Name: size exclusion chromatography to analyze bacterial outer membrane vesicle heterogeneity
Uploaded: 2021-03-31T15:00:00
Description: Watch this Scientific Journal Video about Size Exclusion Chromatography to Analyze Bacterial Outer Membrane Vesicle Heterogeneity at JoVE.com

This work was funded by the National Science Foundation (1554417) and National Institutes of Health (DE027769).

1. Preparation of buffers
<ol>
	<li>To prepare the ELISA wash buffer, add 3.94 g Tris-base, 8.77 g NaCl, and 1 g bovine serum albumin (BSA) to 1 L of deionized (DI) water. Add 500 &#181;L polysorbate-20. Adjust the pH to 7.2 using HCl or NaOH.</li>
	<li>To prepare the blocking buffer, add 3.94 g Tris-base, 8.77 g NaCl, and 10 g BSA. Add 500 &#181;L polysorbate-20 to 1 L of DI water. Adjust the pH to 7.2 using HCl or NaOH.</li>
	<li>To prepare the elution buffer (PBS), add 8.01 g NaCl, 2.7 g KCl, 1.42 g Na2HP...

<ol>
	<li>Kuehn, M. J., Kesty, N. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bacterial+outer+membrane+vesicles+and+the+host-pathogen+interaction.">Bacterial outer membrane vesicles and the host-pathogen interaction.</a> Genes and Development. 19, 2645-2655 (2005).</li><li>Kulp, A., Kuehn, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biological+functions+and+biogenesis+of+secreted+bacterial+outer+membrane+vesicles.">Biological functions and biogenesis of secreted bacterial outer membrane vesicles.</a> Annual Reviews Microbiology. 64, 163-184 (2010).</li><li>Kato, S., Kowashi, Y., Demuth, D. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Outer+membrane-like+vesicles+secreted+by+Actinobacillus+actinomycetemcomitans+are+enriched+in+leukotoxin.">Outer membrane-like vesicles secreted by Actinobacillus actinomycetemcomitans are enriched in leukotoxin.</a> Microbial Pathogenesis. 32 (1), 1-13 (2002).</li><li>Nice, J. 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=Aggregatibacter+actinomycetemcomitans+leukotoxin+is+delivered+to+host+cells+in+an+LFA-1-independent+manner+when+associated+with+outer+membrane+vesicles.">Aggregatibacter actinomycetemcomitans leukotoxin is delivered to host cells in an LFA-1-independent manner when associated with outer membrane vesicles.</a> Toxins. 10 (10), 414 (2018).</li><li>Haurat, M. 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=Selective+sorting+of+cargo+proteins+into+bacterial+membrane+vesicles.">Selective sorting of cargo proteins into bacterial membrane vesicles.</a> Journal of Biological Chemistry. 286 (2), 1269-1276 (2011).</li><li>Horstman, A. L., Kuehn, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enterotoxigenic+Escherichia+coli+secretes+active+heat-labile+enterotoxin+via+outer+membrane+vesicles.">Enterotoxigenic Escherichia coli secretes active heat-labile enterotoxin via outer membrane vesicles.</a> The Journal of Biological Chemistry. 275 (17), 12489-12496 (2000).</li><li>Wai, S. N., 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=Vesicle-mediated+export+and+assembly+of+pore-forming+oligomers+of+the+Enterobacterial+ClyA+cytotoxin.">Vesicle-mediated export and assembly of pore-forming oligomers of the Enterobacterial ClyA cytotoxin.</a> Cell. 115, 25-35 (2003).</li><li>Balsalobre, 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=Release+of+the+Type+I+secreted+&#945;-haemolysin+via+outer+membrane+vesicles+from+Escherichia+coli.">Release of the Type I secreted &#945;-haemolysin via outer membrane vesicles from Escherichia coli.</a> Molecular Microbiology. 59 (1), 99-112 (2006).</li><li>Donato, G. M., 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=Delivery+of+Bordetella+pertussis+adenylate+cyclase+toxin+to+target+cells+via+outer+membrane+vesicles.">Delivery of Bordetella pertussis adenylate cyclase toxin to target cells via outer membrane vesicles.</a> FEBS Letters. 586, 459-465 (2012).</li><li>Kim, Y. 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=Outer+membrane+vesicles+of+Vibrio+vulnificus+deliver+cytolysin-hemolysin+VvhA+into+epithelial+cells+to+induce+cytotoxicity.">Outer membrane vesicles of Vibrio vulnificus deliver cytolysin-hemolysin VvhA into epithelial cells to induce cytotoxicity.</a> Biochemical and Biophysical Research Communications. 399, 607-612 (2010).</li><li>Maldonado, R., Wei, R., Kachlany, S. C., Kazi, M., Balashova, N. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cytotoxic+effects+of+Kingella+kingae+outer+membrane+vesicles+on+human+cells.">Cytotoxic effects of Kingella kingae outer membrane vesicles on human cells.</a> Microbial Pathogenesis. 51 (1-2), 22-30 (2011).</li><li>Turner, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Helicobacter+pylori+outer+membrane+vesicle+size+determines+their+mechanisms+of+host+cell+entry+and+protein+content.">Helicobacter pylori outer membrane vesicle size determines their mechanisms of host cell entry and protein content.</a> Frontiers in Immunology. 9, 1466 (2018).</li><li>Zavan, L., Bitto, N. J., Johnston, E. L., Greening, D. W., Kaparakis-Liaskos, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Helicobacter+pylori+growth+stage+determines+the+size,+protein+composition,+and+preferential+cargo+packaging+of+outer+membrane+vesicles.">Helicobacter pylori growth stage determines the size, protein composition, and preferential cargo packaging of outer membrane vesicles.</a> Proteomics. 19 (1-2), 1800209 (2019).</li><li>Rompikuntal, P. K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Perinuclear+localization+of+internalized+outer+membrane+vesicles+carrying+active+cytolethal+distending+toxin+from+Aggregatibacter+actinomycetemcomitans.">Perinuclear localization of internalized outer membrane vesicles carrying active cytolethal distending toxin from Aggregatibacter actinomycetemcomitans.