This work was supported by grants from the Foundation of Anna and Edwin Berger, Lars Hierta, the O.E. and Edla Johansson Foundation, the Swedish Medical Research Council (grant number K2015-57X-03163-43-4, www.vr.se), the Cancer Foundation at the University Hospital in Malm&#246;, the Physiographical Society (Forssman&#39;s Foundation), and the Sk&#229;ne County Council&#39;s Research and Development Foundation.

1. Analysis of Vn as a Bacterial Surface Protein Ligand
<ol>
	<li>Detection of Vn-binding at the bacterial surface using flow cytometry 
	NOTE: In flow cytometry, we used side scatter and forward scatter to gate positive events. To examine the interactions with Vn, Hif clinical isolates (n=10)7 were selected together with E. coli BL21 (DE3) as a negative control (Figure 1A).
	<ol>
		<li>Culture Hif clinical isolates in brain-heart infusion (BHI) medium supplemented with 10 &#181;g/mL NAD and hemin at 37 &#176;C with shaking at 200 rpm. Use Luria-Bertani medium to culture E. coli14. Harvest Hif at mid-log phase (OD600 = 0.3)15, and resuspend the bacteria in phosphate-buffered saline (PBS), pH 7.2, containing 1% (w/v) bovine serum albumin (BSA) (blocking buffer; PBS-BSA). Adjust the suspension to 109 CFU/mL.</li>
		<li>Transfer the aliquots containing 5 x 106 CFU to 5 mL polystyrene round-bottom tubes (12 x 75 mm2) and add 1 mL of blocking buffer. Centrifuge the suspension at 3,500 &#215; g at room temperature (RT)16 for 5 min to pellet the bacteria, then carefully aspirate to remove the supernatant without disturbing the pellet.</li>
		<li>Resuspend the bacterial pellets with 50 &#956;L of blocking buffer containing 250 nM Vn and incubate the samples for 1 h at RT without shaking. After incubation, pellet the bacteria by centrifugation at 3,500 x g for 5 min, then wash the pellets three times using PBS and similar centrifugation steps.</li>
		<li>To the bacterial pellet, add 50 &#956;L of primary sheep anti-human Vn polyclonal antibodies (pAbs) at 1:100 dilution in PBS-BSA. Incubate the suspension for 1 h at RT, then wash the bacteria three times with PBS to remove unbound antibodies (as described in step 1.1.3).</li>
		<li>Next, add 50 &#956;L of PBS-BSA containing fluorescein isothiocyanate (FITC)-conjugated donkey anti-sheep pAbs (1:100 dilution) and incubate at RT for 1 h in the dark.</li>
		<li>Prepare a blank control by incubating bacteria with blocking buffer only and pAbs without Vn.</li>
		<li>Wash bacteria three times with 1 mL of blocking buffer and pellet the suspension by centrifugation, as described in section 1.1.2. Finally, resuspend the bacterial pellet with 300 &#181;L of PBS and analyze by flow cytometry7.</li>
	</ol>
	</li>
	<li>ELISA analysis of the interaction between recombinant PH and Vn 
	NOTE: Controls need to be included to exclude nonspecific binding. Human Factor H (FH) or C4b-binding protein (C4BP) are used as positive and negative controls, respectively.
	<ol>
		<li>Dilute each of the human proteins (Vn, FH, and C4BP) separately to 50 nM in Tris-HCl, pH 9.0 (coating buffer). Dispense 100 &#181;L of protein solution into each well of a Polysorp microtiter plate. Close the plates with the lid and store at 4 &#176;C overnight (16 h) to facilitate the immobilization of protein onto microtiter plate wells.</li>
		<li>Discard the solution from the microtiter plate by tilting upside down over the sink and wash the wells three times with 300 &#181;L of PBS/well. Block the coated wells for 1 h at RT with PBS containing 2.5% (w/v) BSA (PBS-BSA).</li>
		<li>After removing the blocking solution, wash the wells three times with 300 &#181;L of PBS containing 0.05% (v/v) Tween 20 (PBST) per well. Add 100 &#181;L of 50 nM recombinant His-tagged PH to each sample well and incubate for 1 h at RT. In control wells, add only 100 &#181;L of PBS-BSA. 
		NOTE: The lph gene encoding PH from Hif was amplified by PCR and cloned into the pET26b expression vector that adds a 6&#215; His-tag at the C-terminus of the expressed protein. The recombinant vector was transformed into E. coli BL21(DE3) for expression. Ni-NTA resin was used to purify the recombinant protein15.</li>
		<li>Discard the protein solution and remove the unbound proteins by washing the wells three times with 300 &#181;L of PBST per well. Add 100 &#181;L of PBS-BSA containing horseradish peroxidase (HRP)-conjugated anti-His pAbs (1:10,000 dilution) and incubate for 1 h at RT.</li>
		<li>Prepare 20 mM solution A by dissolving tetramethylbenzidine in a solution of 5% acetone and 45% methanol. To prepare solution B, dissolve 19.2 g of citric acid in 1,000 mL of H2O, adjust the pH to 4.25 by adding KOH, then add 230 &#181;L of 30% H2O2. Store both solutions in the dark at RT. Just before use, mix 500 &#181;L of solution B with 9.5 mL of solution A to prepare the ELISA detection reagent.</li>
		<li>Wash the wells three times with 300 &#181;L of PBST per well and detect antigen-antibody complexes by adding 100 &#181;L of ELISA detection reagent to each well.</li>
		<li>Add 50 &#181;L of 1 M H2SO4/well to stop the reaction. Measure the optical density of the wells at 450 nm using a microplate reader.</li>
	</ol>
	</li>
	<li>Study of the interaction kinetics of recombinant PH and Vn using BLI
	<ol>
		<li>Immobilize human Vn on amine-reactive sensors using the amine coupling method, according to the manufacturer&#39;s guidelines11.</li>
		<li>Using PBS, serially dilute the ligand (recombinant PH) from 0 to 4 &#181;M and transfer the resulting solutions to a 96-well black, flat-bottom microtiter plate. Run the experiment at 30 &#176;C using a BLI instrument17.</li>
		<li>Load the data folder in the BLI data analysis software. Select the &#39;sensor selection&#39; option. Then, select &#39;reference well&#39; (Vn-coated sensor in PBS) for subtraction.</li>
		<li>Select &#39;align Y-axis to baseline&#39; and select &#39;interstep correction and align to association&#39;. Press &#39;process data&#39; that will automatically open the analysis tab.</li>
		<li>In the analysis tab, select the &#39;association and dissociation&#39; option under curve fitting. Select the model &#39;1:1 binding and global fitting&#39;. Press &#39;fit curve&#39; and export fitting data17.</li>
	</ol>
	</li>
</ol>
2. Characterization of The Role of Vn in Bacterial Adherence
<ol>
	<li>Study of bacterial adherence to Vn-coated glass surfaces
	<ol>
		<li>Prepare a 2 &#181;g/mL solution of Vn in PBS and pipet 10 &#181;L of this solution onto a glass microscope slide as a single drop. Allow the drop to dry on the slide for 30 min at RT. Coat a slide with human serum albumin (HSA) as a negative control.</li>
		<li>Wash the protein-coated glass slides three times by dipping the slides for two seconds in a beaker containing PBS to remove excess uncoated protein. Add 20 mL of fresh Hif culture (described in step 1.1.1) into a sterile plastic petri dish and submerge the Vn-/HSA-coated glass slides in the culture medium. Incubate the dishes at 37 &#176;C for 1 h with shaking at 20 rpm. 
