Name: Hücresel ve Biyofilmler Ekstrasellüler Bileşenleri Eşzamanlı Kantitasyonu (Video) | JoVE Journal
Uploaded: 2013-12-10T20:45:00.000+00:00
Duration: 10 min 18 s
Description: Keşfedin biyofilmlerdeki hücresel ve ekstrasellüler bileşenlerin eşzamanlı kantitasyonu için konfokal lazer tarama mikroskobu ve istatistiksel analiz yöntemlerini. Bu protokol antibakteriyal ajanların biyofilm yapısı üzerindeki etkilerini değerlendirmeye yardımcı olur.

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Funding for this study was provided by the National Institutes of Health/NIDCR grant 1R15DE019566-01A1. Dr. Jim Henthorn (OUHSC Flow and Image Cytometry Laboratory) is acknowledged for providing technical assistance with confocal laser scanning microscopy. Dr. Fernando Esteban Florez (Department of Dental Materials) is acknowledged for providing technical assistance during the filming of this video.

1. Preparation of Media and Reagents
<ol>
	<li>Make 300 ml overnight culture medium (THY; 3% Todd Hewitt Broth prepared according to manufacturer's instructions supplemented with 0.3% Yeast Extract in ultrapure water) and autoclave. Store at room temperature for up to 2 months.</li>
	<li>Make 1 L THY agar (3% Todd Hewitt Broth, 0.3% Yeast Extract, and 1.5% agar in ultrapure water), autoclave, and cool to 60 °C before pouring into Petri dishes. Store at 4 °C for up to 3 months.</li>
	<li>Make 150 ml biofilm growth medium (0.5X TY supplemented with 10 mM sucrose; 1.5% Tryptone, 0.5% Yeast Extract, and 10 mM sucrose in ultrapure water) and filter sterilize. Store at room temperature for up to 1 month.</li>
	<li>Make 1 L Phosphate Buffered Saline (PBS; 8 g NaCl, 0.2 g KCl, 1.44 g Na2HPO4, and 0.24 g KH2PO4 in ultrapure water) and autoclave. Store at room temperature for several months.</li>
	<li>Make 600 ml 10 mM Tris HCl buffer supplemented with 10 mM CaCl2 in ultrapure water (TC buffer; pH 7.2) and autoclave. Store at room temperature for several months.</li>
	<li>Autoclave 1 L ultrapure water. Store at room temperature for several months.</li>
</ol>
2. Specimen Fabrication
<ol>
	<li>Fabricate disk-shaped specimens of Point 4 (PF) and TPH3 (TP) dental resin composites in a custom-made stainless steel mold in two increments. Each increment is light-cured for 40 sec using an LED light-curing unit. The two products have slightly different compositions and filler levels, and thereby produce different surface topographies upon which the biofilms will be grown.
	<ol>
		<li>Specimens of relevant substrates could be fabricated using established protocols from other disciplines in lieu of step 2.1.</li>
	</ol>
	</li>
	<li>Finish and polish specimens to an acceptable final surface finish, e.g. by using a semi-automated grinder-polisher. Rinse polished specimens with ultrapure water and dry using compressed air.</li>
	<li>Sterilize specimens using ethylene oxide gas or an alternate sterilization method.</li>
</ol>
3. Biofilm Growth
<ol>
	<li>Inoculate a single colony of S. mutans into 4 ml overnight culture medium (step 1.1). Incubate overnight at 37 °C for 16-18 hr. The optical density (OD600) of the culture should be ≥0.9.
	<ol>
		<li>It is best to use a colony from plate cultures that have been passaged 2x from an original stock, as this results in more consistent biofilm growth.</li>
	</ol>
	</li>
	<li>Create a 1:100 dilution using the overnight culture (step 1.1) in 10 ml of biofilm growth medium (step 1.3).</li>
	<li>Transfer sterile resin composite specimens (e.g. PF, TP) to sterile 12-well plates.</li>
	<li>Add 2.5 ml of diluted culture medium (step 3.2) to wells for treatment (mouthwash) and control groups. Add 2.5 ml of sterile uninoculated biofilm growth medium to sterility control wells.</li>
	<li>Grow the biofilms under microaerophilic conditions. Place plates on a shaker at 100 rpm inside an incubator at 37 °C for 24 hr.</li>
	<li>After 24 hr, aseptically aspirate medium from all wells and wash twice with sterile PBS (step 1.4; 2.5 ml/well), aspirating the PBS after each wash. Replenish 2.5 ml of fresh biofilm growth medium in each well and incubate for an additional 24 hr under identical conditions as the previous step, for total biofilm growth time of 48 hr.</li>
	<li>In lieu of the above steps, biofilms of other species could be grown on substrates using established protocols.</li>
</ol>
4. Antibacterial/Mouthwash Treatments
<ol>
	<li>Aspirate medium after biofilm growth is complete.</li>
	<li>Add 2.5 ml Biotène PBF (BIO) or Listerine Total Care (LTO) mouthwash, or other treatment modality, in wells for the treatment groups, and add 2.5 ml sterile ultrapure water to the control group well. Immerse specimens for 60 sec, as per manufacturers' instructions, while agitating plates on an orbital shaker at 150 rpm. Immediately aspirate both the mouthwash and ultrapure water from the wells.</li>
	<li>Wash the specimens 5x for 15 sec per wash with sterile ultrapure water on the orbital shaker at 150 rpm, aspirating water after each washing step.</li>
	<li>In lieu of the above steps, other antibacterial agents could be tested using established protocols.</li>
</ol>
5. Staining
<ol>
	<li>Prepare the stain dilutions for biofilm analysis.
	<ol>
		<li>Prepare a 5 mg/ml stock solution of Concanavalin A, Alexa Fluor 647 conjugate (AF) in 0.1 M sodium bicarbonate pH 8.3. Store at -20 °C in single-use aliquots for several months because freezing and thawing is discouraged. Using this AF stock solution, prepare a 250 μg/ml dilution in TC buffer.</li>
		<li>Prepare a 10 μM dilution using the 5 mM Syto 9 stock solution (SY), as provided by the manufacturer, in TC buffer. Store the remaining SY stock solution at -20 °C for several months.</li>
		<li>Prepare a 10x dilution using the 5,000x Sypro Red stock solution (SR), as provided by the manufacturer, in sterile ultrapure water. Store the remaining SR stock solution at -20 °C for several months.</li>
	</ol>
	</li>
	<li>Wash all biofilms 2x with TC buffer (2.5 ml/well) using a hand-swirling motion, allowing the second wash to remain in the plate for 30 min at room temperature. Aspirate.</li>
	<li>Place a 50 μl drop of AF stain on each biofilm specimen. Stain for 30 min at room temperature, protected from light. Wash 2x with TC buffer (2.5 ml/well), aspirating after each wash.</li>
	<li>Follow with a 50 μl drop of SY stain on each biofilm specimen. Stain for 30 min at room temperature, protected from light. Wash 2x with sterile ultrapure water (2.5 ml/well), aspirating after each wash</li>
	<li>Finally, place a 50 μl drop of SR stain on each biofilm specimen. Stain for 30 min at room temperature, protected from light. Wash 3x with sterile ultrapure water (2.5 ml/well), aspirating after each wash.</li>
	<li>Transfer the specimens to a 6-well plate, placing one specimen per well in 6 ml sterile ultrapure water to facilitate confocal microscopy.</li>
</ol>
6. Imaging Using Confocal Laser Scanning Microscopy
<ol>
	<li>Acquire images of each component (stain) within biofilms of the treatment and control groups using a confocal laser scanning microscope settings shown in Table 1. A 63X dipping lens with a 0.9 numerical aperture that has a working distance of 2.2 mm was used in this study. 
	<img alt="Biofilm staining chart; laser wavelengths (nm) and emission bands (nm) for EPS, nucleic acids, proteins." fo:content-width="4.75in" src="/files/ftp_upload/50639/50639table1.jpg" data-altupdatedat="1787630408000" data-alt="Table 1"> 
	Table 1. Confocal Laser Scanning Microscope Settings.</li>
</ol>