</a> Infections and Immunity. 80 (1), 31-42 (2012).</li><li>Nice, J. 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=Aggregatibacter+actinomycetemcomitans+leukotoxin+is+delivered+to+host+cells+in+an+LFA-1-independent+manner+when+associated+with+outer+membrane+vesicles.">Aggregatibacter actinomycetemcomitans leukotoxin is delivered to host cells in an LFA-1-independent manner when associated with outer membrane vesicles.</a> Toxins. 10 (10), 414 (2018).</li><li>Stevenson, 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=Immunization+with+outer+membrane+vesicles+displaying+conserved+surface+polysaccharide+antigen+elicits+broadly+antimicrobial+antibodies.">Immunization with outer membrane vesicles displaying conserved surface polysaccharide antigen elicits broadly antimicrobial antibodies.</a> Proceedings of the National Academy of Sciences. 115 (14), 3106-3115 (2018).</li><li>Gujrati, V., 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=Bioengineered+bacterial+outer+membrane+vesicles+as+cell-specific+drug-delivery+vehicles+for+cancer+therapy.">Bioengineered bacterial outer membrane vesicles as cell-specific drug-delivery vehicles for cancer therapy.</a> ACS Nano. 8 (2), 1525-1537 (2014).</li><li>Huang, W., 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=Development+of+novel+nanoantibiotics+using+an+outer+membrane+vesicle-based+drug+efflux+mechanism.">Development of novel nanoantibiotics using an outer membrane vesicle-based drug efflux mechanism.</a> Journal of Controlled Release. 317, 1-22 (2020).</li><li>Chen, D. J., 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=Delivery+of+foreign+antigens+by+engineered+outer+membrane+vesicle+vaccines.">Delivery of foreign antigens by engineered outer membrane vesicle vaccines.</a> Proceedings of the National Academy of Sciences. 107 (7), 3099-3104 (2010).</li><li>Chen, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Outer+membrane+vesicles+displaying+engineered+glycotopes+elicit+protective+antibodies.">Outer membrane vesicles displaying engineered glycotopes elicit protective antibodies.</a> Proceedings of the National Academy of Sciences. 113 (26), 3609-3618 (2016).</li><li>Singorenko, P. D., 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=Isolation+of+membrane+vesicles+from+prokaryotes:+A+technical+and+biological+comparison+reveals+heterogeneity.">Isolation of membrane vesicles from prokaryotes: A technical and biological comparison reveals heterogeneity.</a> Journal of Extracellular Vesicles. 6 (1), 1324731 (2017).</li><li>Zeringer, E., Barta, T., Li, M., Vlassov, A. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Strategies+for+isolation+of+exosomes.">Strategies for isolation of exosomes.</a> Cold Spring Harbor Protocols. 2015 (4), 319-323 (2015).</li><li>Benedikter, B. J., 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=Ultrafiltration+combined+with+size+exclusion+chromatography+efficiently+isolates+extracellular+vesicles+from+cell+culture+media+for+compositional+and+functional+studies.">Ultrafiltration combined with size exclusion chromatography efficiently isolates extracellular vesicles from cell culture media for compositional and functional studies.</a> Science Reports. 7 (1), 15297 (2017).</li><li>Mol, E. A., Goumans, M. J., Doevendans, P. A., Sluijter, J. P. G., Vader, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Higher+functionality+of+extracellular+vesicles+isolated+using+size-exclusion+chromatography+compared+to+ultracentrifugation.">Higher functionality of extracellular vesicles isolated using size-exclusion chromatography compared to ultracentrifugation.</a> Nanomedicine. 13 (6), 2061-2065 (2017).</li><li>Lally, E. T., Golub, E. E., Kieba, I. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+and+immunological+characterization+of+the+domain+of+Actinobacillus+actinomycetemcomitans+leukotoxin+that+determines+its+specificity+for+human+target+cells.">Identification and immunological characterization of the domain of Actinobacillus actinomycetemcomitans leukotoxin that determines its specificity for human target cells.</a> Journal of Biological Chemistry. 269 (49), 31289-31295 (1994).</li><li>Chang, E. H., Giaquinto, P., Huang, J., Balashova, N. V., Brown, A. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Epigallocatechin+gallate+inhibits+leukotoxin+release+by+Aggregatibacter+actinomycetemcomitans+by+promoting+association+with+the+bacterial+membrane.">Epigallocatechin gallate inhibits leukotoxin release by Aggregatibacter actinomycetemcomitans by promoting association with the bacterial membrane.</a> Molecular Oral Microbiology. 35 (1), 29-39 (2020).</li><li>Klimentov&#225;, J., Stul&#237;k, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Methods+of+isolation+and+purification+of+outer+membrane+vesicles+from+gram-negative+bacteria.">Methods of isolation and purification of outer membrane vesicles from gram-negative bacteria.</a> Microbiological Research. 170, 1-9 (2015).</li><li>Dauros Singorenko, P., 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=Isolation+of+membrane+vesicles+from+prokaryotes:+a+technical+and+biological+comparison+reveals+heterogeneity.">Isolation of membrane vesicles from prokaryotes: a technical and biological comparison reveals heterogeneity.</a> Journal of Extracellular Vesicles. 6 (1), 1324731 (2017).</li><li>Mongui&#243;-Tortajada, M., G&#225;lvez-Mont&#243;n, C., Bayes-Genis, A., Roura, S., Borr&#224;s, F. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Extracellular+vesicle+isolation+methods:+rising+impact+of+size-exclusion+chromatography.">Extracellular vesicle isolation methods: rising impact of size-exclusion chromatography.</a> Cellular and Molecular Life Sciences. 76 (12), 2369-2382 (2019).</li></ol>