		&#8203;NOTE: Hif M10 and Hif M10&#916;lph were grown in liquid BHI medium or on chocolate agar plates. The medium for the lph mutant was supplemented with 10 &#181;g/mL kanamycin15.</li>
		<li>After incubation, remove any unbound bacteria by submerging the slides three times in a beaker filled with PBS. Visualize bacteria by Gram staining, as described.
		<ol>
			<li>Remove excess PBS from each slide by tilting it and touching the edge onto tissue paper. Air-dry the slides for 3-5 min at RT, and fix adhered bacteria by passing each slide three times over a flame.</li>
			<li>Hold the slide by the edges with two fingers on a staining tray, then add 3&#8211;4 drops (200&#8211;300 &#181;L) of 2.3% crystal violet solution. Wait 60 s, then wash the slides under a gentle stream of tap water for 3&#8211;4 s.</li>
			<li>Add 3&#8211;4 drops of 0.33% iodine solution onto the slides. Wait 1 min, then rinse the slide under a gentle stream of tap water. Carefully dry the slides by blotting paper.</li>
			<li>Add 3&#8211;4 drops of decolorizing solution containing 75% isopropyl alcohol and 25% acetone onto the slide. After 5&#8211;10 s, wash the slide under a gentle stream of tap water.</li>
			<li>Add 3&#8211;4 drops (200&#8211;300 &#181;L) of basic carbolfuchsin solution. Wait 1 min, then rinse the slides under a gentle stream of tap water. Dry the slides using blotting paper.</li>
			<li>Visualize the bacteria under a light microscope, selecting an oil-immersion objective lens at 100X magnification18. Compare the adherence of Hif WT and mutant bacteria on the Vn- and HSA-coated glass surfaces.</li>
		</ol>
		</li>
	</ol>
	</li>
	<li>Study of Vn-dependent adherence of bacteria to epithelial cells 
	NOTE: This efficient adherence assay was used in our previous studies4,7.
	<ol>
		<li>Culture A549 cells (type II alveolar epithelial cells) in a 75-cm2&#160;tissue culture flask with F12 medium supplemented with 10% (vol/vol) fetal calf serum (FCS) (complete medium) and 5 &#181;g/mL gentamicin. Incubate the flask in an incubator with 5% CO2 at 37 &#176;C for 3 days until 80% confluent (confluency can be estimated by visualizing surface coverage by the cells using inverted microscope). The following four steps describe how to prepare the epithelial cells for the assay19,20.
		<ol>
			<li>Wash the cell monolayer in the flask twice with 20 mL of PBS by gentle swirling. To detach the cells from the flask surface, add 2 mL of cell detachment enzyme solution and incubate the flask for 5 min at 37 &#176;C. Tap the flask with your palm to detach all of the cells from the plastic surface. Pipette up and down a few times to disperse cell clumps.</li>
			<li>Add 18 mL of F12 complete medium to the flask and transfer the entire cell suspension to a 50-mL sterile Falcon tube. Centrifuge the cell suspension for 5 min at 200 x g at RT and discard the supernatant. Resuspend the cell pellet in 10 mL of F12 complete medium.</li>
			<li>Remove 10 &#181;L of the cell suspension and place it in an Eppendorf tube, then add 90 &#181;L of Trypan blue solution. Load the sample into a hemocytometer (depth 0.1 mm) after placing the coverslip.</li>
			<li>Count all viable cells in areas A, B, C, and D (each field consists of 16 squares, and each square has an area of 0.0025 mm2), then calculate the average number of cells ([A+B+C+D]/4). Calculate the number of cells per milliliter using the following equation: 
			Viable cells/mL = average cell count &#215; 104 &#215; dilution factor20. 
			NOTE: Here, the dilution factor is 10.</li>
			<li>Dilute the cell suspension to 5.0 x 103 cells/mL using complete medium containing 5 &#181;g/mL gentamicin. Dispense 500 &#956;L of cell suspension into each well of a 24-well cell culture plate. Incubate the plate at 37 &#176;C in 5% CO2 until the cells are 90% confluent.</li>
		</ol>
		</li>
		<li>Prior to bacterial infection, remove the medium from the wells and add F12 medium (without FCS), then incubate overnight at 37 &#176;C.</li>
		<li>Wash the cell monolayer three times with 500 &#181;L of PBS at RT. Place the plate on ice and add 100 &#181;L of pre-chilled F12 medium containing 10 &#181;g/mL of Vn. Incubate plate at 4 &#176;C for 1 h. For control wells, add only F12 medium.</li>
		<li>After incubation, discard the solution by pipetting and wash the cell layer twice with 1 mL of PBS at RT. Resuspend a culture of freshly grown Hif M10 (step 1.1.1) in F12 medium (2&#215;108 CFU/mL). Add 100 &#181;L of this bacterial suspension to each well and incubate the plate for 2 h at 37 &#176;C. 
		NOTE: Each well contains approximately 2 x 105 A549 cells. For infection, 2 x 107 bacterial CFU were added, corresponding to a multiplicity of infection of 100.</li>
		<li>Remove the medium by pipetting and wash the A549 epithelial cells three times with PBS. Add 50 &#181;L/well of cell detachment solution and incubate the plate for 5 min at 37 &#176;C.</li>
		<li>Next, add 50 &#181;L of F12 complete medium per well to stop the enzymatic reaction. Transfer the epithelial cells (&#8776;100 &#956;L [i.e., the entire volume]) from each well to a 6-mL glass tube containing four glass beads. Lyse the cells at RT by vortexing for 2 min.</li>
		<li>Dilute 10 &#181;L of the cell lysate 100-fold by adding 10 &#181;L of lysate to 990 &#181;L of F12 medium. Plate 10 &#181;L of the diluted sample onto a chocolate agar plate.</li>
		<li>Incubate the chocolate agar plate at 37 &#176;C overnight, then count the colonies. Each colony represents one CFU.</li>
	</ol>
	</li>
</ol>
3. Analysis of Vn-dependent Resistance to the Bactericidal Activity of Human Serum
<ol>
	<li>Purchase NHS from a commercial source. Prepare VDS as previously described12. Replenish the VDS with 180 nM Vn that is equivalent to Vn present in NHS.</li>
	<li>Prepare heat-inactivated serum (HIS) by heating NHS at 56 &#176;C for 30 min in order to inactivate complement proteins. 
	NOTE: The optimal serum concentration (5%) and incubation time (15 min) for the assay described in steps 3.3&#8211;3.7 were determined empirically for Hif15; these parameters could vary for other bacterial pathogens.</li>
	<li>Culture bacteria (in this case, Hif M10 and the mutant Hif M10&#916;lph) to mid-log phase (OD600&#160;= 0.3). Pellet bacteria by centrifugation at 3,500 x g for 10 min.</li>
	<li>Resuspend the bacterial pellet with 1 volume of dextrose gelatin Veronal buffer (DGVB++; pH 7.3) containing 2.5% (w/v) glucose, 2 mM MgCl2, 0.15 mM CaCl2, and 0.1% (wt/vol) gelatin.</li>
	<li>Add 1.5 x 103 CFU of bacteria to 100 &#181;L of DGVB++ containing 5% serum (NHS, HIS, VDS, or VDS+180 nM Vn). Incubate the sample at 37 &#176;C for 15 min with shaking at 300 rpm.</li>
	<li>Remove a 10 &#181;L aliquot from the reaction mixture at 0 min (T0 sample) and 15 min (Tt sample) and plate on chocolate agar. Incubate the plate at 37 &#176;C overnight.</li>
	<li>After incubation, count the colonies appearing on the plate. Calculate the percentage of bacteria killed12 using the following equation: (CFU at Tt)/(CFU at T0) &#215; 100.</li>
</ol>

