</td>
			<td style="width:143px;">2; used to secure nose and remove cortices&#160;</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:233px;">Forcep: Dumont #2 
			(forcep #2)</td>
			<td style="width:149px;">Fine Science Tools</td>
			<td style="width:155px;">11223-20</td>
			<td style="width:143px;">1; used to remove scalp</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:233px;">Forcep: Dumont #3 
			(forcep #3)</td>
			<td style="width:149px;">Fine Science Tools</td>
			<td style="width:155px;">11231-30</td>
			<td style="width:143px;">1; used to remove skull</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:233px;">Forcep: Dumont #5a 
			(forcep #4)</td>
			<td style="width:149px;">Fine Science Tools</td>
			<td style="width:155px;">11253-21</td>
			<td style="width:143px;">1; used to remove meninges</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;"></td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;"></td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Table of specific equipment</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:233px;">Name of Equipment</td>
			<td style="width:149px;">Name of Company</td>
			<td style="width:155px;">Catalogue Number</td>
			<td style="width:143px;">Comments</td>
		</tr>
		<tr height="80">
			<td height="80" style="height:80px;width:233px;">Zoom Stereo Dissection Microscope&#160;</td>
			<td style="width:149px;">Olympus</td>
			<td style="width:155px;">SZ4060</td>
			<td style="width:143px;">Microscope is placed inside Laminar-Horizontal Flow Cabinet</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:233px;">Laminar-Horizontal Flow Cabinet</td>
			<td style="width:149px;">Nuaire</td>
			<td style="width:155px;">NU-201-330</td>
			<td style="width:143px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:233px;">Biological Safety Cabinet</td>
			<td style="width:149px;">Labconco</td>
			<td style="width:155px;">3440001</td>
			<td style="width:143px;">Class II</td>
		</tr>
		<tr height="46">
			<td height="46" style="height:46px;width:233px;">Water-Jacketed CO2 Incubator</td>
			<td style="width:149px;">VWR</td>
			<td>97025-836</td>
			<td style="width:143px;">Set to 37 &#176;C, 5% CO2</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:233px;">Swing-out buckets</td>
			<td style="width:149px;">Fisher Scientific</td>
			<td>75006441</td>
			<td style="width:143px;">To be used with Swing-out rotor</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:233px;">Swing-out Rotor</td>
			<td style="width:149px;">Fisher Scientific</td>
			<td>75006445</td>
			<td style="width:143px;">Max Radius: 19.2 (cm)</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:233px;">Sorvall Legend RT+ Centrifuge 
			(clinical centrifuge)</td>
			<td style="width:149px;">Fisher Scientific</td>
			<td>75-004-377</td>
			<td style="width:143px;">With swing-out rotor</td>
		</tr>
		<tr height="80">
			<td height="80" style="height:80px;width:233px;">AccuSpin Micro 17 microcentrifuge 
			(tabletop microcentrifuge)</td>
			<td style="width:149px;">Fisher Scientific</td>
			<td>S98645</td>
			<td style="width:143px;">With microliter rotor (24 x 1.5/2.0 ml; 
			Cat #: 75003524)&#160;&#160;</td>
		</tr>
	</tbody>
</table>

isolation of cortical microglia with preserved immunophenotype and functionality from murine neonates

Isolation of microglia from CNS tissue is a powerful investigative tool used to study microglial biology ex vivo. The present method details a procedure for isolation of microglia from neonatal murine cortices by mechanical agitation with a rotary shaker. This microglia isolation method yields highly pure cortical microglia that exhibit morphological and functional characteristics indicative of quiescent microglia in normal, nonpathological conditions in vivo. This procedure also preserves the microglial immunophenotype and biochemical functionality as demonstrated by the induction of morphological changes, nuclear translocation of the p65 subunit of NF-&#954;B (p65), and secretion of the hallmark proinflammatory cytokine, tumor necrosis factor-&#945; (TNF-&#945;), upon lipopolysaccharide (LPS) and Pam3CSK4 (Pam) challenges. Therefore, the present isolation procedure preserves the immunophenotype of both quiescent and activated microglia, providing an experimental method of investigating microglia biology in ex vivo conditions.

Retaining the immunophenotype and functionality of microglia ex vivo during isolation is critical to be able to utilize these cells as an investigatory model for microglial biology. In order to demonstrate the successful preservation of microglia immunofunctionality using the present method, we isolated cortical microglia from P3 neonates (CX3CR1-GFP+/-and C57BL/6) and treated cultures with either LPS or Pam.
As illustrated in Figure 1A, isolation of microg...