<ol start="2">
	<li>Set the scan size to 250 μm x 250 μm and a minimum pixel resolution of 512 x 512 to acquire CLSM images at a resolution adequate for quantitative analysis.</li>
	<li>Use the SY stain to set the top and bottom points of the biofilm image stack, then set the z-step to be adequate for quantitative analysis (0.6 μm for this study). Before collecting a scan, optimize the image and stain parameters (i.e. PMT voltage and offset) using the QLUT option. A color look-up table was used to assign pseudo-colors to each stain (green for SY, red for SR, and blue for AF) in order to make each biofilm component more distinguishable in the 3D reconstruction.</li>
	<li>Collect CLSM images at 400 Hz using sequential scanning in the "between stacks" mode to optimize capture of images of multiple stains within the same biofilm.</li>
</ol>
7. Biofilm Structural Analysis
<ol>
	<li>Analyze the CLSM images collected using image analysis software for biofilms. The following steps describe the use of ISA3D software12 to calculate the structural parameters of the biofilm images collected.
	<ol>
		<li>Copy CLSM image files for each biofilm to the Images folder, as specified in the software's manual. Ensure that the naming convention for CLSM files required by the software is followed. The software permits analysis of files within subfolders in batch mode, thus facilitating analysis of treatment and control group biofilms in the same run.</li>
		<li>Enter x-, y-, and z-axis dimensions of CLSM images in the dxy and dz fields of the main dialog box. Select threshold and distance mapping settings, as described in the software's manual (Otsu and Quasi-Euclidean were used for this study, respectively). Input a suitable name for the results file, and then run the program. A results file will be produced in the ISA folder.</li>
		<li>View the results file to obtain values for twenty 3D structural parameters12 such as biovolume and mean biofilm thickness (measured in this study) that quantify the 3D distribution of each component (stain) within the biofilm.</li>
	</ol>
	</li>
</ol>
8. Visualization of Biofilm Structure
<ol>
	<li>Create a reconstruction of overlaid components (stains) within each biofilm using image analysis software. The following steps describe the use of Volocity software to create 3D reconstructions.
	<ol>
		<li>Create a library for each biofilm by copying CLSM image files into the software, as described in the manual.</li>
		<li>Use the 3D Renderer menu option to produce a reconstructed 3D image from the CLSM images of each biofilm (HR Opacity format was used for this study).</li>
		<li>Rotate the 3D image to orient all of the biofilms in a similar manner with regard to the x-, y-, and z-coordinate axes. Capture a snapshot of the correctly oriented biofilm reconstruction, and then export the snapshot in TIFF, JPEG or other suitable format.</li>
	</ol>
	</li>
	<li>Perform visual analysis of the concurrent distribution of EPS, proteins and nucleic acid components within biofilms on the reconstructed images.</li>
	<li>Use Pearson's correlation coefficient and Manders' overlap coefficient to perform a colocalization analysis of multiple biofilm components (colocalization was not measured in this study).</li>
</ol>
9. Statistical Analysis
<ol>
	<li>Use separate mixed models statistical analyses to compare mean values of structural parameters between mouthwash and control groups (α=0.05). For this study, SAS software was used to perform the statistical analysis.</li>
</ol>