<ol>
	<li>Singh, B., Su, Y. C., Riesbeck, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Vitronectin+in+bacterial+pathogenesis:+a+host+protein+used+in+complement+escape+and+cellular+invasion.">Vitronectin in bacterial pathogenesis: a host protein used in complement escape and cellular invasion.</a> Mol. Microbiol. 78 (3), 545-560 (2010).</li><li>Hallstrom, 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=Conserved+Patterns+of+Microbial+Immune+Escape:+Pathogenic+Microbes+of+Diverse+Origin+Target+the+Human+Terminal+Complement+Inhibitor+Vitronectin+via+a+Single+Common+Motif.">Conserved Patterns of Microbial Immune Escape: Pathogenic Microbes of Diverse Origin Target the Human Terminal Complement Inhibitor Vitronectin via a Single Common Motif.</a> PloS one. 11 (1), 0147709 (2016).</li><li>Su, Y. C., Hallstrom, B. M., Bernhard, S., Singh, B., Riesbeck, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Impact+of+sequence+diversity+in+the+Moraxella+catarrhalis.+UspA2/UspA2H+head+domain+on+vitronectin+binding+and+antigenic+variation.">Impact of sequence diversity in the Moraxella catarrhalis. UspA2/UspA2H head domain on vitronectin binding and antigenic variation.</a> Micro. Infect. 15 (5), 375-387 (2013).</li><li>Singh, B., 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=A+fine-tuned+interaction+between+trimeric+autotransporter+haemophilus+surface+fibrils+and+vitronectin+leads+to+serum+resistance+and+adherence+to+respiratory+epithelial+cells.">A fine-tuned interaction between trimeric autotransporter haemophilus surface fibrils and vitronectin leads to serum resistance and adherence to respiratory epithelial cells.</a> Infect. Immun. 82 (6), 2378-2389 (2014).</li><li>Kohler, 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=Binding+of+vitronectin+and+Factor+H+to+Hic+contributes+to+immune+evasion+of+Streptococcus+pneumoniae.+serotype+3.">Binding of vitronectin and Factor H to Hic contributes to immune evasion of Streptococcus pneumoniae. serotype 3.</a> Thromb. haemostasis. 113 (1), 125-142 (2015).</li><li>Onelli, E., Citterio, S., O'Connor, J. E., Levi, M., Sgorbati, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Flow+cytometry,+sorting+and+immunocharacterization+with+proliferating+cell+nuclear+antigen+of+cycling+and+non-cycling+cells+in+synchronized+pea+root+tips.">Flow cytometry, sorting and immunocharacterization with proliferating cell nuclear antigen of cycling and non-cycling cells in synchronized pea root tips.</a> Planta. 202 (2), 188-195 (1997).</li><li>Al-Jubair, 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=Haemophilus+influenzae+Type+f+Hijacks+Vitronectin+Using+Protein+H+To+Resist+Host+Innate+Immunity+and+Adhere+to+Pulmonary+Epithelial+Cells.">Haemophilus influenzae Type f Hijacks Vitronectin Using Protein H To Resist Host Innate Immunity and Adhere to Pulmonary Epithelial Cells.</a> J. Immunol. 195 (12), 5688-5695 (2015).</li><li>Martinez-Martin, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Technologies+for+Proteome-Wide+Discovery+of+Extracellular+Host-Pathogen+Interactions.">Technologies for Proteome-Wide Discovery of Extracellular Host-Pathogen Interactions.</a> J. Immunol. Res. 2017, 2197615 (2017).</li><li>Boleij, A., Laarakkers, C. M., Gloerich, J., Swinkels, D. W., Tjalsma, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Surface-affinity+profiling+to+identify+host-pathogen+interactions.">Surface-affinity profiling to identify host-pathogen interactions.</a> Infect. Immun. 79 (12), 4777-4783 (2011).</li><li>Abdiche, Y., Malashock, D., Pinkerton, A., Pons, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Determining+kinetics+and+affinities+of+protein+interactions+using+a+parallel+real-time+label-free+biosensor,+the+Octet.">Determining kinetics and affinities of protein interactions using a parallel real-time label-free biosensor, the Octet.</a> Anal. Biochem. 377 (2), 209-217 (2008).</li><li>Sultana, A., Lee, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Measuring+protein-protein+and+protein-nucleic+Acid+interactions+by+biolayer+interferometry.">Measuring protein-protein and protein-nucleic Acid interactions by biolayer interferometry.</a> Cur. Prot. Prot. Sc. 79, 11-26 (2015).</li><li>Su, Y. 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=Haemophilus+influenzae+acquires+vitronectin+via+the+ubiquitous+Protein+F+to+subvert+host+innate+immunity.">Haemophilus influenzae acquires vitronectin via the ubiquitous Protein F to subvert host innate immunity.</a> Mol. Microbiol. 87 (6), 1245-1266 (2013).</li><li>Ronander, 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=Nontypeable+Haemophilus+influenzae+adhesin+protein+E:+characterization+and+biological+activity.">Nontypeable Haemophilus influenzae adhesin protein E: characterization and biological activity.</a> J. Infect. Dis. 199 (4), 522-531 (2009).</li><li>Sezonov, G., Joseleau-Petit, D., D'Ari, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Escherichia+coli+physiology+in+Luria-Bertani+broth.">Escherichia coli physiology in Luria-Bertani broth.</a> J. Bact. 189 (23), 8746-8749 (2007).</li><li>Fleury, 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=Identification+of+a+Haemophilus+influenzae+factor+H-Binding+lipoprotein+involved+in+serum+resistance.">Identification of a Haemophilus influenzae factor H-Binding lipoprotein involved in serum resistance.</a> J. Imunol. 192 (12), 5913-5923 (2014).</li><li>Abdiche, Y., Malashock, D., Pinkerton, A., Pons, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Determining+kinetics+and+affinities+of+protein+interactions+using+a+parallel+real-time+label-free+biosensor,+the+Octet.">Determining kinetics and affinities of protein interactions using a parallel real-time label-free biosensor, the Octet.</a> Anal. Biochem. 377 (2), 209-217 (2008).</li><li>Rich, R. L., Myszka, D. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Higher-throughput,+label-free,+real-time+molecular+interaction+analysis.">Higher-throughput, label-free, real-time molecular interaction analysis.</a> Anal. Biochem. 361 (1), 1-6 (2007).</li><li>McNamara, G., Difilippantonio, M. J., Ried, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microscopy+and+image+analysis.">Microscopy and image analysis.</a> Current protoc. Hum. Genet. , 4 (2005).</li><li>Lieber, M., Smith, B., Szakal, A., Nelson-Rees, W., Todaro, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+continuous+tumor-cell+line+from+a+human+lung+carcinoma+with+properties+of+type+II+alveolar+epithelial+cells.">A continuous tumor-cell line from a human lung carcinoma with properties of type II alveolar epithelial cells.</a> International J. Canc. 17 (1), 62-70 (1976).</li><li>Foster, K. A., Oster, C. G., Mayer, M. M., Avery, M. L., Audus, K. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterization+of+the+A549+cell+line+as+a+type+II+pulmonary+epithelial+cell+model+for+drug+metabolism.">Characterization of the A549 cell line as a type II pulmonary epithelial cell model for drug metabolism.</a> Exp. Cell Res. 243 (2), 359-366 (1998).</li><li>Su, Y. 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=Haemophilus+influenzae+P4+Interacts+With+Extracellular+Matrix+Proteins+Promoting+Adhesion+and+Serum+Resistance.">Haemophilus influenzae P4 Interacts With Extracellular Matrix Proteins Promoting Adhesion and Serum Resistance.</a> J. Infect. Dis. 213 (2), 314-323 (2016).</li><li>Singh, B., Al-Jubair, T., Morgelin, M., Thunnissen, M. M., Riesbeck, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+unique+structure+of+Haemophilus+influenzae+protein+E+reveals+multiple+binding+sites+for+host+factors.">The unique structure of Haemophilus influenzae protein E reveals multiple binding sites for host factors.</a> Infect. Immun. 81 (3), 801-814 (2013).</li><li>Vellaiswamy, M., Campagna, B., Raoult, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transmission+electron+microscopy+as+a+tool+for+exploring+bacterial+proteins:+model+of+RickA+in+Rickettsia+conorii.">Transmission electron microscopy as a tool for exploring bacterial proteins: model of RickA in Rickettsia conorii.</a> New Microbiolog. 34 (2), 209-218 (2011).</li><li>Pinne, M., Haake, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Immuno-fluorescence+assay+of+leptospiral+surface-exposed+proteins.">Immuno-fluorescence assay of leptospiral surface-exposed proteins.</a> J. Vis. Exp. JoVE. (53), (2011).</li></ol>