Watch this Scientific Journal Video about Isolation of Cortical Microglia with Preserved Immunophenotype and Functionality From Murine Neonates at JoVE.com

Isolation of Cortical Microglia with Preserved Immunophenotype and Functionality From Murine Neonates

One key to successful investigation of microglial biology is the preservation of microglial immunofunction ex vivo during isolation from CNS tissue. Isolating microglia via rotary shaking results in highly pure and immunofunctional cell cultures as assessed by fluorescent imaging, immunocytochemistry, and ELISA following microglia activation with the proinflammatory stimuli lipopolysaccharide (LPS) and Pam3CSK4 (Pam).

Isolation of microglia from CNS tissue is a powerful investigative tool used to study microglial biology ex vivo. The present method details a procedure ...

isolation-cortical-microglia-with-preserved-immunophenotype

Research

JoVE Journal

Immunology and Infection

15.6K Views.  Georgetown University Medical Center. One key to successful investigation of microglial biology is the preservation of microglial immunofunction ex vivo during isolation from CNS tissue. Isolating microglia via rotary shaking results in highly pure and immunofunctional cell cultures as assessed by fluorescent imaging, immunocytochemistry, and ELISA following microglia activation with the proinflammatory stimuli lipopolysaccharide (LPS) and Pam3CSK4 (Pam).

Video: Isolation of Cortical Microglia with Preserved Immunophenotype and Functionality From Murine Neonates

Primary Microglia Isolation from Mixed Glial Cell Cultures of Neonatal Rat Brain Tissue

Microglia account for approximately 12% of the total cellular population in the mammalian brain. While neurons and astrocytes are considered the major cell types of the nervous system, microglia play a significant role in normal brain physiology by monitoring tissue for debris and pathogens and maintaining homeostasis in the parenchyma via phagocytic activity 1,2. Microglia are activated during a number of injury and disease conditions, including neurodegenerative disease, traumatic brain injury, and nervous system infection 3. Under these activating conditions, microglia increase their phagocytic activity, undergo morpohological and proliferative change, and actively secrete reactive oxygen and nitrogen species, pro-inflammatory chemokines and cytokines, often activating a paracrine or autocrine loop 4-6. As these microglial responses contribute to disease pathogenesis in neurological conditions, research focused on microglia is warranted.
	Due to the cellular heterogeneity of the brain, it is technically difficult to obtain sufficient microglial sample material with high purity during in vivo experiments. Current research on the neuroprotective and neurotoxic functions of microglia require a routine technical method to consistently generate pure and healthy microglia with sufficient yield for study. We present, in text and video, a protocol to isolate pure primary microglia from mixed glia cultures for a variety of downstream applications. Briefly, this technique utilizes dissociated brain tissue from neonatal rat pups to produce mixed glial cell cultures. After the mixed glial cultures reach confluency, primary microglia are mechanically isolated from the culture by a brief duration of shaking. The microglia are then plated at high purity for experimental study.
	The principle and protocol of this methodology have been described in the literature 7,8. Additionally, alternate methodologies to isolate primary microglia are well described 9-12. Homogenized brain tissue may be separated by density gradient centrifugation to yield primary microglia 12. However, the centrifugation is of moderate length (45 min) and may cause cellular damage and activation, as well as, cause enriched microglia and other cellular populations. Another protocol has been utilized to isolate primary microglia in a variety of organisms by prolonged (16 hr) shaking while in culture 9-11. After shaking, the media supernatant is centrifuged to isolate microglia. This longer two-step isolation method may also perturb microglial function and activation. We chiefly utilize the following microglia isolation protocol in our laboratory for a number of reasons: (1) primary microglia simulate in vivo biology more faithfully than immortalized rodent microglia cell lines, (2) nominal mechanical disruption minimizes potential cellular dysfunction or activation, and (3) sufficient yield can be obtained without passage of the mixed glial cell cultures.
	It is important to note that this protocol uses brain tissue from neonatal rat pups to isolate microglia and that using older rats to isolate microglia can significantly impact the yield, activation status, and functional properties of isolated microglia. There is evidence that aging is linked with microglia dysfunction, increased neuroinflammation and neurodegenerative pathologies, so previous studies have used ex vivo adult microglia to better understand the role of microglia in neurodegenerative diseases where aging is important parameter. However, ex vivo microglia cannot be kept in culture for prolonged periods of time. Therefore, while this protocol extends the life of primary microglia in culture, it should be noted that the microglia behave differently from adult microglia and in vitro studies should be carefully considered when translated to an in vivo setting.

Isolating primary microglia from the cellular heterogeneity of the brain is essential to investigate their role in both physiological and pathological conditions. This protocol describes a mechanical isolation and mixed cell culture technique that provides high yield and high purity, viable primary microglial cells for in vitro study and downstream applications.