Here, we have provided a protocol for the simple, fast, and reproducible separation of bacterial OMV subpopulations. Although the technique is relatively straight-forward, there are some steps that must be performed extremely carefully to ensure that efficient separation occurs in the column. First, it is essential that the gel be loaded into the column carefully and slowly to avoid air bubbles. We have observed that leaving the gel at room temperature for several hours before loading the column allows the gel to equilib...

Gram-negative bacteria release vesicles derived from their outer membrane, so-called outer membrane vesicles (OMVs), throughout growth. These OMVs play important roles in cell-to-cell communication, both between bacteria and host as well as between bacterial cells, by carrying a number of important biomolecules, including DNA/RNA, proteins, lipids, and peptidoglycans1,2. In particular, the role of OMVs in bacterial pathogenesis has been extensively studied due to their enrichment in certain virulence factors and toxins3,4,5,6,7,8,9,10,11.
OMVs have been reported to range in size from 20 to 450 nm, depending on the parent bacteria and the growth stage, with several types of bacteria releasing heterogeneously sized OMVs8,12,13,14, which also differ in their protein composition and mechanism of host cell entry12. H. pylori released OMVs ranging in diameter from 20 to 450 nm, with the smaller OMVs containing a more homogeneous protein composition than the larger OMVs. Importantly, the two populations of OMVs were observed to be internalized by host cells via different mechanisms12. In addition, we have demonstrated that Aggregatibacter actinomycetemcomitans releases a population of small (&#60;150 nm) OMVs along with a population of large (&#62;350 nm) OMVs, with the OMVs containing a significant amount of a secreted protein toxin, leukotoxin (LtxA)15. While the role of OMV heterogeneity in cellular processes is clearly important, technical difficulties in separating and analyzing distinct populations of vesicles has limited these studies.
In addition to their importance in bacterial pathogenesis, OMVs have been proposed for use in a number of biotechnological applications, including as vaccines and drug delivery vehicles16,17,18,19,20. For their translational use in such approaches, a clean and monodisperse preparation of vesicles is required. Thus, effective&#160;and efficient methods of separation are necessary.
Most commonly, density gradient centrifugation (DGC) is used to separate heterogeneously sized vesicle populations from cellular debris, including flagellae and secreted proteins21; the method has also been reported as an approach to separate heterogeneously sized OMV subpopulations12,13,14. However, DGC is time-consuming, inefficient, and highly variable user-to-user22 and is, therefore, not ideal for scale-up. In contrast, size exclusion chromatography (SEC) represents a scalable, efficient, and consistent approach to purify OMVs21,23,24. We have found that a long (50-cm), gravity-flow, SEC column, filled with gel filtration medium is sufficient for efficiently purifying and separating subpopulations of OMVs. Specifically, we used this approach to separate A. actinomycetemcomitans OMVs into &#34;large&#34; and &#34;small&#34; subpopulations, as well as to remove protein and DNA contamination. Purification was completed in less than 4 h, and complete separation of the OMV subpopulations and removal of debris was accomplished.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1-Step Ultra TMB-ELISA</td>
			<td>Thermo Scientific</td>
			<td>34028</td>
			<td></td>
		</tr>
		<tr>
			<td>Amicon 50 kDa filters</td>
			<td>Millipore Sigma</td>
			<td>UFC905024</td>
			<td></td>
		</tr>
		<tr>
			<td>Bovine Serum Albumin (BSA)</td>
			<td>Fisher Scientific</td>
			<td>BP9704-100</td>
			<td></td>
		</tr>
		<tr>
			<td>ELISA Immuno Plates</td>
			<td>Thermo Scientific</td>
			<td>442404</td>
			<td></td>
		</tr>
		<tr>
			<td>FM 4-64</td>
			<td>Thermo Scientific</td>
			<td>T13320</td>
			<td>1.5 x 50 cm</td>
		</tr>
		<tr>
			<td>Glass Econo-Column</td>
			<td>BioRad</td>
			<td>7371552</td>
			<td></td>
		</tr>
		<tr>
			<td>Infinite 200 Pro Plate Reader</td>
			<td>Tecan</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium Chloride (KCl)</td>
			<td>Amresco (VWR)</td>
			<td>0395-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium Phosphate Monobasic Anhydrous (KH2PO4)</td>
			<td>Amresco (VWR)</td>
			<td>0781-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>Sephacryl S-1000 Superfine</td>
			<td>GE Healthcare</td>
			<td>17-0476-01</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Chloride (NaCl)</td>
			<td>Fisher Chemical</td>
			<td>S271-3</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Phosphate Dibasic Anhydrous (Na2HPO4)</td>
			<td>Amresco (VWR)</td>
			<td>0404-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris Base</td>
			<td>VWR</td>
			<td>0497-1KG</td>
			<td></td>
		</tr>
		<tr>
			<td>Tween(R) 20</td>
			<td>Acros Organics</td>
			<td>23336-2500</td>
			<td></td>
		</tr>
	</tbody>
</table>