The authors have no financial conflicts of interest.

Bacterial pathogens recruit Vn to the cell surface and utilize this complement regulator to prevent the deposition of complement factors and completion of the membrane attack complex2. Vn also functions as a bridge molecule between bacterial surface proteins and host cell surface receptors, thus enabling pathogens to adhere to the surface of epithelial cells and subsequently mediate internalization. In this study, we describe protocols that can be used to estimate i) binding of Vn to the surface o...

Vitronectin (Vn) is an important human glycoprotein involved in maintaining homeostasis via regulation of the fibrinolytic system. Vn also functions as a complement regulator by inhibiting the terminal complement pathway during C5b6-7 complex formation and C9 polymerization. Several bacterial pathogens have been shown to recruit Vn to the cell surface as a means of resisting complement deposition1,2,3. In addition, Vn functions as a &#34;sandwich&#34; molecule between bacteria and host epithelial cell receptors, thereby promoting adherence and internalization of pathogens2,4,5. Binding of Vn to the bacterial cell surface is mediated by other currently unidentified proteins. Fully elucidating the functional role of Vn-binding in evasion of the hose immune response will therefore require identification of Vn-recruiting proteins.
The initial step in identifying Vn-binding proteins is to test whether a pathogen of interest can bind purified Vn. Flow cytometry is a convenient and straightforward method to determine whether Vn is bound to pathogen cells. In this study, we assessed the binding of Vn to various Haemophilus influenzae type f (Hif) clinical isolates6. The method described herein is quantitative and can be used to distinguish the binding capacity of a wide variety of bacterial strains. In a previous study, we characterized protein H (PH) of Hif as a Vn-binding protein7. Therefore, in the present study, the Vn-binding potential of wild-type (WT) Hif and Hif M10&#916;lph mutants were compared using the described protocols.
Once it is determined that a pathogen binds Vn, the second step is to characterize the surface proteome in order to identify potential Vn-binding proteins. A variety of approaches can be used for this purpose8,9, but these methodologies are not described in this report. The method most suitable for examining protein-protein interactions is to recombinantly express selected bacterial surface proteins in E. coli and purify by affinity chromatography. Here, we use PH and its molecular interaction with Vn to illustrate the method. Interactions between recombinant PH and Vn were characterized using an enzyme-linked immunosorbent assay (ELISA)7 and a recently developed label-free technique known as bio-layer interferometry (BLI)10,11. Whereas ELISAs can be used to confirm protein-protein interactions, BLI provides detailed data regarding the kinetic parameters of the interactions.
To study the functional role of Vn in bacterial adherence, two different assays can be utilized. The first assay described here is direct measurement of bacterial adherence to Vn-coated glass surfaces, whereas the second assay examines adherence to the surface of epithelial cells. For the first assay, glass slides were coated with Vn, and the binding of WT or mutant Hif strains was assessed by Gram-stain and microscopy. This technique readily distinguishes bacteria based on the ability to bind Vn12. Bacterial adhesion to mammalian cells was then analyzed by adding cultured bacteria onto a monolayer of type II alveolar epithelial cells; bacterial attachment was assessed by counting the number of colony-forming units (CFUs). Adhered and internalized bacteria can be distinguished in the presence or absence of Vn4,13.
The role of Vn acquisition in bacterial serum resistance was evaluated using a serum killing assay (i.e., serum bactericidal activity). To assess the significance of Vn acquisition in serum resistance, the bactericidal activity of Vn-depleted serum (VDS) was compared with that of normal human serum (NHS). The method used readily distinguishes Vn-binding versus non-binding bacteria based on serum resistance. We used this method to study the role of Vn in the serum resistance of several bacterial pathogens4,12.
Numerous methods have been reported for studying host-pathogen interactions. Here, we describe a set of protocols that can be easily adapted to the study of any pathogen in order to assess the role of Vn in pathogenesis. We tested these protocols using various pathogens, and Hif was chosen as an example for this report.