Microglia account for approximately 12% of the  total cellular population in the mammalian brain. While neurons and astrocytes are considered  the major ...

Isolation, Processing and Analysis of Murine Gingival Cells

We have developed a technique to precisely isolate and process murine gingival tissue for flow cytometry and molecular studies. The gingiva is a unique and important tissue to study immune mechanisms because it is involved in host immune response against oral biofilm that might cause periodontal diseases. Furthermore, the close proximity of the gingiva to alveolar bone tissue enables also studying bone remodeling under inflammatory conditions. Our method yields large amount of immune cells that allows analysis of even rare cell populations such as Langerhans cells and T regulatory cells as we demonstrated previously 1. Employing mice to study local immune responses involved in alveolar bone loss during periodontal diseases is advantageous because of the availability of various immunological and experimental tools. Nevertheless, due to their small size and the relatively inconvenient access to the murine gingiva, many studies avoided examination of this critical tissue. The method described in this work could facilitate gingival analysis, which hopefully will increase our understating on the oral immune system and its role during periodontal diseases.

This study describes an efficient technique to isolate and process gingival tissues from the mouse oral cavity in order to produce a single-cell culture. The resulting cells can be further used for flow cytometry analysis and molecular studies.

We have developed a technique to precisely isolate and process murine gingival tissue for flow cytometry and molecular studies. The gingiva is a unique ...

Culturing Microglia from the Neonatal and Adult Central Nervous System

Microglia are the resident macrophage-like cells of the central nervous system (CNS) and, as such, have critically important roles in physiological and pathological processes such as CNS maturation in development, multiple sclerosis, and spinal cord injury. Microglia can be activated and recruited to action by neuronal injury or stimulation, such as axonal damage seen in MS or ischemic brain trauma resulting from stroke. These immunocompetent members of the CNS are also thought to have roles in synaptic plasticity under non-pathological conditions. We employ protocols for culturing microglia from the neonatal and adult tissues that are aimed to maximize the viable cell numbers while minimizing confounding variables, such as the presence of other CNS cell types and cell culture debris. We utilize large and easily discernable CNS components (e.g. cortex, spinal cord segments), which makes the entire process feasible and reproducible. The use of adult cells is a suitable alternative to the use of neonatal brain microglia, as many pathologies studied mainly affect the postnatal spinal cord. These culture systems are also useful for directly testing the effect of compounds that may either inhibit or promote microglial activation. Since microglial activation can shape the outcomes of disease in the adult CNS, there is a need for in vitro systems in which neonatal and adult microglia can be cultured and studied.

We outline methods for the efficient and quick isolation/culture of viable microglia from the neonatal cerebral cortex and adult spinal cord. The dissection and plating of cortical microglia can be accomplished within 90 minutes, with the subsequent microglial harvest taking place ~ 10 days following the initial dissection.

Microglia are the resident macrophage-like cells of the central nervous system (CNS) and, as such, have critically important roles in physiological and ...

Isolation of Murine Lymph Node Stromal Cells

Secondary lymphoid organs including lymph nodes are composed of stromal cells that provide a structural environment for homeostasis, activation and differentiation of lymphocytes. Various stromal cell subsets have been identified by the expression of the adhesion molecule CD31 and glycoprotein podoplanin (gp38), T zone reticular cells or fibroblastic reticular cells, lymphatic endothelial cells, blood endothelial cells and FRC-like pericytes within the double negative cell population. For all populations different functions are described including, separation and lining of different compartments, attraction of and interaction with different cell types, filtration of the draining fluidics and contraction of the lymphatic vessels. In the last years, different groups have described an additional role of stromal cells in orchestrating and regulating cytotoxic T cell responses potentially dangerous for the host. 
Lymph nodes are complex structures with many different cell types and therefore require a appropriate procedure for isolation of the desired cell populations. Currently, protocols for the isolation of lymph node stromal cells rely on enzymatic digestion with varying incubation times; however, stromal cells and their surface molecules are sensitive to these enzymes, which results in loss of surface marker expression and cell death. Here a short enzymatic digestion protocol combined with automated mechanical disruption to obtain viable single cells suspension of lymph node stromal cells maintaining their surface molecule expression is proposed.

Isolation of lymph node stromal cells is a multistep procedure including enzymatic digestion and mechanical disaggregation to obtain fibroblastic reticular cells, lymphatic and blood endothelial cells. In the described procedure, a short digestion is combined with automated mechanical disaggregation to minimize surface marker degradation of viable lymph node stromal cells.