<ol><li>Costerton, J. W., Stewart, P. S., Greenberg, E. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Bacterial+biofilms%3A+a+common+cause+of+persistent+infections%5BTitle%5D)+AND+%22Science%22%5BJournal%5D)">Bacterial biofilms: a common cause of persistent infections.</a> Science. 284, 1318-1322 (1999).</li>
<li>Hall-Stoodley, L., Costerton, J. W., Stoodley, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Bacterial+biofilms%3A+from+the+natural+environment+to+infectious+diseases%5BTitle%5D)+AND+%22Nat.+Rev.+Microbiol%22%5BJournal%5D)">Bacterial biofilms: from the natural environment to infectious diseases.</a> Nat. Rev. Microbiol. 2, 95-108 (2004).</li>
<li>Yang, Y., Sreenivasan, P. K., Subramanyam, R., Cummins, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Multiparameter+assessments+to+determine+the+effects+of+sugars+and+antimicrobials+on+a+polymicrobial+oral+biofilm%5BTitle%5D)+AND+%22Appl.+Environ.+Microbiol%22%5BJournal%5D)">Multiparameter assessments to determine the effects of sugars and antimicrobials on a polymicrobial oral biofilm.</a> Appl. Environ. Microbiol. 72, 6734-6742 (2006).</li>
<li>Klein, M. I., Xiao, J., Heydorn, A., Koo, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((An+analytical+tool-box+for+comprehensive+biochemical%2C+structural+and+transcriptome+evaluation+of+oral+biofilms+mediated+by+mutans+streptococci%5BTitle%5D)+AND+%22J.+Vis.+Exp%22%5BJournal%5D)">An analytical tool-box for comprehensive biochemical, structural and transcriptome evaluation of oral biofilms mediated by mutans streptococci.</a> J. Vis. Exp. , (2011).</li>
<li>Conchello, J. A., Lichtman, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Optical+sectioning+microscopy%5BTitle%5D)+AND+%22Nat.+Methods%22%5BJournal%5D)">Optical sectioning microscopy.</a> Nat. Methods. 2, 920-931 (2005).</li>
<li>Robinson, J. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Principles+of+confocal+microscopy%5BTitle%5D)+AND+%22Methods+Cell+Biol%22%5BJournal%5D)">Principles of confocal microscopy.</a> Methods Cell Biol. 63, 89-106 (2001).</li>
<li>Neu, T. R., Kuhlicke, U., Lawrence, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Assessment+of+fluorochromes+for+two-photon+laser+scanning+microscopy+of+biofilms%5BTitle%5D)+AND+%22Appl.+Environ.+Microbiol%22%5BJournal%5D)">Assessment of fluorochromes for two-photon laser scanning microscopy of biofilms.</a> Appl. Environ. Microbiol. 68, 901-909 (2002).</li>
<li>Wood, S. R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Architecture+of+intact+natural+human+plaque+biofilms+studied+by+confocal+laser+scanning+microscopy%5BTitle%5D)+AND+%22J.+Dental+Res%22%5BJournal%5D)">Architecture of intact natural human plaque biofilms studied by confocal laser scanning microscopy.</a> J. Dental Res. 79, 21-27 (2000).</li>
<li>Chen, M. Y., Lee, D. J., Tay, J. H., Show, K. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Staining+of+extracellular+polymeric+substances+and+cells+in+bioaggregates%5BTitle%5D)+AND+%22Appl.+Microbiol.+Biotechnol%22%5BJournal%5D)">Staining of extracellular polymeric substances and cells in bioaggregates.</a> Appl. Microbiol. Biotechnol. 75, 467-474 (2007).</li>
<li>Zinchuk, V., Zinchuk, O., Okada, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Quantitative+colocalization+analysis+of+multicolor+confocal+immunofluorescence+microscopy+images%3A+pushing+pixels+to+explore+biological+phenomena%5BTitle%5D)+AND+%22Acta+Histochem.+Cytochem%22%5BJournal%5D)">Quantitative colocalization analysis of multicolor confocal immunofluorescence microscopy images: pushing pixels to explore biological phenomena.</a> Acta Histochem. Cytochem. 40, 101-111 (2007).</li>
<li>Dunn, K. W., Kamocka, M. M., McDonald, J. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((A+practical+guide+to+evaluating+colocalization+in+biological+microscopy%5BTitle%5D)+AND+%22Am.+J.+Physiol.+Cell+Physiol%22%5BJournal%5D)">A practical guide to evaluating colocalization in biological microscopy.</a> Am. J. Physiol. Cell Physiol. 300, C723-C742 (2011).</li>
<li>Beyenal, H., Donovan, C., Lewandowski, Z., Harkin, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Three-dimensional+biofilm+structure+quantification%5BTitle%5D)+AND+%22J.+Microbiol.+Methods%22%5BJournal%5D)">Three-dimensional biofilm structure quantification.</a> J. Microbiol. Methods. 59, 395-413 (2004).</li>
</ol>

The authors declare that they have no competing financial interests. Production and Free Access to this article is sponsored by Leica Microsystems.