<table border="0" cellpadding="0" cellspacing="0" style="width:1013px;" width="1014">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:335px;">1.5 mL thermomixter</td>
			<td style="width:288px;">Eppendorf</td>
			<td style="width:119px;">5355</td>
			<td style="width:272px;">dry block heating and cooling shaker</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">5 mL polystyrene round-bottom tube&#160;</td>
			<td>BD Falcon</td>
			<td>60819-138</td>
			<td>12 &#215; 75 mm style</td>
		</tr>
		<tr height="25">
			<td height="25" style="height:25px;width:335px;">5% CO2 supplied incubator&#160;</td>
			<td style="width:288px;">Thermo Scientific&#160;</td>
			<td style="width:119px;">BBD6220</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">6 mL polystyrene round-bottom tube&#160;</td>
			<td style="width:288px;">VWR</td>
			<td>89000-478</td>
			<td>12 &#215; 75 mm style with cap</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:335px;">24-well plates</td>
			<td style="width:288px;">BD Falcon</td>
			<td>08-772-1H</td>
			<td style="width:272px;">Cell culture grade</td>
		</tr>
		<tr height="26">
			<td height="26" style="height:26px;width:335px;">30% Hydrogen peroxide (H2O2) solution</td>
			<td style="width:288px;">Sigma-Aldrich</td>
			<td style="width:119px;">H1009-100ML</td>
			<td>Laboratory analysis grade</td>
		</tr>
		<tr height="25">
			<td height="25" style="height:25px;width:335px;">75 cm2 tissue culture flask</td>
			<td style="width:288px;">BD Falcon</td>
			<td>BD353136</td>
			<td>Vented</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">96 well black flat bottom plate</td>
			<td style="width:288px;">Greiner Bio-One</td>
			<td>655090</td>
			<td>Tissue culture treated &#181;Clear black plates</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:335px;">A549 Cell Line human</td>
			<td style="width:288px;">Sigma-Aldrich</td>
			<td style="width:119px;">86012804-1VL</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:335px;">Cell detachment enzyme (Accutase)&#160;</td>
			<td style="width:288px;">Sigma-Aldrich</td>
			<td>A6964-500ML</td>
			<td style="width:272px;">Cell Culture Grade</td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:335px;">AR2G sensors</td>
			<td style="width:288px;">Pall Life Science</td>
			<td>18-5095</td>
			<td style="width:272px;">Sensor to immobilized protein by amino coupling&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:335px;">Acetone</td>
			<td style="width:288px;">VWR</td>
			<td>97064-786</td>
			<td>Analysis grade</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:335px;">Bovine Serum Albumins (BSA)</td>
			<td style="width:288px;">Sigma-Aldrich</td>
			<td>A2058</td>
			<td style="width:272px;">Suitable for cell culture</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:335px;">Bibulous paper&#160;</td>
			<td style="width:288px;">VWR</td>
			<td>28511-007</td>
			<td></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:335px;">Bio-layer interferometer</td>
			<td style="width:288px;">Pall Life Science</td>
			<td style="width:119px;">FB-50258</td>
			<td style="width:272px;">Bilayer interferometry measuring equipment</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Crystal violet solution</td>
			<td style="width:288px;">Sigma-Aldrich</td>
			<td>HT90132-1L</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:335px;">C4BP (C4b binding protein)</td>
			<td style="width:288px;">Complement Technology, Inc.</td>
			<td style="width:119px;">A109</td>
			<td>Bought as Frozen liquid form</td>
		</tr>
		<tr height="26">
			<td height="26" style="height:26px;width:335px;">Calcium chloride (CaCl2)</td>
			<td style="width:288px;">Sigma-Aldrich</td>
			<td>C5670-500G</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:335px;">Carbol-fuchsin solution</td>
			<td style="width:288px;">Sigma-Aldrich</td>
			<td>HT8018-250ML</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:335px;">Citric acid</td>
			<td style="width:288px;">Sigma-Aldrich</td>
			<td>251275-500G</td>
			<td>American Chemical Society (ACS) grade</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:335px;">Decolorizing solution</td>
			<td style="width:288px;">Sigma-Aldrich</td>
			<td>75482-250ML-F</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:335px;">E. coli host (E. Coli BL21)</td>
			<td style="width:288px;">Novagen</td>
			<td>69450-3</td>
			<td>Protein expression host</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:335px;">F12 medium</td>
			<td style="width:288px;">Sigma-Aldrich</td>
			<td>D6421</td>
			<td style="width:272px;">Cell Culture Grade</td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:335px;">Flow cytometer&#160;</td>
			<td style="width:288px;">BD Biosciences</td>
			<td style="width:119px;">651154</td>
			<td style="width:272px;">Cell analysis grade for research applications&#160;</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:335px;">Fetal Calf Serum (FCS)</td>
			<td style="width:288px;">Sigma-Aldrich</td>
			<td>12003C</td>
			<td style="width:272px;">Suitable for cell culture</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:335px;">Normal human serum (NHS)</td>
			<td style="width:288px;">Complement Technology, Inc.</td>
			<td>NHS</td>
			<td style="width:272px;">Pooled human serum</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:335px;">FITC-conjugated donkey anti-sheep antibodies&#160;</td>
			<td style="width:288px;">AbD Serotec</td>
			<td>STAR88F</td>
			<td style="width:272px;">Polyclonal</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:335px;">Gentamicin</td>
			<td style="width:288px;">Sigma-Aldrich</td>
			<td>G1397</td>
			<td style="width:272px;">Cell culture grade</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Glucose</td>
			<td style="width:288px;">Sigma-Aldrich</td>
			<td style="width:119px;">G8270-1KG</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:335px;">Gelatin</td>
			<td style="width:288px;">Sigma-Aldrich</td>
			<td>G9391</td>
			<td>Suitable for cell culture</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Hemocytometer</td>
			<td style="width:288px;">Marienfeld</td>
			<td>640210</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:335px;">HRP-conjugated anti-His tag antibodies</td>
			<td style="width:288px;">Abcam</td>
			<td style="width:119px;">ab1269</td>
			<td style="width:272px;">Polyclonal</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:335px;">Human factor H</td>
			<td style="width:288px;">Complement Technology, Inc.</td>
			<td style="width:119px;">A137</td>
			<td>Bought as Frozen liquid form</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:335px;">C4BP</td>
			<td style="width:288px;">Complement Technology, Inc.</td>
			<td style="width:119px;">A109</td>
			<td>Frozen solution</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:335px;">Human serum albumin</td>
			<td style="width:288px;">Sigma-Aldrich</td>
			<td style="width:119px;">A1653-10G</td>
			<td>lyophilized powder</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Histidine affinity resin column (HisTrap HP)</td>
			<td style="width:288px;">GE Health Care Life Science</td>
			<td style="width:119px;">17-5247-01</td>
			<td>Columns prepacked with Ni Sepharose</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:335px;">His-tagged PH</td>
			<td style="width:288px;"></td>
			<td style="width:119px;"></td>
			<td>Recombinantly expressed and purified in our lab</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:335px;">Iodine solution</td>
			<td style="width:288px;">Sigma-Aldrich</td>
			<td>HT902-8FOZ</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:335px;">Methanol</td>
			<td style="width:288px;">VWR</td>
			<td>BDH1135-1LP</td>
			<td>Analysis grade</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:335px;">&#160;Microscope</td>
			<td style="width:288px;">Olympus</td>
			<td style="width:119px;">IX73</td>
			<td style="width:272px;">Inverted microscope</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:335px;">Microscope slides</td>
			<td style="width:288px;">Sigma-Aldrich</td>
			<td>S8902</td>
			<td style="width:272px;">plain, size 25 mm &#215; 75 mm&#160;</td>
		</tr>
		<tr height="26">
			<td height="26" style="height:26px;width:335px;">Magnesium chloride (MgCl2)</td>
			<td style="width:288px;">Sigma-Aldrich</td>
			<td>M8266-1KG</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Plasmid containg C terminal 6x His-tag on the backbone (pET26(b))</td>
			<td style="width:288px;">Novagen</td>
			<td>69862-3</td>
			<td>DNA vector</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:335px;">Polysorb microtitre plates&#160;</td>
			<td style="width:288px;">Sigma-Aldrich</td>
			<td>M9410</td>
			<td style="width:272px;">For ELISA</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:335px;">Potassium hydroxide (KOH)</td>
			<td style="width:288px;">Sigma-Aldrich</td>
			<td style="width:119px;">6009</td>
			<td>American Chemical Society (ACS) grade</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:335px;">Sheep anti-human Vn antibodies</td>
			<td style="width:288px;">AbD Serotec</td>
			<td>AHP396</td>
			<td style="width:272px;">Polyclonal</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:335px;">Shaker&#160;</td>
			<td style="width:288px;">Stuart Scientific</td>
			<td style="width:119px;">STR6</td>
			<td>Platform shaker</td>
		</tr>
		<tr height="26">
			<td height="26" style="height:26px;width:335px;">Tissue culture flask</td>
			<td style="width:288px;">BD Falcon</td>
			<td style="width:119px;">3175167</td>
			<td style="width:272px;">75 cm2</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:335px;">&#160;Thermomixer&#160;</td>
			<td style="width:288px;">Sigma-Aldrich</td>
			<td>T3317</td>
			<td>Dry block heating and cooling shaker</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:335px;">Tetramethylbenzidine</td>
			<td style="width:288px;">Sigma-Aldrich</td>
			<td>860336-100MG</td>
			<td>ELISA grade</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:335px;">Vitronectin (Vn) from human plasma</td>
			<td style="width:288px;">Sigma-Aldrich</td>
			<td>V8379-50UG</td>
			<td>cell culture grade</td>
		</tr>
	</tbody>
</table>

assays for studying the role of vitronectin in bacterial adhesion and serum resistance

