This research was funded in parts by NIH grants HL66299 to TS, RB, and SL, HL60024 to TS, and HL136869 to MF.

All animal procedures were reviewed and approved by the Institutional and Animal Care Committee of the University of South Alabama and were performed in accordance with all federal, state, and local regulations. Primary cultures of rat pulmonary microvascular endothelial cells (PMVECs) were obtained from the Cell Culture Core Facility at the University of South Alabama&#8217;s Center for Lung Biology. Cells were prepared using previously described procedures16.
1. Generation of Cytotoxic Supernatants
Note: Here, we use two different strains of P. aeruginosa: PA103, which has an intact type III secretion system capable of transferring the exoenzymes ExoU and ExoT to target cells during infection, and &#8710;PcrV, which lacks a type III secretion system and is incapable of transferring exoenzymes to target cells following inoculation.
<ol>
	<li>Streak bacteria onto Vogel-Bonner (VB) agar plates17 and grow overnight at 37 &#176;C.
	<ol>
		<li>To prepare plates, make the following stock solution (Vogel-Bonner salts; 10x&#160;stock): measure 2 g MgSO4, 20 g citric acid (free acid), 100 g K2PO4, and 35 g NaH2PO4. Add ddH2O to 1 L and autoclave for 15 min with slow exhaust.</li>
		<li>Place 7.5 g agar in 450 mL ddH2O and autoclave as above.</li>
		<li>Following autoclaving, place both solutions into a 50 &#176;C water bath to cool.</li>
		<li>Add 50 mL of the 10x VB stock salt solution to the agar.</li>
		<li>Add carbenicillin to 400 &#181;g/mL (for the strains of P. aeruginosa being used) and mix well by swirling the flask.</li>
		<li>Place 5 mL of the VB agar solution into individual sterile culture dishes, allow the agar to solidify, and then store at 4 &#176;C until the day of bacterial seeding.</li>
		<li>On the day of bacterial seeding, pre-warm a plate to 37 &#176;C and then streak bacteria onto the plate using a sterile loop. Place the plate in a 37 &#176;C incubator overnight.</li>
	</ol>
	</li>
	<li>Verify PMVEC purity by positive staining with fluorescent Griffonia simplicifolia lectin and negative staining with fluorescent Helix pomatia lectin (a marker for arterial endothelial cells). Aliquot cells and freeze in liquid nitrogen.</li>
	<li>For experiments, maintain cells in Dulbecco&#8217;s Modified Eagle&#8217;s Medium (DMEM) supplemented with 10% fetal bovine serum, and grow cells in a 37 &#176;C incubator containing 5% CO2. Use cells at passages 5 - 15.
	<ol>
		<li>For generation of cytotoxic supernatants, plate 2 x 106 cells into individual 150 cm dishes and grow for 3 - 4 days until confluence is achieved. Use two plates per experiment (see below).</li>
		<li>For analysis of cytotoxic supernatants, plate 1 x 105 cells into individual wells of a 6-well dish and grow for four days until confluence is achieved.</li>
	</ol>
	</li>
	<li>To produce supernatant, wash one of the two 150 cm dishes of PMVECs from step 1.3.1 with phosphate-buffered saline, trypsinize, and then count the cells (we use an automated cell counter and follow the manufacturer&#8217;s protocol; see Table of Materials). Wash the other dish of PMVECs with Hank&#8217;s Balanced Salt Solution (HBSS) and then infect with either strain of P. aeruginosa at a multiplicity of infection (MOI) of 20:1. This is achieved as follows:
	<ol>
		<li>For P. aeruginosa, OD540 0.25 = 2 x 108 CFUs/mL. To prepare this dilution, add 1 mL HBSS to a 1 mL disposable cuvette. Scrape enough bacteria off of the plate that was prepared in step 1.1 until an OD540 of 0.25 is achieved when measured using a spectrophotometer. The next step will provide a calculation of how much bacteria will be needed.</li>
		<li>Once the number of PMVECs in the culture dish is determined (step 1.4 above), determine the appropriate number of bacteria to be added to the second, non-trypsinized culture dish containing the PMVECs. For example, if it is determined that the culture dish of PMVECs contains 1.3 x 107 cells, then prepare 1.3 x 107 cells x 20 bacteria/cell x 1 mL/2 x 108 CFUs = 1.3 mL bacteria.</li>
		<li>Dilute the 1.3 mL of bacteria into HBSS to a final volume of 20 mL, so that the entire surface of a 150 cm dish can be covered with fluid, then add the diluted bacteria to the plate of PMVECs.</li>
		<li>Incubate the PMVECs inoculated with the bacteria at 37 &#176;C in a 5% CO2 incubator for 4 - 5 h, until gaps can be seen forming in the cell monolayer when the plate is observed microscopically (See Figure 1 for proper level of gap formation).</li>
		<li>Collect the supernatant, then centrifuge for 10 min at 2,000 x g in a tabletop centrifuge to remove cellular debris. 
		Note: Any table top centrifuge capable of generating sufficient g force to pellet unlysed cells and large cell fragments can be used for this step.</li>
		<li>Pour the supernatant into a syringe that has a 0.2 &#181;m filter attached to its end, then pass the supernatant through the filter to remove bacteria.</li>
		<li>Use an aliquot of the sterile supernatant to test cytotoxicity (see 2.1) and freeze the rest of the supernatant at -80 &#176;C for future use.</li>
	</ol>
	</li>
</ol>
2. Analysis of Cytotoxic Supernatants
<ol>
	<li>Cytotoxicity Assay
	<ol>
		<li>Grow PMVECs in 6-well dishes until confluence. Wash wells once with HBSS, then add 1.5 mL of filter-sterilized supernatant (collected from either PA103- or &#8710;PcrV-inoculated cells) to individual wells. Add sterile HBSS to another well as a negative control.</li>
		<li>Place the plate into the CO2 incubator for 21 - 24 h, then observe for cell killing/cytotoxicity (see next step). Use supernatants that exhibit cytotoxicity for further experimentation, and discard those that do not show cell killing.</li>
		<li>Quantitation of cell killing
		<ol>
			<li>Measure lactate dehydrogenase (LDH) release from dead cells using commercially available LDH Assay Kits and manufacturer&#8217;s recommended procedures.</li>
			<li>Alternatively, quantify cell killing microscopically using ImageJ software. For this, record microscopic images and areas of the culture dish containing intact cells, then quantify regions lacking cells (indicative of cell death in a monolayer) using a custom ImageJ (National Institutes of Health) macro (see Supplementary Coding File). If desired, carry out the macro steps manually as follows:
			<ol>
				<li>Input images (RGB or Tiff format) into the macro and adjust contrast to 15% saturated pixels. Duplicate contrast-adjusted images and perform the &#8220;subtract background&#8221; command to obtain a high-contrast image of both cell and gap area within the field of view.</li>
				<li>Subtract this image from the original image and combine the resulting image with the original image using the image calculator &#8220;AND&#8221; function. Convert the resultant image to black (gaps) and white (cells) mask with the threshold function (minimum 0, maximum 5), and use the &#8220;binary erode&#8221; function to remove noise from the image.</li>
				<li>Measure the ratio of black to white pixels within the resultant image using the &#8220;area fraction&#8221; measurement. Plot and express fractional areas for each treatment time point as percent of maximal gap area.</li>
				<li>Calculate means and compare using one-way ANOVA with Tukey&#8217;s post hoc test, with p values less than 0.05 considered significant.</li>
			</ol>
			</li>
		</ol>
		</li>
		<li>Use immunoblot analysis to establish the presence of amyloid, oligomeric tau, and A&#946; in culture supernatants. Perform immunoblot analysis using standard procedures10,11,12, except for concentrating culture supernatants at least 10-fold prior to electrophoresis.
		<ol>
			<li>To concentrate supernatant, place 1 - 2 mL of supernatant into a centrifugation filter unit whose membrane has a molecular weight cut-off of 10 kDa. Then, place the filter unit into a table top centrifuge and centrifuge at 2,000 x g until the required degree of concentration is achieved (usually 45 - 60 min).</li>
			<li>Determine the amount of protein in the concentrated supernatant11 and load equal amounts of samples into individual wells of the gel.</li>
			<li>Run gels, transfer the proteins to nitrocellulose, then probe blots with either A11 anti-amyloid antibody, T22 anti-oligomeric tau antibody, or MOAB2 anti-A&#946; antibody followed by appropriate secondary antibodies. Develop the blots using standard chemiluminescence procedures.</li>
		</ol>
		</li>
		<li>To do a thioflavin T Assay, use thioflavin T fluorescence (ThT) to quantify amyloids in supernatants. For these measurements, use filter-sterilized supernatants.
		<ol>
			<li>Prepare a stock solution (50x) of thioflavin T by suspending 8 mg thioflavin T (ThT) into 10 mL phosphate buffered saline (PBS). After mixing, filter the solution through a 0.22 &#181;m filter to remove particulates.</li>
			<li>For measurements, add 20 &#181;L of ThT stock to 1 mL of PBS in a 1 mL spectrophotometer cuvette. Place the diluted sample into a spectrofluorimeter.</li>
			<li>Measure the baseline fluorescence emission using 425 nm excitation and scanning the fluorescence emission from 450-575 nm in 2 nm increments.</li>
			<li>Perform a time-lapse scan using 425 nm excitation and 482 nm emission, with data acquired every 0.2 s for 60 s.</li>
			<li>The initial 20 s of the time-lapse scan measures fluorescence in the blank cuvette. At 20 s, pause the scan and add 10 &#181;L of the filter-sterilized supernatant to the cuvette. Mix the cuvette by inversion and then place back into the spectrofluorimeter.</li>
			<li>Resume the time-based scan, acquiring the final 40 s of data.</li>
			<li>Upon completion of the time-lapse scan, perform a final fluorescence emission spectrum scan using identical settings, as detailed in 2.1.5.3.</li>
		</ol>
		</li>
	</ol>
	</li>
</ol>