The acquisition of CLSM images has to be performed in the manner and format necessary for the quantification of biofilms and for colocalization analysis, such that the distribution of signal intensity in each image is a reliable representation of the distribution of each fluorochrome in the biofilm stack. The signal intensity should be distinguishable from noise and background10,11, unaffected by autofluorescence from the substrate, and having minimal bleed-through due to spectral interference between the fluorochromes used11. Noise is an inevitable limitation of fluorescence microscopy11, and image quality can sometimes be limited for technical or logistical reasons. Identification of fluorochromes with minimal spectral overlap is critical to the success of this method, but can be complicated. Furthermore, the quantification of multiple fluorochromes poses a multifactorial problem. Therefore, it is not surprising that very few investigations have successfully quantified the concurrent distribution of more than two components within the structures of biofilms.
The objective of this study was to report a methodology consisting of distinct but interconnected steps for the quantification and comparison of the concurrent 3-dimensional distributions of three cellular and extracellular components within biofilms. The biofilm growth assay described permits biofilm growth on relevant substrates and produces biofilm structures that are reproducible, as demonstrated by the results reported in Table 1. The combination of novel simultaneous staining of EPS, proteins and nucleic acid components with the measurement of 3D biofilm structural parameters results in quantifiable distributions of components within biofilms. Qualitative visual analysis of the concurrent distribution of EPS, proteins and nucleic acid within the biofilms is possible via the reconstruction of overlaid stains within each biofilm. The ISA3D software12 contains several unique structural parameters such as fractal dimension, homogeneity, and biofilm roughness coefficient in addition to traditionally-measured parameters such as porosity and biofilm thickness to enhance quantification of the 3D structures of biofilms. Statistical analysis of the biofilm structural parameters facilitates relevant comparisons of biofilms under specific experimental conditions such as antibacterial/antifouling efficacy (e.g.&#160;after treatment with mouthwashes) or over time (temporal effects).
This methodology efficiently and successfully quantified and compared the concurrent 3D distributions of three major components within S. mutans biofilms that were grown on relevant substrates, thus overcoming two challenges to the simultaneous assessment of biofilm components. This method can also be used to determine the efficacy of antibacterial treatments or antifouling measures against multiple biofilm components, as shown using mouthwashes in this study. Furthermore, the majority of the protocols described above can be replaced with protocols for the fabrication of relevant substrates and biofilm growth assays of relevant microorganisms. Therefore, this method has broad application because it facilitates comparison of 3D structures/architecture of in vitro and in vivo biofilms in a variety of disciplines including the medical, dental, geological and marine sciences.

Biofilms are structured microbial communities that are encapsulated in a self-produced extracellular matrix, and are attached to biological or inert surfaces1. Biofilms represent a common lifestyle for many bacteria, and form by transitioning in stages from free-floating (planktonic) cells to complex multispecies communities. The inherent resistance of biofilms to antimicrobial agents is at the root of many persistent and chronic bacterial infections1,2, as demonstrated by oral biofilms (dental plaque). Cariogenic microorganisms such as mutans streptococci process sucrose and other carbohydrates to produce an extracellular matrix and generate acids that can demineralize tooth structure and cause dental caries. Most biofilm matrices are biopolymers consisting of cellular and extracellular components such as exopolysaccharides (EPS), proteins, and nucleic acids3,4.
Confocal laser scanning microscopy (CLSM), the most widely used technique for fluorescence imaging, has radically transformed optical imaging in biology because it has the ability to collect 3D images of hydrated biological structures without fixation5,6,7. This nondestructive technique involves collecting images of thin sections within a region of interest on the specimen in such a manner that the contribution of out-of-focus light is removed. The quality and resolution of images captured by CLSM is beyond what is achievable using widefield fluorescence microscopy. One major drawback of CLSM is that scanning of images occurs at a slower rate than with widefield microscopy techniques, in which entire images are collected simultaneously5. However, with a widening selection of fluorochromes, lasers, and filters, CLSM has become one of the prevailing techniques for multispectral imaging5,7.
Previous studies have shown CLSM to be a useful tool for examining the structure or architecture of biofilms by using one or two fluorescent tags or stains to provide a better understanding of the distribution of EPS and cells within biofilms, and especially within the extracellular matrix7,8. In theory, fluorescent staining/labeling of multiple components is desirable for exploring the detailed structure and colocalization of cellular and extracellular components within biofilms. However, concurrent analysis of various components within biofilms can be challenging because: 1)&#160;selection of fluorescent dyes having minimal spectral overlap is complicated, and 2)&#160;quantification of multiple fluorochromes poses a multifactorial problem. Colocalization using multiple fluorochromes requires the use of highly specific stains with minimal spectral interference to avoid any bleed-through effects, which occurs when two fluorochromes have significant overlap in their spectral peak, causing one to be more strongly excited than the other9. Ideally, fluorochromes having excitation spectra that do not overlap would provide the best results, however it is very difficult to find stains that meet this criterion. Instead, the selection of stains is optimized by choosing fluorochromes whose emission spectra have minimal overlap, allowing the stains to be viewed one by one within a limited observation wavelength band9.
Superimposition of fluorescence images is probably the most widely used method for evaluating concurrent distribution of fluorochromes. Colocalization of the various components appears as an overlap of different colors through multiple channels created by the fluorochromes being examined10. The tools for displaying multiple-channel fluorescence images as merged color images are available in most CLSM software and biological image analysis software. Although superimposition of images is useful for spatial evaluation of colocalization, the images can only be examined qualitatively by visual analysis. This provides a limited amount of information, as these representations are generally not helpful for quantifying colocalization under different experimental conditions nor do they determine whether the colocalization exceeds random coincidence11. Very few investigations so far have used quantitative methods to analyze the 3-dimensional structure of biofilms and biofilm components, and even fewer have quantified the effect of antibacterial treatments or antifouling measures on biofilm components.
The objective of this study was to report a methodology for quantification and comparison of the concurrent 3-dimensional distributions of three cellular and extracellular components of biofilms. The method consists of distinct but interconnected steps involving biofilm growth, staining, CLSM imaging of biofilms, biofilm structural analysis and visualization, and statistical analysis of structural parameters. The biofilm growth assay permits biofilm growth on relevant substrates, and produces biofilm structures that are reproducible. The combination of novel simultaneous staining of EPS, proteins and nucleic acid components with the measurement of 3D biofilm structural parameters results in quantifiable distributions of components within biofilms. Statistical analysis of the biofilm structural parameters facilitates evaluation of biofilms under specific experimental conditions (e.g.&#160;after treatment with mouthwashes), as will be described in the next section.