size exclusion chromatography to analyze bacterial outer membrane vesicle heterogeneity

The cell wall of Gram-negative bacteria consists of an inner (cytoplasmic) and outer membrane (OM), separated by a thin peptidoglycan layer. Throughout growth, the outer membrane can bleb to form spherical outer membrane vesicles (OMVs). These OMVs are involved in numerous cellular functions including cargo delivery to host cells and communication with bacterial cells. Recently, the therapeutic potential of OMVs has begun to be explored, including their use as vaccines and drug delivery vehicles. Although OMVs are derived from the OM, it has long been appreciated that the lipid and protein cargo of the OMV differs, often significantly, from that of the OM. More recently, evidence that bacteria can release multiple types of OMVs has been discovered, and evidence exists that size can impact the mechanism of their uptake by host cells. However, studies in this area are limited by difficulties in efficiently separating the heterogeneously sized OMVs. Density gradient centrifugation (DGC) has traditionally been used for this purpose; however, this technique is time-consuming and difficult to scale-up. Size exclusion chromatography (SEC), on the other hand, is less cumbersome and lends itself to the necessary future scale-up for therapeutic use of OMVs. Here, we describe a SEC approach that enables reproducible separation of heterogeneously sized vesicles, using as a test case, OMVs produced by Aggregatibacter actinomycetemcomitans, which range in diameter from less than 150 nm to greater than 350 nm. We demonstrate separation of &#34;large&#34; (350 nm) OMVs and &#34;small&#34; (&#60;150 nm) OMVs, verified by dynamic light scattering (DLS). We recommend SEC-based techniques over DGC-based techniques for separation of heterogeneously sized vesicles due to its ease of use, reproducibility (including user-to-user), and possibility for scale-up.

Figure 2&#160;shows representative results from this method. OMVs produced by A. actinomycetemcomitans strain JP2 were first purified from the culture supernatant using ultracentrifugation15. We previously found that this strain produces two populations of OMVs, one with diameters of about 300 nm and one with diameters of about 100 nm15. To separate these OMV populations, we purified the sample using the SEC protocol described above. E...

Watch this Scientific Journal Video about Size Exclusion Chromatography to Analyze Bacterial Outer Membrane Vesicle Heterogeneity at JoVE.com

Size Exclusion Chromatography to Analyze Bacterial Outer Membrane Vesicle Heterogeneity

Bacterial vesicles play important roles in pathogenesis and have promising biotechnological applications. The heterogeneity of vesicles complicates analysis and use; therefore, a simple, reproducible method to separate varying sizes of vesicles is necessary. Here, we demonstrate the use of size exclusion chromatography to separate heterogeneous vesicles produced by Aggregatibacter actinomycetemcomitans.

The cell wall of Gram-negative bacteria consists of an inner (cytoplasmic) and outer membrane (OM), separated by a thin peptidoglycan layer. Throughout ...