<ol>
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E., Vasilakis, C., Jick, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Acute+respiratory+tract+infections+and+risk+of+first-time+acute+myocardial+infarction.">Acute respiratory tract infections and risk of first-time acute myocardial infarction.</a> Lancet. 351 (9114), 1467-1471 (1998).</li><li>Waterer, G. W., Kessler, L. A., Wunderink, R. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Medium-term+survival+after+hospitalization+with+community-acquired+pneumonia.">Medium-term survival after hospitalization with community-acquired pneumonia.</a> Am J Resp Crit Care Med. 169 (8), 910-914 (2003).</li><li>Yende, 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=Inflammatory+markers+at+hospital+discharge+predict+subsequent+mortality+after+pneumonia+and+sepsis.">Inflammatory markers at hospital discharge predict subsequent mortality after pneumonia and sepsis.</a> Am J Resp Crit Care Med. 177 (11), 1242-1247 (2008).</li><li>Corrales-Medina, V. F., 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=Association+between+hospitalization+for+pneumonia+and+subsequent+risk+of+cardiovascular+disease.">Association between hospitalization for pneumonia and subsequent risk of cardiovascular disease.</a> J Am Med Assoc. 313 (3), 264-274 (2015).</li><li>Frank, D. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+exoenzyme+S+regulon+of+Pseudomonas+aeruginosa.">The exoenzyme S regulon of Pseudomonas aeruginosa.</a> Mol Microbiol. 26 (4), 621-629 (1997).</li><li>Engel, J., Balachandran, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Role+of+Pseudomonas+aeruginosa+type+III+effectors+in+disease.">Role of Pseudomonas aeruginosa type III effectors in disease.</a> Curr Opin Microbiol. 12 (1), 61-66 (2009).</li><li>Ochoa, C. D., Alexeyev, M., Pastukh, V., Balczon, R., Stevens, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pseudomonas+aeruginosa+exotoxin+Y+is+a+promiscuous+cyclase+that+increases+endothelial+tau+phosphorylation+and+permeability.">Pseudomonas aeruginosa exotoxin Y is a promiscuous cyclase that increases endothelial tau phosphorylation and permeability.</a> J. Biol. Chem. 287 (30), 25407-25418 (2012).</li><li>Balczon, R., 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=Pseudomonas+aeruginosa+exotoxin+Y-mediated+tau+hyperphosphorylation+impairs+microtubule+assembly+in+pulmonary+microvascular+endothelial+cells.">Pseudomonas aeruginosa exotoxin Y-mediated tau hyperphosphorylation impairs microtubule assembly in pulmonary microvascular endothelial cells.</a> PLoS One. 8, e74343 (2013).</li><li>Morrow, K. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pseudomonas+aeruginosa+exoenzymes+U+and+Y+induce+a+transmissible+endothelial+proteinopathy.">Pseudomonas aeruginosa exoenzymes U and Y induce a transmissible endothelial proteinopathy.</a> Am J Physiol Lung Cell Molec Physiol. 310 (4), L337-L353 (2016).</li><li>Balczon, R., 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=Pseudomonas+aeruginosa+infection+liberates+transmissible,+cytotoxic+prion+amyloids.">Pseudomonas aeruginosa infection liberates transmissible, cytotoxic prion amyloids.</a> FASEB Journal. 31 (7), 2785-2796 (2017).</li><li>Stevens, T. C., 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=The+Pseudomonas+aeruginosa+exoenzyme+Y+impairs+endothelial+cell+proliferation+and+vascular+repair+following+lung+injury.">The Pseudomonas aeruginosa exoenzyme Y impairs endothelial cell proliferation and vascular repair following lung injury.</a> Am J Physiol Lung Cell Molec Physiol. 306 (10), L915-L924 (2014).</li><li>Prusiner, S. 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None to report.