Secondary lymphoid organs including lymph nodes are composed of stromal cells that provide a structural environment for homeostasis, activation and ...

Isolation of Leukocytes from the Murine Tissues at the Maternal-Fetal Interface

Immune tolerance in pregnancy requires that the immune system of the mother undergoes distinctive changes in order to accept and nurture the developing fetus. This tolerance is initiated during coitus, established during fecundation and implantation, and maintained throughout pregnancy. Active cellular and molecular mediators of maternal-fetal tolerance are enriched at the site of contact between fetal and maternal tissues, known as the maternal-fetal interface, which includes the placenta and the uterine and decidual tissues. This interface is comprised of stromal cells and infiltrating leukocytes, and their abundance and phenotypic characteristics change over the course of pregnancy. Infiltrating leukocytes at the maternal-fetal interface include neutrophils, macrophages, dendritic cells, mast cells, T cells, B cells, NK cells, and NKT cells that together create the local micro-environment that sustains pregnancy. An imbalance among these cells or any inappropriate alteration in their phenotypes is considered a mechanism of disease in pregnancy. Therefore, the study of leukocytes that infiltrate the maternal-fetal interface is essential in order to elucidate the immune mechanisms that lead to pregnancy-related complications. Described herein is a protocol that uses a combination of gentle mechanical dissociation followed by a robust enzymatic disaggregation with a proteolytic and collagenolytic enzymatic cocktail to isolate the infiltrating leukocytes from the murine tissues at the maternal-fetal interface. This protocol allows for the isolation of high numbers of viable leukocytes (&#62;70%) with sufficiently conserved antigenic and functional properties. Isolated leukocytes can then be analyzed by several techniques, including immunophenotyping, cell sorting, imaging, immunoblotting, mRNA expression, cell culture, and in vitro functional assays such as mixed leukocyte reactions, proliferation, or cytotoxicity assays.

Described herein is a protocol to isolate and analyze the infiltrating leukocytes of tissues at the maternal-fetal interface (uterus, decidua, and placenta) of mice. This protocol maintains the integrity of most cell surface markers and yields enough viable cells for downstream applications including flow cytometry analysis.

Immune tolerance in pregnancy requires that the immune system of the mother undergoes distinctive changes in order to accept and nurture the developing ...

Isolation and Activation of Murine Lymphocytes

B and T cells, with their extremely diverse antigen-receptor repertoires, have the ability to mount specific immune responses against almost any invading pathogen1,2. Understandably, such intricate abilities are controlled by a large number of molecules involved in various cellular processes to ensure timely and spatially regulated immune responses3. Here, we describe experimental procedures that allow rapid isolation of highly purified murine lymphocytes using magnetic cell sorting technology. The resulting purified lymphocytes can then be subjected to various in vitro or in vivo functional assays, such as the determination of lymphocyte signaling capacity upon stimulation by immunoblotting4 and the investigation of proliferative abilities by 3H-thymidine incorporation or carboxyfluorescein diacetate succinimidyl ester (CFSE) labeling5-7. In addition to comparing the functional capacities of control and genetically modified lymphocytes, we can also determine the T cell stimulatory capacity of antigen-presenting cells (APCs) in vivo, as shown in our representative results using transplanted CFSE-labeled OT-I T cells.

Lymphocytes are the major players in adaptive immune responses. Here, we present a lymphocyte purification protocol to determine the physiological functions of the desired molecules in lymphocyte activation in vitro and in vivo. The described experimental procedures are suitable for comparing functional capacities between control and genetically modified lymphocytes.

B and T cells, with their extremely diverse antigen-receptor repertoires, have the ability to mount specific immune responses against almost any invading ...

Isolation of Extracellular Vesicles from Murine Bronchoalveolar Lavage Fluid Using an Ultrafiltration Centrifugation Technique

Extracellular vesicles (EVs) are newly discovered subcellular components that play important roles in many biological signaling functions during physiological and pathological states. The isolation of EVs continues to be a major challenge in this field, due to limitations intrinsic to each technique. The differential ultracentrifugation with density gradient centrifugation method is a commonly used approach and is considered to be the gold standard procedure for EV isolation. However, this procedure is time-consuming, labor-intensive, and generally results in low scalability, which may not be suitable for small-volume samples such as bronchoalveolar lavage fluid. We demonstrate that an ultrafiltration centrifugation isolation method is simple and time- and labor-efficient yet provides a high recovery yield and purity. We propose that this isolation method could be an alternative approach that is suitable for EV isolation, particularly for small-volume biological specimens.