<table><tbody><tr><td>Bacto Agar</td><td>Becton, Dickinson and Company</td><td>214010</td><td></td></tr><tr><td>Bacto Todd Hewitt Broth</td><td>Becton, Dickinson and Company</td><td>249240</td><td></td></tr><tr><td>Yeast Extract, Granulated</td><td>EMD Millipore</td><td>1.03753.0500</td><td></td></tr><tr><td>Bacto Tryptone</td><td>Becton, Dickinson and Company</td><td>211705</td><td></td></tr><tr><td>OmniPur Sucrose</td><td>EMD Millipore</td><td>8510</td><td></td></tr><tr><td>Potassium Chloride, ACS reagent, 99.0-100.5%</td><td>Sigma-Aldrich</td><td>P3911-500G</td><td></td></tr><tr><td>Potassium Phosphate, monobasic, &amp;ge;99.0%, ACS reagent</td><td>Sigma-Aldrich</td><td>P0662-500G</td><td></td></tr><tr><td>Sodium Chloride</td><td>Sigma-Aldrich</td><td>S9888-500G</td><td></td></tr><tr><td>Sodium Phosphate, Monobasic, Monohydrate</td><td>EMD Millipore</td><td>SX0710-1</td><td></td></tr><tr><td>Tris(hydroxymethyl)aminomethane, 99.8+%, ACS reagent</td><td>Sigma-Aldrich</td><td>252859-500G</td><td></td></tr><tr><td>Concanavalin A, Alexa Fluor 647 Conjugate</td><td>Invitrogen</td><td>C21421</td><td></td></tr><tr><td>Syto 9</td><td>Invitrogen</td><td>S34854</td><td></td></tr><tr><td>Sypro Red</td><td>Invitrogen</td><td>S12012 or S6653</td><td></td></tr><tr><td>Biot&amp;egrave;ne PBF Oral Rinse</td><td>GlaxoSmithKline</td><td>N/A</td><td></td></tr><tr><td>Listerine Total Care</td><td>McNeil-PPC, Inc.</td><td>N/A</td><td></td></tr></tbody></table>

concurrent quantification of cellular and extracellular components of biofilms

Concurrent Quantification of Cellular and Extracellular Components of Biofilms

Confocal laser scanning microscopy (CLSM) is a powerful tool for investigation of biofilms. Very few investigations have successfully quantified concurrent distribution of more than two components within biofilms because: 1)&#160;selection of fluorescent dyes having minimal spectral overlap is complicated, and 2)&#160;quantification of multiple fluorochromes poses a multifactorial problem. Objectives: Report a methodology to quantify and compare concurrent 3-dimensional distributions of three cellular/extracellular components of biofilms grown on relevant substrates. Methods: The method consists of distinct, interconnected steps involving biofilm growth, staining, CLSM imaging, biofilm structural analysis and visualization, and statistical analysis of structural parameters. Biofilms of Streptococcus mutans (strain UA159) were grown for 48 hr on sterile specimens of Point 4 and TPH3 resin composites. Specimens were subsequently immersed for 60 sec in either Biot&#232;ne PBF (BIO) or Listerine Total Care (LTO) mouthwashes, or water (control group; n=5/group). Biofilms were stained with fluorochromes for extracellular polymeric substances, proteins and nucleic acids before imaging with CLSM. Biofilm structural parameters calculated using ISA3D image analysis software were biovolume and mean biofilm thickness. Mixed models statistical analyses compared structural parameters between mouthwash and control groups (SAS software; &#945;=0.05). Volocity software permitted visualization of 3D distributions of overlaid biofilm components (fluorochromes). Results: Mouthwash BIO produced biofilm structures that differed significantly from the control (p&#60;0.05) on both resin composites, whereas LTO did not produce differences (p&#62;0.05) on either product. Conclusions: This methodology efficiently and successfully quantified and compared concurrent 3D distributions of three major components within S. mutans biofilms on relevant substrates, thus overcoming two challenges to simultaneous assessment of biofilm components. This method can also be used to determine the efficacy of antibacterial/antifouling agents against multiple biofilm components, as shown using mouthwashes. Furthermore, this method has broad application because it facilitates comparison of 3D structures/architecture of biofilms in a variety of disciplines.