Size exclusion chromatography is a useful approach for separating the subpopulations of heterogeneously-sized bacterial vesicles and for removing nucleic acids and proteins from bacterial supernatants. Size exclusion chromatography is less expensive, faster, and more reproducible than other separation techniques, including density gradient ultracentrifugation. We've demonstrated the potential of this approach using A.actinomycetemcomitans vesicles, but we expect that it could be applied to other heterogeneously-sized bacterial vesicle populations as well.Be sure to properly degas all of the buffer and bead solutions and to pipette the solution slowly without introducing bubbles but quickly enough that the beads pack homogeneously without drying out. To begin, use a glass rod to mix a stock bottle of gel filtration medium and pour the volume required to fill the column plus approximately 50%excess into a glass bottle. Allow the beads to settle and decant the excess liquid.Resuspend the beads in elution buffer to a final solution of approximately 70%gel and 30%buffer and degas the solution under vacuum. Mount the column on a ring stand in the vertical position and fill the column with elution buffer to wet the walls before draining the buffer until only about one centimeter remains. Then carefully pipette the gel beads into the column while simultaneously draining the excess buffer to prevent the beads from settling until the column is packed to a height of approximately two centimeters below the bottom of the column reservoir.Before loading the sample, degas the elution buffer under vacuum. Wash the column with approximately two times the column volume of elution buffer. Once the buffer reaches the top of gel layer, carefully add two milliliters of a 100 to 200 nanomolar per liter outer membrane vesicle sample on top of the gel layer without disturbing the surface and let the sample enter the gel.Slowly add the elution buffer to the column without disturbing the gel layer and place a 50 milliliter tube under the column. To prevent the column from drying, simultaneously add elution buffer to the top of the column. After collecting 20 milliliters of eluate, place a rack of 1.5 milliliter tubes under the column.Collect a total of 96 one-milliliter fractions in each tube. While collecting the samples, continuously add elution buffer to the column. To clean the column, run one column volume of 0.1 molar sodium hydroxide through the column followed by two column volumes of elution buffer.To measure the lipid concentrations, pipette 50 microliters of each fraction into a 96 well plate. Add 2.5 microliters of lipophilic dye to each well. After 15 seconds, measure the florescence intensity.To measure the concentration of a protein of interest, add 100 microliters of each fraction into individual wells of an ELISA immuno plate. After three hours at 25 degrees Celsius, decant the plate contents. Wash the plate five times with 200 microliters of ELISA wash buffer per wash decanting the plate after each wash.Add 200 microliters of blocking buffer to each well for a one hour incubation at 25 degrees Celsius. At the end of incubation, decant the plate and add 100 microliters of primary antibody in blocking buffer for an overnight incubation at four degrees Celsius. The next day, decant the plate and wash the plate five times with ELISA wash buffer as demonstrated.After the last wash, add 100 microliters of secondary antibody in ELISA wash buffer to each well for a one hour incubation at 25 degrees Celsius. At the end of the incubation, wash the plate as demonstrated and add 100 microliters of TMB solution to each well for a 15 to 30 minute incubation at room temperature. When a blue color develops, add 50 microliters of stopping solution to each well and measure the absorbance at 450 nanometers.After size exclusion column purification of an A.actinomycetemcomitans culture supernatant as demonstrated, two distinct lipid peaks were observed, corresponding to the large and small outer membrane vesicles produced by this strain. ELISA analysis of the sample fractions revealed that the toxin is associated primarily with the subpopulation of large outer membrane vesicles. Immuno blot analysis gave similar but more noisy results, indicating that this approach is less sensitive than ELISA.As observed, this chromatography technique is able to remove significant amounts of free proteins from the outer membrane vesicles'preparations. However, it is important to note that the total protein concentration does not necessarily correlate with the concentration of specific proteins. It is important to be very careful during the packing and running of the column to avoid bubbles and to prevent the column from drying out.Dynamic light scattering, particle tracking, and bicroscopy can be performed following size exclusion chromatography to determine the size and other characteristics of the separated outer membrane vesicles.

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Bioengineering

Design of a Cyclic Pressure Bioreactor for the Ex Vivo Study of Aortic Heart Valves

The aortic valve, located between the left ventricle and the aorta, allows for unidirectional blood flow, preventing backflow into the ventricle. Aortic valve leaflets are composed of interstitial cells suspended within an extracellular matrix (ECM) and are lined with an endothelial cell monolayer. The valve withstands a harsh, dynamic environment and is constantly exposed to shear, flexion, tension, and compression. Research has shown calcific lesions in diseased valves occur in areas of high mechanical stress as a result of endothelial disruption or interstitial matrix damage1-3. Hence, it is not surprising that epidemiological studies have shown high blood pressure to be a leading risk factor in the onset of aortic valve disease4. 
The only treatment option currently available for valve disease is surgical replacement of the diseased valve with a bioprosthetic or mechanical valve5. Improved understanding of valve biology in response to physical stresses would help elucidate the mechanisms of valve pathogenesis. In turn, this could help in the development of non-invasive therapies such as pharmaceutical intervention or prevention. Several bioreactors have been previously developed to study the mechanobiology of native or engineered heart valves6-9. Pulsatile bioreactors have also been developed to study a range of tissues including cartilage10, bone11 and bladder12. The aim of this work was to develop a cyclic pressure system that could be used to elucidate the biological response of aortic valve leaflets to increased pressure loads. 
The system consisted of an acrylic chamber in which to place samples and produce cyclic pressure, viton diaphragm solenoid valves to control the timing of the pressure cycle, and a computer to control electrical devices. The pressure was monitored using a pressure transducer, and the signal was conditioned using a load cell conditioner. A LabVIEW program regulated the pressure using an analog device to pump compressed air into the system at the appropriate rate. The system mimicked the dynamic transvalvular pressure levels associated with the aortic valve; a saw tooth wave produced a gradual increase in pressure, typical of the transvalvular pressure gradient that is present across the valve during diastole, followed by a sharp pressure drop depicting valve opening in systole. The LabVIEW program allowed users to control the magnitude and frequency of cyclic pressure. The system was able to subject tissue samples to physiological and pathological pressure conditions. This device can be used to increase our understanding of how heart valves respond to changes in the local mechanical environment.