Bacteria utilize complement regulators as a means of evading the host immune response. Here, we describe protocols for evaluating the role vitronectin acquisition at the bacterial cell surface plays in resistance to the host immune system. Flow cytometry experiments identified human plasma vitronectin as a ligand for the bacterial receptor outer membrane protein H of Haemophilus influenzae type f. An enzyme-linked immunosorbent assay was employed to characterize the protein-protein interactions between purified recombinant protein H and vitronectin, and binding affinity was assessed using bio-layer interferometry. The biological importance of the binding of vitronectin to protein H at the bacterial cell surface in evasion of the host immune response was confirmed using a serum resistance assay with normal and vitronectin-depleted human serum. The importance of vitronectin in bacterial adherence was analyzed using glass slides with and without vitronectin coating, followed by Gram staining. Finally, bacterial adhesion to human alveolar epithelial cell monolayers was investigated. The protocols described here can be easily adapted to the study of any bacterial species of interest.

Vn-binding to the surface of bacteria was determined by flow cytometry. All Hif clinical isolates tested in this study recruited Vn to the cell surface. No interaction of Vn with the cell surface was observed for the E. coli negative control strain (Figure 1A). As shown in Figure 1B, PH is a major Vn-binding protein on the surface of Hif cells. Binding of Vn by the WT Hif strain M10 caus...

Watch this Scientific Journal Video about Assays for Studying the Role of Vitronectin in Bacterial Adhesion and Serum Resistance at JoVE.com

Assays for Studying the Role of Vitronectin in Bacterial Adhesion and Serum Resistance

This report describes protocols for characterizing interactions between bacterial outer membrane proteins and the human complement regulator vitronectin. The protocols can be used to study the binding reactions and biological function of vitronectin in any bacterial species.

Bacteria utilize complement regulators as a means of evading the host immune response. Here, we describe protocols for evaluating the role vitronectin ...

assays-for-studying-role-vitronectin-bacterial-adhesion-serum

Research

JoVE Journal

Immunology and Infection

8.0K Views.  Lund University. This report describes protocols for characterizing interactions between bacterial outer membrane proteins and the human complement regulator vitronectin. The protocols can be used to study the binding reactions and biological function of vitronectin in any bacterial species.

Video: Assays for Studying the Role of Vitronectin in Bacterial Adhesion and Serum Resistance

In Vitro Assay of Bacterial Adhesion onto Mammalian Epithelial Cells

To cause infections, bacteria must colonize their host. Bacterial pathogens express various molecules or structures able to promote attachment to host cells1. These adhesins rely on interactions with host cell surface receptors or soluble proteins acting as a bridge between bacteria and host. Adhesion is a critical first step prior to invasion and/or secretion of toxins, thus it is a key event to be studied in bacterial pathogenesis. Furthermore, adhered bacteria often induce exquisitely fine-tuned cellular responses, the studies of which have given birth to the field of 'cellular microbiology'2. Robust assays for bacterial adhesion on host cells and their invasion therefore play key roles in bacterial pathogenesis studies and have long been used in many pioneer laboratories3,4. These assays are now practiced by most laboratories working on bacterial pathogenesis.
Here, we describe a standard adherence assay illustrating the contribution of a specific adhesin. We use the Escherichia coli strain 27875, a human pathogenic strain expressing the autotransporter Adhesin Involved in Diffuse Adherence (AIDA). As a control, we use a mutant strain lacking the aidA gene, 2787&Delta;aidA (F. Berthiaume and M. Mourez, unpublished), and a commercial laboratory strain of E. coli, C600 (New England Biolabs). The bacteria are left to adhere to the cells from the commonly used HEp-2 human epithelial cell line. This assay has been less extensively described before6.

In Vitro Assay of Bacterial Adhesion onto Mammalian Epithelial Cells

This protocol is a simple bacterial adhesion assay consisting in counting the numbers of bacterial colony forming units that are adhered onto cultured cells. The assay is robust, independent of the adhesin studied, and numerous variations are used in most laboratories working on bacterial pathogenesis.

To cause infections, bacteria must colonize their host. Bacterial pathogens express various molecules or structures able to promote attachment to host ...

Amplifying and Quantifying HIV-1 RNA in HIV Infected Individuals with Viral Loads Below the Limit of Detection by Standard Clinical Assays

Amplifying viral genes and quantifying HIV-1 RNA in HIV-1 infected individuals with viral loads below the limit of detection by standard assays (below 50-75 copies/ml) is necessary to gain insight to viral dynamics and virus host interactions in patients who naturally control the infection and those who are on combination antiretroviral therapy (cART). 
Here we describe how to amplify viral genomes by single genome sequencing (the SGS protocol) 13, 19 and how to accurately quantify HIV-1 RNA in patients with low viral loads (the single-copy assay (SCA) protocol) 12, 20. 
The single-copy assay is a real-time PCR assay with sensitivity depending on the volume of plasma being assayed. If a single virus genome is detected in 7 ml of plasma, then the RNA copy number is reported to be 0.3 copies/ml. The assay has an internal control testing for the efficiency of RNA extraction, and controls for possible amplification from DNA or contamination. Patient samples are measured in triplicate.
The single-genome sequencing assay (SGS), now widely used and considered to be non-labor intensive 3, 7, 12, 14, 15,is a limiting dilution assay, in which endpoint diluted cDNA product is spread over a 96-well plate. According to a Poisson distribution, when less than 1/3 of the wells give product, there is an 80% chance of the PCR product being resultant of amplification from a single cDNA molecule. SGS has the advantage over cloning of not being subjected to resampling and not being biased by PCR-introduced recombination 19. However, the amplification success of SCA and SGS depend on primer design. Both assays were developed for HIV-1 subtype B, but can be adapted for other subtypes and other regions of the genome by changing primers, probes, and standards.

Quantifying levels of HIV-1 RNA in plasma and sequencing single HIV-1 genomes from individuals with viral loads below the limit of detection (50-75 copies/ml) is difficult. Here we describe how to extract and quantify plasma viral RNA using a real time PCR assay that reliably measures HIV-1 RNA down to 0.3 copies/ml and how to amplify viral genomes by single genome sequencing, from samples with very low viral loads.

Amplifying viral genes and quantifying HIV-1 RNA in HIV-1 infected individuals with viral loads below the limit of detection by standard assays (below ...

