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All procedures involving sample collection have been performed in accordance with the institute&#39;s IRB guidelines.
1. Collection of In Situ Grown Dental Biofilm Samples
<ol>
	<li>Select volunteers that fulfill inclusion and exclusion criteria relevant for the study. Make alginate impressions of their upper and lower dental arch. Make cast models from these impressions and manufacture an acrylic splint in the lower jaw. Design the splint with buccal acrylic flanges connected by a lingual orthodontic wire that allows the volunteer to bite into normal occlusion.</li>
	<li>Drill recessions in the buccal flanges of the acrylic splint with the help of dental acrylic burs to allow insertion of glass slabs for biofilm collection. The depth of the recessions should be at least 1.5 mm, while the width and length of the recessions may vary depending on the number of glass slabs to be inserted.</li>
	<li>For biofilm collection, use custom-made non-fluorescent glass slabs (4 x 4 x 1 mm3) with a surface roughness of grit 1,200 in order to mimic the colonization pattern on natural enamel.</li>
	<li>Sterilize the glass slabs by autoclaving prior to mounting. Mount the glass slabs with sticky wax in the depressions in the buccal flanges of each side slightly recessed to the surface of the acrylic surface in order to protect the biofilm from shear forces exerted by movement of the cheeks. 
	Note: The number of glass slabs placed in a recession may vary between 3 and 14, depending on the aim of the study.</li>
	<li>Insert the appliance in the mouth of the volunteer. Instruct the volunteer to retain the appliance intra-orally throughout the experimental period. Instruct the volunteer to store the appliance in an orthodontic retainer container with a piece of wet paper tissue (to keep it humid) at room temperature during tooth brushing and intake of food and beverages other than water. Instruct the volunteer to not touch the buccal acrylic flanges with the glass slabs while placing and removing the appliance. 
	Note: The experimental period may vary depending on the aim of the study (one day to several weeks).</li>
	<li>Carefully remove the glass slabs from the appliance at the end of the experimental period. Remove the sticky wax around the slabs with a knife and transfer them with a pair of tweezers to a closed container, the biofilm facing upward, until microscopic analysis. Keep the container humid with wet paper tissue. Perform pH imaging within few hours after biofilm collection.</li>
</ol>
2. Biofilm pH Imaging
<ol>
	<li>Prepare salivary solution by adding dithiothreitol to collected saliva according to the method of de Jong et al. Titrate the salivary solution to pH 7.0 and add glucose to a concentration of 0.4 % (wt/vol). Pipette 100 &#181;l per biofilm to be analyzed into a glass-bottom 96-well plate for microscopy. Add 5 &#181;l of the ratiometric dye per well.</li>
	<li>Place the 96-well plate on the microscope stage. Turn on the microscope and the 543 nm laser line. Warm up the incubator to 37 &#176;C. Use the same microscope settings as for the calibration of the dye. Wait for 30 min, until the 96-well plate has reached working temperature.</li>
	<li>Pick up one or more glass slabs with a slim set of tweezers and place them in the saliva-filled wells, one slab per well, with the biofilms facing downward.</li>
	<li>Acquire single images (&#34;Scan Control&#34; &#8594; &#34;Single&#34;) or z-stacks (&#34;Scan Control&#34; &#8594; &#34;Start&#34;) spanning the depth of the biofilms in different areas. To acquire z-stacks choose the number of slices to be imaged (&#34;Scan Control&#34; &#8594; &#34;Z Settings&#34; &#8594; &#34;Num Slices&#34;) and mark the z-position for the first and the last slice in the microscope software (&#34;Scan Control&#34; &#8594; &#34;Z Settings&#34; &#8594; &#34;Mark First&#34;; &#34;Mark Last&#34;). 
	Note: Z-stacks with a depth of up to 75 &#181;m can be acquired with good contrast between extracellular and intracellular areas.</li>
	<li>To follow pH changes in a microscopic field of view over time, mark the x-y-position in the microscope software (&#34;Stage and Focus Control&#34; &#8594; &#34;Mark Pos&#34;) and take repeated images at consecutive time points (&#34;Scan Control&#34; &#8594; &#34;Single&#34;). Regularly take images with the laser power set to zero for background subtraction.</li>
</ol>
3. Digital Image Analysis
<ol>
	<li>To export the microscopic images as TIF files, use the file batch export of the microscope software (&#34;Macro&#34; &#8594; &#34;File Batch Export&#34;). Mark the files to be exported and save red and green channel images in separate folders as TIF-files (&#34;Start Batch Export&#34;). Rename the files in both folders giving them sequential numbers.</li>
	<li>Import the red and green image series into software such as daime (digital image analysis in microbial ecology). Segment the green channel images with individually chosen brightness thresholds (Segment &#8594; Automatic segmentation &#8594; Custom threshold). Choose the brightness thresholds with care (typically between 20 and 80), so that all bacteria (brighter than the extracellular matrix), but not the matrix will be recognized as objects during segmentation. Verify visually that the areas recognized as objects correspond well to the bacterial biomass.</li>
	<li>Transfer the object layer of the segmented green channel images to the corresponding red channel images (Segment &#8594; Transfer object layer). Use the object editor function to reject and delete all objects in the red and green channel images. Now only the extracellular matrix is left in the biofilm images. Export the processed image series as TIF files.</li>
	<li>Import the image series into ImageJ (http://rsb.info.nih.gov/ij; v.1.47). Determine the average fluorescence intensity in the background images taken with the laser turned off (Analyze &#8594;Histogram). Subtract the appropriate background from the red and green images (Process &#8594;Math &#8594;Subtract).</li>
	<li>Still in ImageJ, divide the green image series (G1) by itself (Process &#8594; Image calculator). Then multiply the resulting image series (G2) with the green image series (G1). This will yield an image series (G3), where NaN is assigned to all pixels belonging to areas that were recognized as objects in daime. Proceed in the same way with the red image series (R1/R1 = R2; R2 x R1 = R3). 
	Note: As the bacterial biomass was removed from the images in step 3.3, the fluorescent intensity is 0 in these areas. Step 3.5 is necessary to convert the value 0 to NaN, which allows for ratio calculation in step 3.6.</li>
	<li>Apply the &#39;Mean&#39; filter (Process &#8594;Filters &#8594;Mean; radius: 1 pixel) to compensate for detector noise. Divide the green image series by the red image series (Process &#8594;Image calculator). This results in a green/red ratio for every remaining pixel in the extracellular space of the images. Use false coloring for graphic representation of the ratios in the images (Image &#8594;Lookup Tables). Calculate the mean ratio for each image (Analyze &#8594;Histogram).</li>
	<li>Convert the green/red ratios to pH values according to the function fitted.</li>
</ol>