Here, simple in vitro methods are outlined which allow demonstration of the generation of cytotoxic amyloids during infection with a pneumonia causing organism. These methods include a cell culture cytotoxicity assay, immunoblotting, quantitation of cell killing using a novel microscopic method, and ThT binding. Analyses of the cytotoxic agents have demonstrated that they are amyloid in nature (Figure 2 and Figure 4) and exhibit charact...

Patients who survive pneumonia have elevated death rates in the months following hospital discharge1,2,3,4,5,6. In most cases, death occurs by some type of end-organ failure including renal, pulmonary, cardiac, or liver events, as well as stroke5,6. The reason for the elevated death rate in this patient population has never been established.
Pneumonia is classified as being either community-acquired or hospital-acquired (nosocomial), and agents that can cause pneumonia include bacteria, viruses, fungi, and chemicals. One of the major causes of nosocomial pneumonia is the bacterium Pseudomonas aeruginosa. P. aeruginosa is a gram-negative organism that uses a type III secretion system to transfer various effector molecules, termed exoenzymes, directly to the cytoplasm of target cells7,8. During infection of pulmonary endothelial cells, the exoenzymes target various intracellular proteins, including an endothelial form of the microtubule-associated protein tau9,10,11,12, leading to endothelial barrier breakdown resulting in severe pulmonary edema, decreased pulmonary function and, oftentimes, death.
As stated previously, patients who survive the initial pneumonia have elevated death rates in the first 12 months following hospital discharge. A potential mechanism for explaining this phenomenon is that some type of long-lived toxin is generated during the initial infection that leads to poor long-term outcome. Two observations support this possibility. First, cultured pulmonary endothelial cells that are treated initially with P. aeruginosa fail to proliferate for up to a week after the bacteria are killed by antibiotics13. Second, long-lived prions and agents with prion characteristics have been demonstrated in various human and animal diseases, particularly diseases associated with the nervous system14,15.
Methods for examining the potential production of long-lived cytotoxic agents during pulmonary infection have never been described. Here a series of simple in vitro assays are outlined that can be used for investigating cytotoxin production and activity following infection using a common pneumonia causing agent, P. aeruginosa. These assays should be readily adaptable to investigate possible cytotoxin induction following infection using other agents that cause pneumonia, and the supernatants that are generated also should be useful for investigating effects of the cytotoxins in whole organs or animals. Finally, the assays that are outlined here most likely will be adaptable to test animal and human biological fluids for the production of cytotoxins during pneumonia.