Design of a Cyclic Pressure Bioreactor for the Ex Vivo Study of Aortic Heart Valves

A cyclic pressure bioreactor capable of subjecting heart valve tissue to physiological and pathological pressure conditions has been designed. A LabVIEW program allows users to control pressure magnitude, amplitude and frequency. This device can be used to study the mechanobiology of heart valve tissue or isolated cells.

The aortic valve, located between the left ventricle and the aorta, allows for unidirectional blood flow, preventing backflow into the ventricle. Aortic ...

Bacterial Detection &amp; Identification Using Electrochemical Sensors

Electrochemical sensors are widely used for rapid and accurate measurement of blood glucose and can be adapted for detection of a wide variety of analytes. Electrochemical sensors operate by transducing a biological recognition event into a useful electrical signal. Signal transduction occurs by coupling the activity of a redox enzyme to an amperometric electrode. Sensor specificity is either an inherent characteristic of the enzyme, glucose oxidase in the case of a glucose sensor, or a product of linkage between the enzyme and an antibody or probe.
Here, we describe an electrochemical sensor assay method to directly detect and identify bacteria. In every case, the probes described here are DNA oligonucleotides. This method is based on sandwich hybridization of capture and detector probes with target ribosomal RNA (rRNA). The capture probe is anchored to the sensor surface, while the detector probe is linked to horseradish peroxidase (HRP). When a substrate such as 3,3',5,5'-tetramethylbenzidine (TMB) is added to an electrode with capture-target-detector complexes bound to its surface, the substrate is oxidized by HRP and reduced by the working electrode. This redox cycle results in shuttling of electrons by the substrate from the electrode to HRP, producing current flow in the electrode.

We describe an electrochemical sensor assay method for rapid bacterial detection and identification. The assay involves a sensor array functionalized with DNA oligonucleotide capture probes for ribosomal RNA (rRNA) species-specific sequences. Sandwich hybridization of target rRNA with the capture probe and a horseradish peroxidase-linked DNA oligonucleotide detector probe produces a measurable amperometric current.

Electrochemical  sensors are widely used for rapid and accurate measurement of blood glucose and  can be adapted for detection of a wide variety of ...

Membrane-SPINE: A Biochemical Tool to Identify Protein-protein Interactions of Membrane Proteins In Vivo

Membrane proteins are essential for cell viability and are therefore important therapeutic targets1-3. Since they function in complexes4, methods to identify and characterize their interactions are necessary5. To this end, we developed the Membrane Strep-protein interaction experiment, called Membrane-SPINE6. This technique combines in vivo cross-linking using the reversible cross-linker formaldehyde with affinity purification of a Strep-tagged membrane bait protein. During the procedure, cross-linked prey proteins are co-purified with the membrane bait protein and subsequently separated by boiling. Hence, two major tasks can be executed when analyzing protein-protein interactions (PPIs) of membrane proteins using Membrane-SPINE: first, the confirmation of a proposed interaction partner by immunoblotting, and second, the identification of new interaction partners by mass spectrometry analysis. Moreover, even low affinity, transient PPIs are detectable by this technique. Finally, Membrane-SPINE is adaptable to almost any cell type, making it applicable as a powerful screening tool to identify PPIs of membrane proteins.

Membrane-SPINE: A Biochemical Tool to Identify Protein-protein Interactions of Membrane Proteins In Vivo

A biochemical approach is described to identify in vivo protein-protein interactions (PPI) of membrane proteins. The method combines protein cross-linking, affinity purification and mass spectrometry, and is adaptable to almost any cell type or organism. With this approach, even the identification of transient PPIs becomes possible.

Membrane proteins are essential for cell viability and are therefore important therapeutic targets1-3. Since they function in complexes4, methods to ...

Lipid Bilayer Vesicle Generation Using Microfluidic Jetting

Bottom-up synthetic biology presents a novel approach for investigating and reconstituting biochemical systems and, potentially, minimal organisms. This emerging field engages engineers, chemists, biologists, and physicists to design and assemble basic biological components into complex, functioning systems from the bottom up. Such bottom-up systems could lead to the development of artificial cells for fundamental biological inquiries and innovative therapies1,2. Giant unilamellar vesicles (GUVs) can serve as a model platform for synthetic biology due to their cell-like membrane structure and size. Microfluidic jetting, or microjetting, is a technique that allows for the generation of GUVs with controlled size, membrane composition, transmembrane protein incorporation, and encapsulation3. The basic principle of this method is the use of multiple, high-frequency fluid pulses generated by a piezo-actuated inkjet device to deform a suspended lipid bilayer into a GUV. The process is akin to blowing soap bubbles from a soap film. By varying the composition of the jetted solution, the composition of the encompassing solution, and/or the components included in the bilayer, researchers can apply this technique to create customized vesicles. This paper describes the procedure to generate simple vesicles from a droplet interface bilayer by microjetting.