Representative results for the treatments (mouthwashes) and untreated control group are shown in Table 2, and Figures 1 and 2. Table 2 displays the mean and standard deviation values of biofilm structural parameters biovolume (μm3) and mean biofilm thickness (μm) that were calculated using ISA3D software. Structural parameters of biofilms treated with mouthwash that differed significantly from those of biofilms in the control group (p&lt;0.05) have mean and standard deviation values highlighted in red. The results of the mixed models statistical analyses demonstrated that mouthwash BIO produced biofilm structures that differed significantly from the control (p&lt;0.05) on both resin composites, whereas mouthwash LTO did not produce significant differences (p&gt;0.05) on either resin composite. The results clearly show that the cellular and extracellular biofilm components remaining after the two mouthwash treatments differed. It should also be noted that the S. mutans biofilms grown on the two substrates (PF and TP) differed in 3D structure even though they were grown under similar conditions and both substrates were polished with similar abrasives.
The concurrent distribution of EPS, proteins and nucleic acid within biofilms can be visualized via the 3D reconstructions generated using Volocity software. Figures 1 and 2 demonstrate representative reconstructions of control group biofilms grown on PF and TP resin composites, respectively. The blue stain represents EPS within S. mutans biofilms, the green stain demonstrates nucleic acids, and the red stain shows proteins. The intervening space may be occupied by water or other nonfluorescently labeled biofilms components.
<img alt="3D scatter plot, dynamic data visualization, graph, interactive research tool, analytics display." fo:content-width="4.75in" fo:src="/files/ftp_upload/50639/50639fig1highres.jpg" src="/files/ftp_upload/50639/50639fig1.jpg" data-altupdatedat="1787630408000" data-alt="Figure 1"> 
Figure 1. A representative 3D reconstruction of S. mutans biofilm grown on PF resin composite in the control group (not treated with mouthwash). Concurrent overlay of the three stains within a single biofilm permits the simultaneous visualization of EPS (blue stain), nucleic acid (green stain), and protein (red stain) components within S. mutans biofilms. (1 Unit = 24 μm). <a href="https://www.jove.com/files/ftp_upload/50639/50639fig1large.jpg" target="_blank"> Click here to view larger figure</a>.
<img alt="3D cellular structure visualization, fluorescence microscopy, spatial data analysis, scientific graph." fo:content-width="4.75in" fo:src="/files/ftp_upload/50639/50639fig2highres.jpg" src="/files/ftp_upload/50639/50639fig2.jpg" data-altupdatedat="1787630408000" data-alt="Figure 2"> 
Figure 2. A representative 3D reconstruction of S. mutans biofilm grown on TP resin composite in the control group (not treated with mouthwash). Concurrent overlay of the three stains within a single biofilm permits the simultaneous visualization of EPS (blue stain), nucleic acid (green stain), and protein (red stain) components within S. mutans biofilms. (1 Unit = 24 μm). <a href="https://www.jove.com/files/ftp_upload/50639/50639fig2large.jpg" target="_blank"> Click here to view larger figure</a>.
<table border="1">
	<tbody>
		<tr>
			<td>Resin composite</td>
			<td></td>
			<td colspan="2">Point 4</td>
			<td colspan="2">TPH3</td>
		</tr>
		<tr>
			<td>Mouthwash</td>
			<td>Component</td>
			<td>BV (μm3)</td>
			<td>MT (μm)</td>
			<td>BV (μm3)</td>
			<td>MT (μm)</td>
		</tr>
		<tr>
			<td>Biotène PBF</td>
			<td>Nucleic Acids</td>
			<td>279,517±53,291</td>
			<td>9.32±2.80</td>
			<td>195,033±42,014</td>
			<td>7.45±3.70</td>
		</tr>
		<tr>
			<td></td>
			<td>EPS</td>
			<td>344,902±56,386</td>
			<td>35.22±17.19</td>
			<td>197,840±62,351</td>
			<td>9.83±7.26</td>
		</tr>
		<tr>
			<td></td>
			<td>Proteins</td>
			<td>298,796±62,868</td>
			<td>54.21±21.65</td>
			<td>216,033±66,654</td>
			<td>24.33±39.64</td>
		</tr>
		<tr>
			<td>Listerine Total Care</td>
			<td>Nucleic Acids</td>
			<td>355,707±110,444</td>
			<td>26.45±14.21</td>
			<td>273,296±47,323</td>
			<td>13.43±2.89</td>
		</tr>
		<tr>
			<td></td>
			<td>EPS</td>
			<td>494,099±180,592</td>
			<td>64.90± 26.68</td>
			<td>329,150±47,145</td>
			<td>34.35±30.32</td>
		</tr>
		<tr>
			<td></td>
			<td>Proteins</td>
			<td>348,416±161,316</td>
			<td>58.68±47.28</td>
			<td>303,150±54,705</td>
			<td>34.18±41.46</td>
		</tr>
		<tr>
			<td>Control (untreated)</td>
			<td>Nucleic Acids</td>
			<td>388,375±42,152</td>
			<td>51.15±40.66</td>
			<td>327,809±39,400</td>
			<td>17.08±1.65</td>
		</tr>
		<tr>
			<td></td>
			<td>EPS</td>
			<td>660,448±173,197</td>
			<td>91.37±74.84</td>
			<td>363,850±67,612</td>
			<td>28.33± 15.07</td>
		</tr>
		<tr>
			<td></td>
			<td>Proteins</td>
			<td>517,274±119,475</td>
			<td>127.96±73.84</td>
			<td>353,161±56,518</td>
			<td>21.17±4.41</td>
		</tr>
	</tbody>
</table>
Table 2. Mean and standard deviation values of Biovolume (BV) and Mean biofilm thickness (MT) of biofilms treated with BIO or LTO, or left untreated (control group). Structural parameters of biofilms treated with mouthwashes that differed significantly from those of biofilms in the control group (p&lt;0.05) have mean and standard deviation values highlighted in red.