<table>
	<tbody>
		<tr>
			<td>Rabbit anti beta amyloid</td>
			<td>Thermo</td>
			<td>71-5800</td>
			<td></td>
		</tr>
		<tr>
			<td>A11 amyloid oligomer antibody</td>
			<td>StressMarq</td>
			<td>SPC-506D</td>
			<td></td>
		</tr>
		<tr>
			<td>T22 anti-tau oligomer antibody</td>
			<td>EMD Millipore</td>
			<td>ABN454</td>
			<td></td>
		</tr>
		<tr>
			<td>Thioflavin T</td>
			<td>Sigma Aldrich</td>
			<td>T3516</td>
			<td></td>
		</tr>
		<tr>
			<td>HBSS</td>
			<td>Gibco</td>
			<td>14025-092</td>
			<td></td>
		</tr>
		<tr>
			<td>PBS</td>
			<td>Gibco</td>
			<td>10010-023</td>
			<td></td>
		</tr>
		<tr>
			<td>0.22 micron syringe filters</td>
			<td>Millipore</td>
			<td>SLGP033RS</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM</td>
			<td>Gibco</td>
			<td>11965-092</td>
			<td></td>
		</tr>
		<tr>
			<td>HRP Goat antirabbit IgG</td>
			<td>Abcam</td>
			<td>ab6721-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Strains PA103 and &#916;PcrV</td>
			<td></td>
			<td></td>
			<td>These strains of P. aeruginosa were obtained from Dr. Dara Frank, University of Wisconsin Medical College, Milwaukee, WI</td>
		</tr>
		<tr>
			<td>FITC Griffonia lectin</td>
			<td>Sigma Aldrich</td>
			<td>L9381</td>
			<td></td>
		</tr>
		<tr>
			<td>TRITC Helix pomatia lectin</td>
			<td>Sigma Aldrich</td>
			<td>L1261</td>
			<td></td>
		</tr>
		<tr>
			<td>Agar</td>
			<td>Fisher</td>
			<td>BP1423-500</td>
			<td></td>
		</tr>
		<tr>
			<td>0.22 micron nitrocellulose</td>
			<td>BioRad</td>
			<td>162-0112</td>
			<td></td>
		</tr>
		<tr>
			<td>Type 2 collagenase</td>
			<td>Worthington</td>
			<td>LS004176</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal bovine serum</td>
			<td>Hyclone</td>
			<td>SH30898.03IH</td>
			<td></td>
		</tr>
		<tr>
			<td>PenStrep</td>
			<td>Gibco</td>
			<td>15070063</td>
			<td></td>
		</tr>
		<tr>
			<td>Carbenicillin Disodium salt</td>
			<td>Sigma&#160;</td>
			<td>C1389</td>
			<td></td>
		</tr>
		<tr>
			<td>Microcetrifugation concentrators- 10,000 MW cut-off</td>
			<td>Millipore</td>
			<td>UFC801008</td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium phosphate dibasic</td>
			<td>Sigma&#160;</td>
			<td>795496-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>Magnesium phosphate heptahydrate</td>
			<td>MP Biomedicals</td>
			<td>MP021914221</td>
			<td></td>
		</tr>
		<tr>
			<td>Citric Acid</td>
			<td>G Biosciences</td>
			<td>50-103-5801</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium phosphate dibasic heptahydrate</td>
			<td>Sigma</td>
			<td>S9506-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>Countess Automated Cell Counter</td>
			<td>Invitrogen</td>
			<td>C10277</td>
			<td></td>
		</tr>
	</tbody>
</table>

methods for detecting cytotoxic amyloids following infection of pulmonary endothelial cells by pseudomonas aeruginosa

Patients who survive pneumonia have elevated death rates in the months following hospital discharge. It has been hypothesized that infection of pulmonary tissue during pneumonia results in the production of long-lived cytotoxins that can lead to subsequent end organ failure. We have developed in vitro assays to test the hypothesis that cytotoxins are produced during pulmonary infection. Isolated rat pulmonary endothelial cells and the bacterium Pseudomonas aeruginosa are used as model systems, and the production of cytoxins following infection of the endothelial cells by the bacteria is demonstrated using cell culture followed by direct quantitation using lactate dehydrogenase assays and a novel microscopic method utilizing ImageJ technology. The amyloid nature of these cytotoxins was demonstrated by thioflavin T binding assays and by immunoblotting and immunodepletion using A11 anti-amyloid antibody. Further analyses using immunoblotting demonstrated that oligomeric tau and A&#946; were produced and released by endothelial cells following infection by P. aeruginosa. These methods should be readily adaptable to analyses of human clinical samples.

A simple in vitro assay has been developed to assay for the presence of cytotoxins in supernatants of cells infected with the bacterium P. aeruginosa. Basically, culture medium from infected cells is collected 4 h after bacterial addition, the bacteria are removed by filter sterilization of the culture supernatant, and then the sterile supernatant is added to a new population of cells. The cells are then observed 21 - 24 h after the addition of supernatant and cell killi...

Watch this Scientific Journal Video about Methods for Detecting Cytotoxic Amyloids Following Infection of Pulmonary Endothelial Cells by Pseudomonas aeruginosa at JoVE.com

Methods for Detecting Cytotoxic Amyloids Following Infection of Pulmonary Endothelial Cells by Pseudomonas aeruginosa

Simple methods are described for demonstrating the production of cytotoxic amyloids following infection of pulmonary endothelium by Pseudomonas aeruginosa.