Introducing Shear Stress in the Study of Bacterial Adhesion

During bacterial infections a sequence of interactions occur between the pathogen and its host. Bacterial adhesion to the host cell surface is often the initial and determining step of the pathogenesis. Although experimentally adhesion is mostly studied in static conditions adhesion actually takes place in the presence of flowing liquid. First encounters between bacteria and their host often occur at the mucosal level, mouth, lung, gut, eye, etc. where mucus flows along the surface of epithelial cells. Later in infection, pathogens occasionally access the blood circulation causing life-threatening illnesses such as septicemia, sepsis and meningitis. A defining feature of these infections is the ability of these pathogens to interact with endothelial cells in presence of circulating blood. The presence of flowing liquid, mucus or blood for instance, determines adhesion because it generates a mechanical force on the pathogen. To characterize the effect of flowing liquid one usually refers to the notion of shear stress, which is the tangential force exerted per unit area by a fluid moving near a stationary wall, expressed in dynes/cm2. Intensities of shear stress vary widely according to the different vessels type, size, organ, location etc. (0-100 dynes/cm2). Circulation in capillaries can reach very low shear stress values and even temporarily stop during periods ranging between a few seconds to several minutes 1. On the other end of the spectrum shear stress in arterioles can reach 100 dynes/cm2 2. The impact of shear stress on different biological processes has been clearly demonstrated as for instance during the interaction of leukocytes with the endothelium 3. To take into account this mechanical parameter in the process of bacterial adhesion we took advantage of an experimental procedure based on the use of a disposable flow chamber 4. Host cells are grown in the flow chamber and fluorescent bacteria are introduced in the flow controlled by a syringe pump. We initially focused our investigations on the bacterial pathogen Neisseria meningitidis, a Gram-negative bacterium responsible for septicemia and meningitis. The procedure described here allowed us to study the impact of shear stress on the ability of the bacteria to: adhere to cells 1, to proliferate on the cell surface 5and to detach to colonize new sites 6 (Figure 1). Complementary technical information can be found in reference 7. Shear stress values presented here were chosen based on our previous experience1 and to represent values found in the literature. The protocol should be applicable to a wide range of pathogens with specific adjustments depending on the objectives of the study.

During the infection process, a key step is the adhesion of pathogens with host cells. In most instances this adhesion step occurs in the presence of mechanical stress generated by flowing liquid. We describe a technique that introduces shear stress as an important parameter in the study of bacterial adhesion.

During bacterial infections a sequence of interactions occur between the pathogen and its host. Bacterial adhesion to the host cell surface is often the ...

Multiplex PCR Assay for Typing of Staphylococcal Cassette Chromosome Mec Types I to V in Methicillin-resistant Staphylococcus aureus

Staphylococcal Cassette Chromosome mec (SCCmec) typing is a very important molecular tool for understanding the epidemiology and clonal strain relatedness of methicillin-resistant Staphylococcus aureus (MRSA), particularly with the emerging outbreaks of community-associated MRSA (CA-MRSA) occurring on a worldwide basis. Traditional PCR typing schemes classify SCCmec by targeting and identifying the individual mec and ccr gene complex types, but require the use of many primer sets and multiple individual PCR experiments. We designed and published a simple multiplex PCR assay for quick-screening of major SCCmec types and subtypes I to V, and later updated it as new sequence information became available. This simple assay targets individual SCCmec types in a single reaction, is easy to interpret and has been extensively used worldwide. However, due to the sophisticated nature of the assay and the large number of primers present in the reaction, there is the potential for difficulties while adapting this assay to individual laboratories. To facilitate the process of establishing a MRSA SCCmec assay, here we demonstrate how to set up our multiplex PCR assay, and discuss some of the vital steps and procedural nuances that make it successful.

Multiplex PCR Assay for Typing of Staphylococcal Cassette Chromosome Mec Types I to V in Methicillin-resistant Staphylococcus aureus

We demonstrate a simple multiplex PCR assay for quick-screening and typing of Staphylococcal Cassette Chromosome mec (SCCmec) types I-V for methicillin-resistant Staphylococcus aureus, and provide some of the vital steps and procedural nuances that make it successful for adapting this assay to individual laboratories.

Staphylococcal Cassette Chromosome mec (SCCmec) typing  is a very important molecular tool for understanding the epidemiology and  clonal strain ...

VIGS-Mediated Forward Genetics Screening for Identification of Genes Involved in Nonhost Resistance

Nonhost disease resistance of plants against bacterial pathogens is controlled by complex defense pathways. Understanding this mechanism is important for developing durable disease-resistant plants against wide range of pathogens. Virus-induced gene silencing (VIGS)-based forward genetics screening is a useful approach for identification of plant defense genes imparting nonhost resistance. Tobacco rattle virus (TRV)-based VIGS vector is the most efficient VIGS vector to date and has been efficiently used to silence endogenous target genes in Nicotiana benthamiana.

	In this manuscript, we demonstrate a forward genetics screening approach for silencing of individual clones from a cDNA library in N. benthamiana and assessing the response of gene silenced plants for compromised nonhost resistance against nonhost pathogens, Pseudomonas syringae pv. tomato T1, P. syringae pv. glycinea, and X. campestris pv. vesicatoria. These bacterial pathogens are engineered to express GFPuv protein and their green fluorescing colonies can be seen by naked eye under UV light in the nonhost pathogen inoculated plants if the silenced target gene is involved in imparting nonhost resistance. This facilitates reliable and faster identification of gene silenced plants susceptible to nonhost pathogens. Further, promising candidate gene information can be known by sequencing the plant gene insert in TRV vector. Here we demonstrate the high throughput capability of VIGS-mediated forward genetics to identify genes involved in nonhost resistance. Approximately, 100 cDNAs can be individually silenced in about two to three weeks and their relevance in nonhost resistance against several nonhost bacterial pathogens can be studied in a week thereafter. In this manuscript, we enumerate the detailed steps involved in this screening. VIGS-mediated forward genetics screening approach can be extended not only to identifying genes involved in nonhost resistance but also to studying genes imparting several biotic and abiotic stress tolerances in various plant species.

Virus-induced gene silencing is an useful tool for identifying genes involved in nonhost resistance of plants. We demonstrate the use of bacterial pathogens expressing GFPuv in identifying gene silenced plants susceptible to nonhost pathogens. This approach is easy, fast and facilitates large scale screening and similar protocol can be applied to studying various other plant-microbe interactions.


	Nonhost disease resistance of plants against bacterial pathogens is controlled by complex defense pathways. Understanding this mechanism is important ...

Rapid Screening of HIV Reverse Transcriptase and Integrase Inhibitors

Although a number of anti HIV drugs have been approved, there are still problems with toxicity and drug resistance. This demonstrates a need to identify new compounds that can inhibit infection by the common drug resistant HIV-1 strains with minimal toxicity. Here we describe an efficient assay that can be used to rapidly determine the cellular cytotoxicity and efficacy of a compound against WT and mutant viral strains.
The desired target cell line is seeded in a 96-well plate and, after a 24 hr incubation, serially dilutions of the compounds to be tested are added. No further manipulations are necessary for cellular cytotoxicity assays; for anti HIV assays a predetermined amount of either a WT or drug resistant HIV-1 vector that expresses luciferase is added to the cells. Cytotoxicity is measured by using an ATP dependent luminescence assay and the impact of the compounds on infectivity is measured by determining the amount of luciferase in the presence or the absence of the putative inhibitors.
This screening assay takes 4 days to complete and multiple compounds can be screened in parallel. Compounds are screened in triplicate and the data are normalized to the infectivity/ATP levels in absence of target compounds. This technique provides a quick and accurate measurement of the efficacy and toxicity of potential anti HIV compounds.