Microfluidic jetting against a droplet interface lipid bilayer provides a reliable way to generate vesicles with control over membrane asymmetry, incorporation of transmembrane proteins, and encapsulation of material. This technique can be applied to study a variety of biological systems where compartmentalized biomolecules are desired.

Bottom-up synthetic biology presents a novel approach for investigating and reconstituting biochemical systems and, potentially, minimal organisms. This ...

Luminescence Resonance Energy Transfer to Study Conformational Changes in Membrane Proteins Expressed in Mammalian Cells

Luminescence Resonance Energy Transfer, or LRET, is a powerful technique used to measure distances between two sites in proteins within the distance range of 10-100 &#197;. By measuring the distances under various ligated conditions, conformational changes of the protein can be easily assessed. With LRET, a lanthanide, most often chelated terbium, is used as the donor fluorophore, affording advantages such as a longer donor-only emission lifetime, the flexibility to use multiple acceptor fluorophores, and the opportunity to detect sensitized acceptor emission as an easy way to measure energy transfer without the risk of also detecting donor-only signal. Here, we describe a method to use LRET on membrane proteins expressed and assayed on the surface of intact mammalian cells. We introduce a protease cleavage site between the LRET fluorophore pair. After obtaining the original LRET signal, cleavage at that site removes the specific LRET signal from the protein of interest allowing us to quantitatively subtract the background signal that remains after cleavage. This method allows for more physiologically relevant measurements to be made without the need for purification of protein.

We describe here an improved Luminescence Resonance Energy Transfer (LRET) method where we introduce a protease cleavage site between the donor and acceptor fluorophore sites. This modification allows us to obtain specific LRET signals arising from membrane proteins of interest, allowing for the study of membrane proteins without protein purification.

Luminescence Resonance Energy Transfer, or LRET, is a powerful technique used to measure distances between two sites in proteins within the distance range ...

Methods for Characterizing the Co-development of Biofilm and Habitat Heterogeneity

Biofilms are surface-attached microbial communities that have complex structures and produce significant spatial heterogeneities. Biofilm development is strongly regulated by the surrounding flow and nutritional environment. Biofilm growth also increases the heterogeneity of the local microenvironment by generating complex flow fields and solute transport patterns. To investigate the development of heterogeneity in biofilms and interactions between biofilms and their local micro-habitat, we grew mono-species biofilms of Pseudomonas aeruginosa and dual-species biofilms of P. aeruginosa and Escherichia coli under nutritional gradients in a microfluidic flow cell. We provide detailed protocols for creating nutrient gradients within the flow cell and for growing and visualizing biofilm development under these conditions. We also present protocols for a series of optical methods to quantify spatial patterns in biofilm structure, flow distributions over biofilms, and mass transport around and within biofilm colonies. These methods support comprehensive investigations of the co-development of biofilm and habitat heterogeneity.

Biofilms have complex interactions with their surrounding environment. To comprehensively investigate biofilm-environment interactions, we present here a series of methods to create heterogeneous chemical environment for biofilm development, to quantify local flow velocity, and to analyze mass transport in and around biofilm colonies.

Biofilms are surface-attached microbial communities that have complex structures and produce significant spatial heterogeneities. Biofilm development is ...

A Microfluidic Platform for Precision Small-volume Sample Processing and Its Use to Size Separate Biological Particles with an Acoustic Microdevice

A major advantage of microfluidic devices is the ability to manipulate small sample volumes, thus reducing reagent waste and preserving precious sample. However, to achieve robust sample manipulation it is necessary to address device integration with the macroscale environment. To realize repeatable, sensitive particle separation with microfluidic devices, this protocol presents a complete automated and integrated microfluidic platform that enables precise processing of 0.15&#8211;1.5 ml samples using microfluidic devices. Important aspects of this system include modular device layout and robust fixtures resulting in reliable and flexible world to chip connections, and fully-automated fluid handling which accomplishes closed-loop sample collection, system cleaning and priming steps to ensure repeatable operation. Different microfluidic devices can be used interchangeably with this architecture. Here we incorporate an acoustofluidic device, detail its characterization, performance optimization, and demonstrate its use for size-separation of biological samples. By using real-time feedback during separation experiments, sample collection is optimized to conserve and concentrate sample. Although requiring the integration of multiple pieces of equipment, advantages of this architecture include the ability to process unknown samples with no additional system optimization, ease of device replacement, and precise, robust sample processing.

This protocol describes a system architecture for performing automated small volume (0.15&#8211;1.5 ml) particle separations using a microfluidic device, and discusses methods to optimize acoustofluidic device performance and operation.

A major advantage of microfluidic devices is the ability to manipulate small sample volumes, thus reducing reagent waste and preserving precious sample. ...