Methods for Detecting Cytotoxic Amyloids Following Infection of Pulmonary Endothelial Cells by Pseudomonas aeruginosa

Patients who survive pneumonia have elevated death rates in the months following hospital discharge. It has been hypothesized that infection of pulmonary ...

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Immunology and Infection

5.5K Views.  University of South Alabama. Simple methods are described for demonstrating the production of cytotoxic amyloids following infection of pulmonary endothelium by Pseudomonas aeruginosa.

Video: Methods for Detecting Cytotoxic Amyloids Following Infection of Pulmonary Endothelial Cells by Pseudomonas aeruginosa

Co-culture Models of Pseudomonas aeruginosa Biofilms Grown on Live Human Airway Cells

Bacterial biofilms have been associated with a number of different human diseases, but biofilm development has generally been studied on non-living surfaces. In this paper, we describe protocols for forming Pseudomonas aeruginosa biofilms on human airway epithelial cells (CFBE cells) grown in culture. In the first method (termed the Static Co-culture Biofilm Model), P. aeruginosa is incubated with CFBE cells grown as confluent monolayers on standard tissue culture plates. Although the bacterium is quite toxic to epithelial cells, the addition of arginine delays the destruction of the monolayer long enough for biofilms to form on the CFBE cells. The second method (termed the Flow Cell Co-culture Biofilm Model), involves adaptation of a biofilm flow cell apparatus, which is often used in biofilm research, to accommodate a glass coverslip supporting a confluent monolayer of CFBE cells. This monolayer is inoculated with P. aeruginosa and a peristaltic pump then flows fresh medium across the cells. In both systems, bacterial biofilms form within 6-8 hours after inoculation. Visualization of the biofilm is enhanced by the use of P. aeruginosa strains constitutively expressing green fluorescent protein (GFP). The Static and Flow Cell Co-culture Biofilm assays are model systems for early P. aeruginosa infection of the Cystic Fibrosis (CF) lung, and these techniques allow different aspects of P. aeruginosa biofilm formation and virulence to be studied, including biofilm cytotoxicity, measurement of biofilm CFU, and staining and visualizing the biofilm.

Co-culture Models of Pseudomonas aeruginosa Biofilms Grown on Live Human Airway Cells

This paper describes different methods of growing Pseudomonas aeruginosa biofilms on cultured human airway epithelial cells. These protocols can be adapted to study different aspects of biofilm formation, including visualization of the biofilm, staining of the biofilm, measuring the colony forming units (CFU) of the biofilm, and studying biofilm cytotoxicity.

Bacterial biofilms have been associated with a number of different human diseases, but biofilm development has generally been studied on non-living ...

Pseudomonas aeruginosa and Saccharomyces cerevisiae Biofilm in Flow Cells

Many microbial cells have the ability to form sessile microbial communities defined as biofilms that have altered physiological and pathological properties compared to free living microorganisms. Biofilms in nature are often difficult to investigate and reside under poorly defined conditions1. Using a transparent substratum it is possible to device a system where simple biofilms can be examined in a non-destructive way in real-time: here we demonstrate the assembly and operation of a flow cell model system, for in vitro 3D studies of microbial biofilms generating high reproducibility under well-defined conditions2,3.
The system consists of a flow cell that serves as growth chamber for the biofilm. The flow cell is supplied with nutrients and oxygen from a medium flask via a peristaltic pump and spent medium is collected in a waste container. This construction of the flow system allows a continuous supply of nutrients and administration of e.g. antibiotics with minimal disturbance of the cells grown in the flow chamber. Moreover, the flow conditions within the flow cell allow studies of biofilm exposed to shear stress. A bubble trapping device confines air bubbles from the tubing which otherwise could disrupt the biofilm structure in the flow cell.
The flow cell system is compatible with Confocal Laser Scanning Microscopy (CLSM) and can thereby provide highly detailed 3D information about developing microbial biofilms. Cells in the biofilm can be labeled with fluorescent probes or proteins compatible with CLSM analysis. This enables online visualization and allows investigation of niches in the developing biofilm. Microbial interrelationship, investigation of antimicrobial agents or the expression of specific genes, are of the many experimental setups that can be investigated in the flow cell system.

Pseudomonas aeruginosa and Saccharomyces cerevisiae Biofilm in Flow Cells

Protocol describing the application of a flow cell system for growing and analyzing microbial biofilms for Confocal Laser Scanning Microscopy (CLSM).

Many microbial cells have the ability to form sessile microbial communities defined as biofilms that have altered physiological and pathological ...