A protocol for the concurrent quantification and comparison of three cellular and extracellular components within biofilms is presented. The methodology involves the use of confocal laser scanning microscopy, biofilm structural analysis and visualization software, and statistical analysis software.

Confocal laser scanning microscopy (CLSM) is a powerful tool for investigation of biofilms. Very few investigations have successfully quantified ...

The overall goal of this procedure is to quantify and compare concurrent three dimensional distributions of three cellular and extracellular biofilm components after treatment with antibacterial agents. This is accomplished by first fabricating and then polishing resin composite specimens. In the second step, the biofilms of interest are grown on the specimens and then treated with antibacterial agents.Next, the biofilms are stained with fluorochromes for extracellular polymeric substances, nucleic acids and proteins, and then imaged by confocal laser scanning microscopy. In the final step, three dimensional images of the overlaid fluorochromes are reconstructed to facilitate the concurrent visualization of the biofilm components and structural parameters are calculated from the biofilm images. Ultimately, statistical analysis of the biofilm structural parameters such as bio volume and mean biofilm thickness can be performed to compare differences between the treatment and control groups.The main advantage of this procedure over existing methods is that it uses distinct but interconnected techniques to characterize the distribution of multiple components within the structure of biofilms grown under specific conditions, demonstrating the procedure will be Dr.Fernando Flores, a postdoctoral research fellow, and Ms.Kristen Smart, a research assistant from my laboratory To create the specimens begin by placing one increment of 0.4 or TPH three dental resin composite into custom made stainless steel molds. Next, polymerize the first increment with an LED light curing unit for 40 seconds. After repeating the procedure for the second increment, use a semi-automated grinder polisher to polish the cured specimens to an acceptable final surface finish.Finally, sterilize the specimens to grow the biofilm. First, inoculate a single colony of S mutans in four milliliters of overnight culture medium, and then incubate the culture at 37 degrees Celsius for 16 to 18 hours to achieve an optical density of at least 0.9. Next, dilute the culture at a one to 100 ratio in 10 milliliters of biofilm growth.Medium aseptically transfer the sterile resin composite specimens to sterile 12 well plates, and then add 2.5 milliliters of the diluted culture to each of the wells. For mouthwash treatment and control groups, add 2.5 milliliters of sterile un inoculated biofilm growth, medium to the sterility control wells, and then grow the biofilms at 37 degrees Celsius under micro paraphilic conditions on a shaker at 100 RPM. After 24 hours, aseptically aspirate the medium from all the wells and wash each well twice with 2.5 milliliters of sterile PBS aspirating the saline after each wash, then replenish each well with 2.5 milliliters of fresh biofilm growth media and incubate the plate for an additional 24 hours as just demonstrated for a total biofilm growth Duration of 48 hours after the biofilm growth is complete, aspirate the growth media and then dispense 2.5 milliliters of mouthwash into each treatment group well and 2.5 milliliters of sterile ultrapure water into the control group.Well agitate the plates on an orbital shaker at 150 RPM, and then after 60 seconds, aspirate both the mouthwash and ultrapure water from the wells to stain the exo polysaccharide component of the biofilms. Incubate each biofilm with 50 microliters of LOR conjugate for 30 minutes at room temperature protected from light. Then wash the specimens two times with 2.5 milliliters of TC buffer aspirating after each wash and stain the nucleic acids in each biofilm with a 50 microliter drop of cyto nine for 30 minutes at room temperature protected from light.After washing the specimens twice, stain the protein components in each biofilm with 50 microliters of Cipro red for 30 minutes at room temperature, protected from light. After washing the specimens three times, transfer them to individual wells of a six well plate containing six milliliters of sterile ultrapure water per well to facilitate their visualization by confocal microscopy to acquire images of each of the component stains within the biofilms of the treatment and control groups. Set the lasers of a confocal laser scanning microscope to the following settings for the detection of exo polysaccharides by Exor conjugate stain, use a 633 nanometer laser and a 659 to 749 nanometer emission band for the detection of nucleic acids by cyto nine stain.Use a 488 nanometer laser and a 495 to 500 nanometer emission band, and for the detection of proteins by Cipro red stain, use a 543 nanometer laser and a 615 to 651 nanometer emission band. Then using a 63 x dipping lens with a 0.9 numerical aperture and a working distance of 2.2 millimeters. Collect confocal laser scanning microscopy images at 400 hertz using sequential scanning in the between stacks mode to optimize the capture of images of multiple stains within the same biofilm.After analyzing the confocal laser scanning microscopy images, use the 3D renderer menu option in velocity image analysis software to create a reconstructed 3D image of the overlaid component stains within each biofilm. Next, rotate the 3D image to obtain an optimal view of the biofilm. Then capture a snapshot of the biofilm reconstruction and export the snapshot in a suitable image file format.Finally, perform a visual analysis of the concurrent distribution of the exo polysaccharide nucleic acid and protein components within the biofilms. In the reconstructed images, calculate biofilm structural parameters such as bio volume and mean biofilm thickness using ISA 3D software in this table, the mean and standard deviation values of biofilm structural parameters calculated using statistical analysis software are displayed. The mean and standard deviation values for the structural parameters of the biofilms treated with mouthwash that differed significantly from those of the biofilms in the control group are highlighted in red mixed models.Statistical analyses demonstrated that the Biotene PBF mouthwash produced biofilm structures that differed significantly from the control group on both resin composites, whereas Listerine total care mouthwash did not produce significant differences on either resin composite clearly indicating differences in the cellular and extracellular biofilm components remaining after the two mouthwash treatments. The concurrent distribution of exo polysaccharides nucleic acids and proteins within the biofilms can be visualized via 3D reconstructions generated using velocity software. In this figure, a representative reconstruction of control group biofilms grown on 0.4 is shown the blue color was assigned to exo polysaccharide.Within S mutans biofilms, the green color was assigned to nucleic acids and the red color to proteins. The intervening space may be occupied by water or other biofilm components that have not been fluorescently labeled. In this figure, a representative reconstruction of control group biofilms grown on TPH three resin composites with the colors representing the same components as the previous figure is shown.This procedure has brought application in a variety of disciplines such as the medical, dental, geological, and marine sciences. Since many substrates and biofilms can be substituted for the ones used here.