Here we describe cellular cytotoxicity and single round infectivity assays that allow for the rapid and accurate screening of compounds to determine their cellular cytotoxicity (CC50) and IC50 values against WT and drug resistant HIV-1.

Although a number of anti HIV drugs have been approved, there are still problems with toxicity and drug resistance. This demonstrates a need to identify ...

Static Adhesion Assay for the Study of Integrin Activation in T Lymphocytes

T lymphocyte adhesion is required for multiple T cell functions, including migration to sites of inflammation and formation of immunological synapses with antigen presenting cells. T cells accomplish regulated adhesion by controlling the adhesive properties of integrins, a class of cell adhesion molecules consisting of heterodimeric pairs of transmembrane proteins that interact with target molecules on partner cells or extracellular matrix. The most prominent T cell integrin is lymphocyte function associated antigen (LFA)-1, composed of subunits &#945;L and &#946;2, whose target is the intracellular adhesion molecule (ICAM)-1. The ability of a T cell to control adhesion derives from the ability to regulate the affinity states of individual integrins. Inside-out signaling describes the process whereby signals inside a cell cause the external domains of integrins to assume an activated state. Much of our knowledge of these complex phenomena is based on mechanistic studies performed in simplified in&#160;vitro model systems. The T lymphocyte adhesion assay described here is an excellent tool that allows T cells to adhere to target molecules, under static conditions, and then utilizes a fluorescent plate reader to quantify adhesiveness. This assay has been useful in defining adhesion-stimulatory or inhibitory substances that act on lymphocytes, as well as characterizing the signaling events involved. Although described here for LFA-1 - ICAM-1 mediated adhesion; this assay can be readily adapted to allow for the study of other adhesive interactions (e.g.&#160;VLA-4 - fibronectin).

Static adhesion assay is a powerful tool that can be used to model the interactions between T lymphocytes and other cell types. Interactions are generated by injecting labeled T cells into wells coated with adhesion molecules, while a plate reader is used to quantify the number of adherent cells following serial washes.

T lymphocyte adhesion is required for multiple T cell functions, including migration to sites of inflammation and formation of immunological synapses with ...

In Vitro and In Vivo Model to Study Bacterial Adhesion to the Vessel Wall Under Flow Conditions

In order to cause endovascular infections and infective endocarditis, bacteria need to be able to adhere to the vessel wall while being exposed to the shear stress of flowing blood.
To identify the bacterial and host factors that contribute to vascular adhesion of microorganisms, appropriate models that study these interactions under physiological shear conditions are needed. Here, we describe an in vitro flow chamber model that allows to investigate bacterial adhesion to different components of the extracellular matrix or to endothelial cells, and an intravital microscopy model that was developed to directly visualize the initial adhesion of bacteria to the splanchnic circulation in vivo. These methods can be used to identify the bacterial and host factors required for the adhesion of bacteria under flow. We illustrate the relevance of shear stress and the role of von Willebrand factor for the adhesion of Staphylococcus aureus using both the in vitro and in vivo model.

In Vitro and In Vivo Model to Study Bacterial Adhesion to the Vessel Wall Under Flow Conditions

To study the interaction of bacteria with the blood vessels under shear stress, a flow chamber and an in vivo mesenteric intravital microscopy model are described that allow to dissect the bacterial and host factors contributing to vascular adhesion.

In order to cause endovascular infections and infective endocarditis, bacteria need to be able to adhere to the vessel wall while being exposed to the ...

Assay of Adhesion Under Shear Stress for the Study of T Lymphocyte-Adhesion Molecule Interactions

Overall, T cell adhesion is a critical component of function, contributing to the distinct processes of cellular recruitment to sites of inflammation and interaction with antigen presenting cells (APC) in the formation of immunological synapses. These two contexts of T cell adhesion differ in that T cell-APC interactions can be considered static, while T cell-blood vessel interactions are challenged by the shear stress generated by circulation itself. T cell-APC interactions are classified as static in that the two cellular partners are static relative to each other. Usually, this interaction occurs within the lymph nodes. As a T cell interacts with the blood vessel wall, the cells arrest and must resist the generated shear stress.1,2 These differences highlight the need to better understand static adhesion and adhesion under flow conditions as two distinct regulatory processes. The regulation of T cell adhesion can be most succinctly described as controlling the affinity state of integrin molecules expressed on the cell surface, and thereby regulating the interaction of integrins with the adhesion molecule ligands expressed on the surface of the interacting cell. Our current understanding of the regulation of integrin affinity states comes from often simplistic in vitro model systems. The assay of adhesion using flow conditions described here allows for the visualization and accurate quantification of T cell-epithelial cell interactions in real time following a stimulus. An adhesion under flow assay can be applied to studies of adhesion signaling within T cells following treatment with inhibitory or stimulatory substances. Additionally, this assay can be expanded beyond T cell signaling to any adhesive leukocyte population and any integrin-adhesion molecule pair.

This flow adhesion assay provides a simple, high impact model of T cell-epithelial cell interactions. A syringe pump is used to generate shear stress, and confocal microscopy captures images for quantification. The goal of these studies is to effectively quantify T cell adhesion using flow conditions.

Overall, T cell adhesion is a critical component of function, contributing to the distinct processes of cellular recruitment to sites of inflammation and ...

Rapid, Safe, and Simple Manual Bedside Nucleic Acid Extraction for the Detection of Virus in Whole Blood Samples

The rapid diagnosis of an infection is essential for the outbreak management, risk containment, and patient care. We have previously shown a method for the rapid bedside inactivation of the Ebola virus during blood sampling for safe nucleic acid (NA) tests by adding a commercial lysis/binding buffer directly into the vacuum blood collection tubes. Using this bedside inactivation approach, we have developed a safe, rapid, and simplified bedside NA extraction method for the subsequent detection of a virus in lysis/binding buffer-inactivated whole blood. The NA extraction is directly performed in the blood collection tubes and requires no equipment or electricity. 
After the blood is collected into the lysis/binding buffer, the contents are mixed by flipping the tube by hand, and the mixture is incubated for 20 min at room temperature. Magnetic glass particles (MGPs) are added to the tube, and the contents are mixed by flipping the collection tube by hand. The MGPs are then collected on the side of the blood collection tube using a magnetic holder or a magnet and a rubber band. The MGPs are washed three times, and after the addition of elution buffer directly into the collection tube, the NAs are ready for NA tests, such as qPCR or isothermal loop amplification (LAMP), without the removal of the MGPs from the reaction. The NA extraction method is not dependent on any laboratory facilities and can easily be used anywhere (e.g., in field hospitals and hospital isolation wards). When this NA extraction method is combined with LAMP and a portable instrument, a diagnosis can be obtained within 40 min of the blood collection.

Here, we present a protocol for the rapid virus nucleic acid extraction from the virus-inactivated whole blood. The extraction is performed directly in the blood collection tubes and requires no equipment or electricity. The method is not dependent on laboratory facilities and can be used anywhere (e.g., in field hospitals).

The rapid diagnosis of an infection is essential for the outbreak management, risk containment, and patient care. We have previously shown a method for ...