Methods to Assess Beta Cell Death Mediated by Cytotoxic T Lymphocytes

Type 1 diabetes (T1D) is a T cell mediated autoimmune disease. During the pathogenesis, patients become progressively more insulinopenic as 
insulin production is lost, presumably this results from the destruction of pancreatic beta cells by T cells. Understanding the mechanisms of beta cell death during 
the development of T1D will provide insights to generate an effective cure for this disease. Cell-mediated lymphocytotoxicity (CML) assays have historically used the 
radionuclide Chromium 51 (51Cr) to label target cells. These targets are then exposed to effector cells and the release of 51Cr from target 
cells is read as an indication of lymphocyte-mediated cell death. Inhibitors of cell death result in decreased release of 51Cr.
 As effector cells, we used an activated autoreactive clonal population of CD8+ Cytotoxic T lymphocytes (CTL) isolated from a mouse stock transgenic for both the alpha and beta chains of the AI4 T cell receptor (TCR). Activated AI4 T cells were co-cultured with 51Cr labeled target NIT cells for 16 hours, release of 51Cr was recorded to calculate specific lysis 
Mitochondria participate in many important physiological events, such as energy production, regulation of signaling transduction, and apoptosis. The study of beta cell mitochondrial functional changes during the development of T1D is a novel area of research. Using the mitochondrial membrane potential dye Tetramethyl Rhodamine Methyl Ester (TMRM) and confocal microscopic live cell imaging, we monitored mitochondrial membrane potential over time in the beta cell line NIT-1. For imaging studies, effector AI4 T cells were labeled with the fluorescent nuclear staining dye Picogreen. NIT-1 cells and T cells were co-cultured in chambered coverglass and mounted on the microscope stage equipped with a live cell chamber, controlled at 37&deg;C, with 5% CO2, and humidified. During these experiments images were taken of each cluster every 3 minutes for 400 minutes.
Over a course of 400 minutes, we observed the dissipation of mitochondrial membrane potential in NIT-1 cell clusters where AI4 T cells were attached. In the simultaneous control experiment where NIT-1 cells were co-cultured with MHC mis-matched human lymphocyte Jurkat cells, mitochondrial membrane potential remained intact. This technique can be used to observe real-time changes in mitochondrial membrane potential in cells under attack of cytotoxic lymphocytes, cytokines, or other cytotoxic reagents.

Cell-mediated lymphocytotoxicity (CML) assays can be used to test autoreactive responses and study mechanisms of cell death in vitro. However, using live-cell confocal microscopic imaging techniques with fluorescent dyes, the type and kinetics of cell death as well as the pathways utilized can be studied in greater detail.

Type 1 diabetes (T1D) is a T cell mediated autoimmune disease.  During the pathogenesis, patients become progressively more insulinopenic as 
insulin ...

Selection of Plasmodium falciparum Parasites for Cytoadhesion to Human Brain Endothelial Cells

Most human malaria deaths are caused by blood-stage Plasmodium falciparum parasites. Cerebral malaria, the most life-threatening complication of the disease, is characterised by an accumulation of Plasmodium falciparum infected red blood cells (iRBC) at pigmented trophozoite stage in the microvasculature of the brain2-4. This microvessel obstruction (sequestration) leads to acidosis, hypoxia and harmful inflammatory cytokines (reviewed in 5). Sequestration is also found in most microvascular tissues of the human body2, 3. The mechanism by which iRBC attach to the blood vessel walls is still poorly understood.
The immortalized Human Brain microvascular Endothelial Cell line (HBEC-5i) has been used as an in vitro model of the blood-brain barrier6. However, Plasmodium falciparum iRBC attach only poorly to HBEC-5i in vitro, unlike the dense sequestration that occurs in cerebral malaria cases. We therefore developed a panning assay to select (enrich) various P. falciparum strains for adhesion to HBEC-5i in order to obtain populations of high-binding parasites, more representative of what occurs in vivo.
A sample of a parasite culture (mixture of iRBC and uninfected RBC) at the pigmented trophozoite stage is washed and incubated on a layer of HBEC-5i grown on a Petri dish. After incubation, the dish is gently washed free from uRBC and unbound iRBC. Fresh uRBC are added to the few iRBC attached to HBEC-5i and incubated overnight. As schizont stage parasites burst, merozoites reinvade RBC and these ring stage parasites are harvested the following day. Parasites are cultured until enough material is obtained (typically 2 to 4 weeks) and a new round of selection can be performed. Depending on the P. falciparum strain, 4 to 7 rounds of selection are needed in order to get a population where most parasites bind to HBEC-5i. The binding phenotype is progressively lost after a few weeks, indicating a switch in variant surface antigen gene expression, thus regular selection on HBEC-5i is required to maintain the phenotype.
In summary, we developed a selection assay rendering P. falciparum parasites a more "cerebral malaria adhesive" phenotype. We were able to select 3 out of 4 P. falciparum strains on HBEC-5i. This assay has also successfully been used to select parasites for binding to human dermal and pulmonary endothelial cells. Importantly, this method can be used to select tissue-specific parasite populations in order to identify candidate parasite ligands for binding to brain endothelium. Moreover, this assay can be used to screen for putative anti-sequestration drugs7.

Selection of Plasmodium falciparum Parasites for Cytoadhesion to Human Brain Endothelial Cells

An in vitro model for cerebral malaria sequestration is described1. Plasmodium falciparum infected red blood cells are selected for binding to immortalized human brain microvascular endothelial cells. The selected parasites show a distinct phenotype. The selection process can be applied using various P. falciparum strains and endothelial cell lines.

Most human malaria deaths are caused by blood-stage Plasmodium falciparum parasites. Cerebral malaria, the most life-threatening complication of the ...