concurrent-quantification-cellular-extracellular-components

Research

JoVE Journal

Immunology and Infection

Biofilms formed on tooth surfaces are highly complex and exposed to constant innate and exogenous environmental challenges, which modulate their architecture, physiology and transcriptome. We developed a toolbox to examine the composition, structural organization and gene expression of oral biofilms, which can be adapted to other areas of biofilm research.

An Analytical Tool-box for Comprehensive Biochemical, Structural and Transcriptome Evaluation of Oral Biofilms Mediated by Mutans Streptococci

The video showcases a biofilm dispersion assay using a multi-well plate. Buffer and glucose treatment disassemble the biofilm, releasing bacteria, while bile salts induce stress, retaining bacteria in the protective extracellular polymeric substance. Higher dispersion with buffer and glucose confirms successful biofilm disassembly, estimated by colony forming units measurement.

Detection of Biofilm Disassembly Through a Dispersion Assay

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.

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

A pH-sensitive ratiometric dye is used in combination with confocal laser scanning microscopy and digital image analysis to monitor extracellular pH in dental biofilms in real-time.

Ratiometric Imaging of Extracellular pH in Dental Biofilms

This protocol describes a new method to grow and qualitatively analyze bacterial biofilms on fungal hyphae by confocal and electron microscopy.

A New Method for Qualitative Multi-scale Analysis of Bacterial Biofilms on Filamentous Fungal Colonies Using Confocal and Electron Microscopy

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Characterization of Aquatic Biofilms with Flow Cytometry

The protocol describes the cultivation of cross-kingdom biofilms consisting of Candida albicans and Streptococcus mutans and presents a confocal microscopy-based method for the monitoring of extracellular pH inside these biofilms.

Monitoring Extracellular pH in Cross-Kingdom Biofilms using Confocal Microscopy

Antimicrobial-induced changes to Pseudomonas aeruginosa biofilm architecture differ among clinical isolates cultured from patients with cystic fibrosis and chronic pulmonary infection. Following confocal microscopy, COMSTAT software can be utilized to quantify variations in biofilm architecture (e.g., surface area, thickness, biomass) for individual isolates to assess the efficacy of anti-infective agents.

Quantifying the Effects of Antimicrobials on In vitro Biofilm Architecture using COMSTAT Software

This protocol describes the preparation of the inoculum, the biofilm quantification on microtiter plates using crystal violet dye, the viable count in biofilms, and the visualization of biofilms of Acinetobacter.

Quantification, Viability Assessment, and Visualization Strategies for Acinetobacter Biofilms

This protocol delivers a modular, BSL-2 workflow combining crystal-violet biomass assays, time-lapse phase-contrast kinetics, confocal 3-D/matrix mapping, SEM ultrastructure, and an in vivo hamster infection module to cultivate, quantify, characterize and investigate Leptospira biofilm functional role, enabling standardized evaluation of mutants and anti-biofilm interventions across laboratories.

A Modular Workflow for Quantitative, Structural and Functional Analysis of Leptospira Biofilms

Keşfedin biyofilmlerdeki hücresel ve ekstrasellüler bileşenlerin eşzamanlı kantitasyonu için konfokal lazer tarama mikroskobu ve istatistiksel analiz yöntemlerini. Bu protokol antibakteriyal ajanların biyofilm yapısı üzerindeki etkilerini değerlendirmeye yardımcı olur.

Concurrent Quantification of Cellular and Extracellular Components of Biofilms

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