Here, we describe two extracellular vesicle isolation protocols, ultrafiltration centrifugation and ultracentrifugation with density gradient centrifugation, to isolate extracellular vesicles from murine bronchoalveolar lavage fluid samples. The extracellular vesicles derived from murine bronchoalveolar lavage fluid by both methods are quantified and characterized.

Extracellular vesicles (EVs) are newly discovered subcellular components that play important roles in many biological signaling functions during ...

Application of Consistent Massage-Like Perturbations on Mouse Calves and Monitoring the Resulting Intramuscular Pressure Changes

Massage is generally recognized to be beneficial for relieving pain and inflammation. Although previous studies have reported anti-inflammatory effects of massage on skeletal muscles, the molecular mechanisms behind are poorly understood. We have recently developed a simple device to apply local cyclical compression (LCC), which can generate intramuscular pressure waves with varying amplitudes. Using this device, we have demonstrated that LCC modulates inflammatory responses of macrophages in situ and alleviates immobilization-induced muscle atrophy. Here, we describe protocols for the optimization and application of LCC as a massage-like intervention against immobilization-induced inflammation and atrophy of skeletal muscles of mouse hindlimbs. The protocol that we have developed can be useful for investigating the mechanism underlying beneficial effects of physical exercise and massage. Our experimental system provides a prototype of the analytical approach to elucidate the mechanical regulation of muscle homeostasis, although further development needs to be made for more comprehensive studies.

Here we describe the protocols for applying defined mechanical loads to mouse calves and for monitoring the concomitant intramuscular pressure changes. The experimental systems that we have developed can be useful for investigating the mechanism behind the beneficial effects of physical exercise and massage.

Massage is generally recognized to be beneficial for relieving pain and inflammation. Although previous studies have reported anti-inflammatory effects of ...

Isolation of Lamina Propria Mononuclear Cells from Murine Colon Using Collagenase E

The intestine is the home to the largest number of immune cells in the body. The small and large intestinal immune systems police exposure to exogenous antigens and modulate responses to potent microbially derived immune stimuli. For this reason, the intestine is a major target site of immune dysregulation and inflammation in many diseases including but, not limited to inflammatory bowel diseases such as Crohn&#8217;s disease and ulcerative colitis, graft-versus-host disease (GVHD) after bone marrow transplantation (BMT), and many allergic and infectious conditions. Murine models of gastrointestinal inflammation and colitis are heavily used to study GI complications and to pre-clinically optimize strategies for prevention and treatment. Data gleaned from these models via isolation and phenotypic analysis of immune cells from the intestine is critical to further immune understanding that can be applied to ameliorate gastrointestinal and systemic inflammatory disorders. This report describes a highly effective protocol for the isolation of mononuclear cells (MNC) from the colon using a mixed silica-based density gradient interface. This method reproducibly isolates a significant number of viable leukocytes while minimizing contaminating debris, allowing subsequent immune phenotyping by flow cytometry or other methods.

The goal of this protocol is to isolate mononuclear cells that reside in the lamina propria of the colon by enzymatic digestion of the tissue using collagenase. This protocol allows for the efficient isolation of mononuclear cells resulting in a single cell suspension which in turn can be used for robust immunophenotyping.

The intestine is the home to the largest number of immune cells in the body. The small and large intestinal immune systems police exposure to exogenous ...

Concomitant Isolation of Primary Astrocytes and Microglia for Protozoa Parasite Infection

Astrocytes and microglia are the most abundant glial cells. They are responsible for physiological support and homeostasis maintenance in the central nervous system (CNS). The increasing evidences of their involvement in the control of infectious diseases justify the emerging interest in the improvement of methodologies to isolate primary astrocytes and microglia in order to evaluate their responses to infections that affect the CNS. Considering the impact of Trypanosoma cruzi (T. cruzi) and Toxoplasma gondii (T. gondii) infection in the CNS, here we provide a method to extract, maintain, dissociate and infect murine astrocytes and microglia cells with protozoa parasites. Extracted cells from newborn cortices are maintained in vitro for 14 days with periodic differential media replacement. Astrocytes and microglia are obtained from the same extraction protocol by mechanical dissociation. After phenotyping by flow cytometry, cells are infected with protozoa parasites. The infection rate is determined by fluorescence microscopy at different time points, thus enabling the evaluation of differential ability of glial cells to control protozoan invasion and replication. These techniques represent simple, cheap and efficient methods to study the responses of astrocytes and microglia to infections, opening the field for further neuroimmunology analysis.

The overall goal of this protocol is to instruct how to extract, maintain, and dissociate murine astrocyte and microglia cells from the central nervous system, followed by infection with protozoa parasites.

Astrocytes and microglia are the most abundant glial cells. They are responsible for physiological support and homeostasis maintenance in the central ...