RNA Isolation of Pseudomonas aeruginosa Colonizing the Murine Gastrointestinal Tract

Pseudomonas aeruginosa (PA) infections result in significant morbidity and mortality in hosts with compromised immune systems, such as patients with leukemia, severe burn wounds, or organ transplants1. In patients at high-risk for developing PA bloodstream infections, the gastrointestinal (GI) tract is the main reservoir for colonization2, but the mechanisms by which PA transitions from an asymptomatic colonizing microbe to an invasive, and often deadly, pathogen are unclear. Previously, we performed in vivo transcription profiling experiments by recovering PA mRNA from bacterial cells residing in the cecums of colonized mice 3 in order to identify changes in bacterial gene expression during alterations to the host&#x2019;s immune status.
As with any transcription profiling experiment, the rate-limiting step is in the isolation of sufficient amounts of high quality mRNA. Given the abundance of enzymes, debris, food residues, and particulate matter in the GI tract, the challenge of RNA isolation is daunting. Here, we present a method for reliable and reproducible isolation of bacterial RNA recovered from the murine GI tract. This method utilizes a well-established murine model of PA GI colonization and neutropenia-induced dissemination4. Once GI colonization with PA is confirmed, mice are euthanized and cecal contents are recovered and flash frozen. RNA is then extracted using a combination of mechanical disruption, boiling, phenol/chloroform extractions, DNase treatment, and affinity chromatography. Quantity and purity are confirmed by spectrophotometry (Nanodrop Technologies) and bioanalyzer (Agilent Technologies) (Fig 1). This method of GI microbial RNA isolation can easily be adapted to other bacteria and fungi as well.

RNA Isolation of Pseudomonas aeruginosa Colonizing the Murine Gastrointestinal Tract

A reliable method for the RNA isolation of Pseudomonas aeruginosa recovered from murine cecums is described. The RNA recovered is of sufficient quantity and quality for subsequent qPCR, transcription profiling, and RNA Seq experiments. This technique can be adapted for RNA isolation of other intestinal microbes.

Pseudomonas aeruginosa (PA) infections result in significant morbidity and mortality in hosts with compromised immune systems, such as patients with ...

Following Cell-fate in E. coli After Infection by Phage Lambda

The system comprising bacteriophage (phage) lambda and the bacterium E. coli has long served as a paradigm for cell-fate determination1,2. Following the simultaneous infection of the cell by a number of phages, one of two pathways is chosen: lytic (virulent) or lysogenic (dormant)3,4. We recently developed a method for fluorescently labeling individual phages, and were able to examine the post-infection decision in real-time under the microscope, at the level of individual phages and cells5. Here, we describe the full procedure for performing the infection experiments described in our earlier work5. This includes the creation of fluorescent phages, infection of the cells, imaging under the microscope and data analysis. The fluorescent phage is a "hybrid", co-expressing wild- type and YFP-fusion versions of the capsid gpD protein. A crude phage lysate is first obtained by inducing a lysogen of the gpD-EYFP (Enhanced Yellow Fluorescent Protein) phage, harboring a plasmid expressing wild type gpD. A series of purification steps are then performed, followed by DAPI-labeling and imaging under the microscope. This is done in order to verify the uniformity, DNA packaging efficiency, fluorescence signal and structural stability of the phage stock. The initial adsorption of phages to bacteria is performed on ice, then followed by a short incubation at 35&deg;C to trigger viral DNA injection6. The phage/bacteria mixture is then moved to the surface of a thin nutrient agar slab, covered with a coverslip and imaged under an epifluorescence microscope. The post-infection process is followed for 4 hr, at 10 min interval. Multiple stage positions are tracked such that ~100 cell infections can be traced in a single experiment. At each position and time point, images are acquired in the phase-contrast and red and green fluorescent channels. The phase-contrast image is used later for automated cell recognition while the fluorescent channels are used to characterize the infection outcome: production of new fluorescent phages (green) followed by cell lysis, or expression of lysogeny factors (red) followed by resumed cell growth and division. The acquired time-lapse movies are processed using a combination of manual and automated methods. Data analysis results in the identification of infection parameters for each infection event (e.g. number and positions of infecting phages) as well as infection outcome (lysis/lysogeny). Additional parameters can be extracted if desired.

Following Cell-fate in E. coli After Infection by Phage Lambda

This article describes the procedure for preparing a fluorescently-labeled version of bacteriophage lambda, infection of E. coli bacteria, following the infection outcome under the microscope, and analysis of infection results.

The system comprising bacteriophage (phage) lambda and the bacterium E. coli has long served as a paradigm for cell-fate determination1,2. Following the ...

Long Term Chronic Pseudomonas aeruginosa Airway Infection in Mice

A mouse model of chronic airway infection is a key asset in cystic fibrosis (CF) research, although there are a number of concerns regarding the model itself. Early phases of inflammation and infection have been widely studied by using the Pseudomonas aeruginosa agar-beads mouse model, while only few reports have focused on the long-term chronic infection in vivo. The main challenge for long term chronic infection remains the low bacterial burden by P. aeruginosa and the low percentage of infected mice weeks after challenge, indicating that bacterial cells are progressively cleared by the host.
This paper presents a method for obtaining efficient long-term chronic infection in mice. This method is based on the embedding of the P. aeruginosa clinical strains in the agar-beads in vitro, followed by intratracheal instillation in C57Bl/6NCrl mice. Bilateral lung infection is associated with several measurable read-outs including weight loss, mortality, chronic infection, and inflammatory response. The P. aeruginosa RP73 clinical strain was preferred over the PAO1 reference laboratory strain since it resulted in a comparatively lower mortality, more severe lesions, and higher chronic infection. P. aeruginosa colonization may persist in the lung for over three months. Murine lung pathology resembles that of CF patients with advanced chronic pulmonary disease.
This murine model most closely mimics the course of the human disease and can be used both for studies on the pathogenesis and for the evaluation of novel therapies.