A Facile and Eco-friendly Route to Fabricate Poly(Lactic Acid) Scaffolds with Graded Pore Size

Over the recent years, functionally graded scaffolds (FGS) gaineda crucial role for manufacturing of devices for tissue engineering. The importance of this new field of biomaterials research is due to the necessity to develop implants capable of mimicking the complex functionality of the various tissues, including a continuous change from one structure or composition to another. In this latter context, one topic of main interest concerns the design of appropriate scaffolds for bone-cartilage interface tissue. In this study, three-layered scaffolds with graded pore size were achieved by melt mixing poly(lactic acid) (PLA), sodium chloride (NaCl) and polyethylene glycol (PEG). Pore size distributions were controlled by NaCl granulometry and PEG solvation. Scaffolds were characterized from a morphological and mechanical point of view. A correlation between the preparation method, the pore architecture and compressive mechanical behavior was found. The interface adhesion strength was quantitatively evaluated by using a custom-designed interfacial strength test. Furthermore, in order to imitate the human physiology, mechanical tests were also performed in phosphate buffered saline (PBS) solution at 37 &#176;C. The method herein presented provides a high control of porosity, pore size distribution and mechanical performance, thus offering the possibility to fabricate three-layered scaffolds with tailored properties by following a simple and eco-friendly route.

A Facile and Eco-friendly Route to Fabricate PolyLactic Acid Scaffolds with Graded Pore Size

In this work, poly(lactic acid)/polyethylene glycol (PLA/PEG) scaffolds were prepared by using a combination of melt mixing and selective leaching. The method herein discussed permitted to develop three-layer scaffolds by highly controlling both porosity and pore size. The mechanical properties were also evaluated in a physiological environment.

Over the recent years, functionally graded scaffolds (FGS) gaineda crucial role for manufacturing of devices for tissue engineering. The importance of ...

Treatment of Ligament Constructs with Exercise-conditioned Serum: A Translational Tissue Engineering Model

In vitro experiments are essential to understand biological mechanisms; however, the gap between monolayer tissue culture and human physiology is large, and translation of findings is often poor. Thus, there is ample opportunity for alternative experimental approaches. Here we present an approach in which human cells are isolated from human anterior cruciate ligament tissue remnants, expanded in culture, and used to form engineered ligaments. Exercise alters the biochemical milieu in the blood such that the function of many tissues, organs and bodily processes are improved. In this experiment, ligament construct culture media was supplemented with experimental human serum that has been &#39;conditioned&#39; by exercise. Thus the intervention is more biologically relevant since an experimental tissue is exposed to the full endogenous biochemical milieu, including binding proteins and adjunct compounds that may be altered in tandem with the activity of an unknown agent of interest. After treatment, engineered ligaments can be analyzed for mechanical function, collagen content, morphology, and cellular biochemistry. Overall, there are four major advantages versus traditional monolayer culture and animal models, of the physiological model of ligament tissue that is presented here. First, ligament constructs are three-dimensional, allowing for mechanical properties (i.e., function) such as ultimate tensile stress, maximal tensile load, and modulus, to be quantified. Second, the enthesis, the interface between boney and sinew elements, can be examined in detail and within functional context. Third, preparing media with post-exercise serum allows for the effects of the exercise-induced biochemical milieu, which is responsible for the wide range of health benefits of exercise, to be investigated in an unbiased manner. Finally, this experimental model advances scientific research in a humane and ethical manner by replacing the use of animals, a core mandate of the National Institutes of Health, the Center for Disease Control, and the Food and Drug Administration.

We present a model of ligament tissue in which three-dimensional constructs are treated with the human exercise-conditioned serum and analyzed for collagen content, function, and cellular biochemistry.

In vitro experiments are essential to understand biological mechanisms; however, the gap between monolayer tissue culture and human physiology is large, ...

Outer-Boundary Assisted Segmentation and Quantification of Trabecular Bones by an Imagej Plugin

Micro-computed tomography (micro-CT) is routinely used to assess bone quantity and trabecular microstructural properties in small animals under different bone loss conditions. However, the standard approach for trabecular analysis of micro-CT images is slice-by-slice semi-automatic hand-contouring, which is labor intensive and error prone. Described here is an efficient method for automatic segmentation of trabecular bones according to the bone's outer boundaries, where trabecular bones can be identified and segmented automatically with accuracy with less operator bias when appropriate segmentation parameters are set. To profile satisfactory segmentation parameters, an image stack of segmentation results is displayed, where all possible combinations of the segmentation parameters are changed one by one in sequence, and segmentation results with associated parameters can easily be visually checked. As a quality-control feature of the plugin, simulated standard objects are quantified where the measured quantities can be compared with theoretical values. Layer-by-layer quantification of trabecular properties and trabecular thicknesses are reported by such a plugin, and the distributions of such properties within the selected regions can be profiled easily. Although layer-by-layer quantification retains more information about trabecular bones and facilitates further statistical analysis of structural changes, such measures are unavailable from the output of current commercial software, where only a single quantified value for each parameter is reported for each sample. Therefore, the described workflows are better approaches for analyzing trabecular bones with accuracy and efficiency.

We present a workflow for segmenting and quantifying trabecular bones for 2D and 3D images based on the bone&#39;s outer boundary using an ImageJ plugin. This approach is more efficient and accurate than the current manual hand-contouring approach, and provides layer-by-layer quantifications, which are not available in current commercial software.

Micro-computed tomography (micro-CT) is routinely used to assess bone quantity and trabecular microstructural properties in small animals under different ...