Long Term Chronic Pseudomonas aeruginosa Airway Infection in Mice

We describe the agar-beads method to establish persistent long-term chronic Pseudomonas aeruginosa airway infection in the mouse model.

A mouse model of chronic airway infection is a key asset in cystic fibrosis (CF) research, although there are a number of concerns regarding the model ...

Pseudomonas aeruginosa Induced Lung Injury Model

In order to study human acute lung injury and pneumonia, it is important to develop animal models to mimic various pathological features of this disease. Here we have developed a mouse lung injury model by intra-tracheal injection of bacteria Pseudomonas aeruginosa (P. aeruginosa or PA). Using this model, we were able to show lung inflammation at the early phase of injury. In addition, alveolar epithelial barrier leakiness was observed by analyzing bronchoalveolar lavage (BAL); and alveolar cell death was observed by Tunel assay using tissue prepared from injured lungs. At a later phase following injury, we observed cell proliferation required for the repair process. The injury was resolved 7 days from the initiation of P. aeruginosa injection. This model mimics the sequential course of lung inflammation, injury and repair during pneumonia. This clinically relevant animal model is suitable for studying pathology, mechanism of repair, following acute lung injury, and also can be used to test potential therapeutic agents for this disease.

Pseudomonas aeruginosa Induced Lung Injury Model

We have developed a mouse lung injury model by intra-tracheal injection of bacteria Pseudomonas aeruginosa. This model mimics lung injury during pneumonia and is clinically relevant.

In order to study human acute lung injury and pneumonia, it is important to develop animal models to mimic various pathological features of this disease. ...

Pneumococcus Infection of Primary Human Endothelial Cells in Constant Flow

Interaction of Streptococcus pneumoniae with the surface of endothelial cells is mediated in blood flow via mechanosensitive proteins such as the Von Willebrand Factor (VWF). This glycoprotein changes its molecular conformation in response to shear stress, thereby exposing binding sites for a broad spectrum of host-ligand interactions. In general, culturing of primary endothelial cells under a defined shear flow is known to promote the specific cellular differentiation and the formation of a stable and tightly linked endothelial layer resembling the physiology of the inner lining of a blood vessel. Thus, the functional analysis of interactions between bacterial pathogens and the host vasculature involving mechanosensitive proteins requires the establishment of pump systems that can simulate the physiological flow forces known to affect the surface of vascular cells.
The microfluidic device used in this study enables a continuous and pulseless recirculation of fluids with a defined flow rate. The computer-controlled air-pressure pump system applies a defined shear stress on endothelial cell surfaces by generating a continuous, unidirectional, and controlled medium flow. Morphological changes of the cells and bacterial attachment can be microscopically monitored and quantified in the flow by using special channel slides that are designed for microscopic visualization. In contrast to static cell culture infection, which in general requires a sample fixation prior to immune labeling and microscopic analyses, the microfluidic slides enable both the fluorescence-based detection of proteins, bacteria, and cellular components after sample fixation; serial immunofluorescence staining; and direct fluorescence-based detection in real time. In combination with fluorescent bacteria and specific fluorescence-labeled antibodies, this infection procedure provides an efficient multiple component visualization system for a huge spectrum of scientific applications related to vascular processes.

This study describes the microscopic monitoring of pneumococcus adherence to von Willebrand factor strings produced on the surface of differentiated human primary endothelial cells under shear stress in defined flow conditions. This protocol can be extended to detailed visualization of specific cell structures and quantification of bacteria by applying differential immunostaining procedures.

Interaction of Streptococcus pneumoniae with the surface of endothelial cells is mediated in blood flow via mechanosensitive proteins such as the Von ...

Culture of Small Colony Variant of Pseudomonas aeruginosa and Quantitation of its Alginate

Pseudomonas aeruginosa, an opportunistic Gram-negative bacterial pathogen, can overproduce an exopolysaccharide alginate resulting in a unique phenotype called mucoidy. Alginate is linked to chronic lung infections resulting in poor prognosis in patients with cystic fibrosis (CF). Understanding the pathways that regulate the production of alginate can aid in the development of novel therapeutic strategies targeting the alginate formation. Another disease-related phenotype is the small colony variant (SCV). SCV is due to the slow growth of bacteria and often associated with increased resistance to antimicrobials. In this paper, we first show a method of culturing a genetically defined form of P. aeruginosa SCV due to pyrimidine biosynthesis mutations. Supplementation of nitrogenous bases, uracil or cytosine, returns the normal growth to these mutants, demonstrating the presence of a salvage pathway that scavenges free bases from the environment. Next, we discuss two methods for the measurement of bacterial alginate. The first method relies on the hydrolysis of the polysaccharide to its uronic acid monomer followed by derivatization with a chromogenic reagent, carbazole, while the second method uses an ELISA based on a commercially available, alginate-specific mAb. Both methods require a standard curve for quantitation. We also show that the immunological method is specific for alginate quantification and may be used for the measurement of alginate in the clinical specimens.

Culture of Small Colony Variant of Pseudomonas aeruginosa and Quantitation of its Alginate

Here, we describe a growth condition to culture the small colony variant of Pseudomonas aeruginosa. We also describe two separate methods for the detection and quantitation of the exopolysaccharide alginate produced by P. aeruginosa using a traditional uronic acid carbazole assay and an alginate-specific monoclonal antibody (mAb) based ELISA.

Pseudomonas aeruginosa, an opportunistic Gram-negative bacterial pathogen, can overproduce an exopolysaccharide alginate resulting in a unique phenotype ...