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Zeiss LSM 510 META</td>
			<td>Zeiss</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>C-Apochromat 63X water immersion objective</td>
			<td>Zeiss</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>XL Incubator</td>
			<td>PeCON</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>SNARF-4F 5-(and-6)-Carboxylic Acid</td>
			<td>Life Technologies</td>
			<td>S23920</td>
			<td></td>
		</tr>
		<tr>
			<td>Dimethyl sulfoxide</td>
			<td>Life Technologies</td>
			<td>D12345</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>Life Technologies</td>
			<td>11344-041</td>
			<td></td>
		</tr>
		<tr>
			<td>Costar 96-well black clear-bottom plate</td>
			<td>Fisher Scientific</td>
			<td>07-200-567</td>
			<td></td>
		</tr>
		<tr>
			<td>Custom-made glass slabs (4x4x1 mm; 1,200 grit)</td>
			<td>Menzel</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Alginate impression material</td>
			<td>GC Corporation</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Acrylic Adjusting Logic Sets/set of acrylic dental burs</td>
			<td>Axis Dental</td>
			<td>LS-906</td>
			<td></td>
		</tr>
		<tr>
			<td>Orthodontic retainer containers</td>
			<td>Spark Medical Equipment Co., Ltd</td>
			<td>SK-WDTC01</td>
			<td></td>
		</tr>
		<tr>
			<td>Sticky wax</td>
			<td>Dentsply</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Chewing paraffin wax</td>
			<td>Ivoclar Vivadent AG</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Dithiothreitol</td>
			<td>Sigma Aldrich</td>
			<td>D0632</td>
			<td>Used during preparation of salivary solution</td>
		</tr>
		<tr>
			<td>0.45 &#181;m and 0.2 &#181;m syringe filters</td>
			<td>Sigma Aldrich</td>
			<td>CLS431220; CLS431219</td>
			<td></td>
		</tr>
		<tr>
			<td>daime</td>
			<td>University of Vienna, Austria</td>
			<td>http://dome.csb.univie.ac.at/daime</td>
			<td></td>
		</tr>
		<tr>
			<td>ImageJ</td>
			<td>NIH, Bethesda, Maryland, USA</td>
			<td>http://imagej.nih.gov/ij/</td>
			<td></td>
		</tr>
	</tbody>
</table>

an assay for real-time monitoring of extracellular ph in dental biofilms

Source: Schlafer, S., et al. <a href="https://app.jove.com/v/53622">Ratiometric Imaging of Extracellular pH in Dental Biofilms.</a> J. Vis. Exp. (2016)
This video demonstrates a real-time assay for monitoring extracellular pH in dental biofilms using a pH-sensitive ratiometric probe. When an in situ-grown bacterial biofilm is exposed to glucose, a reduction in extracellular pH near the bacterial biomass protonates the probe, leading to its increased concentration inside the bacteria. The disparity in emission wavelength between the protonated and unprotonated probe is utilized to calculate the pH across the extracellular matrix of the biofilm and track pH changes over time.

An Assay for Real-Time Monitoring of Extracellular pH in Dental Biofilms

All procedures involving sample collection have been performed in accordance with the institute&#39;s IRB guidelines.
1. Collection of In Situ Grown ...

Take a multi-well plate containing a neutral pH salivary solution supplemented with glucose.
Add a dual-emission ratiometric, pH-sensitive dye.
Place the plate on a confocal microscope stage.
Introduce a glass slab with an adhered dental biofilm into the well facing down.
Bacteria in the biofilm ferment glucose, generating organic acids and lowering pH in the vicinity.
The acidic pH protonates the dye, causing its internalization and up-concentration within bacteria, staining them, while the deprotonated dye remains extracellular.
Over time, the pH becomes acidic in other areas of the biofilm.
Upon laser excitation, the protonated dye exhibits a shift in fluorescence emission compared to its deprotonated form.
Capture fluorescent images at specified intervals.
Using appropriate software, eliminate bacterial-derived fluorescence signals.
Calculate the ratio of fluorescent emission intensities from the extracellular matrix at two specific wavelengths, correlating to pH values.
Determine the decrease in extracellular biofilm pH following glucose metabolism by bacteria.

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51 Views. Source: Schlafer, S., et al. Ratiometric Imaging of Extracellular pH in Dental Biofilms. J. Vis. Exp. (2016) This video demonstrates a real-time assay for monitoring extracellular pH in dental biofilms using a pH-sensitive ratiometric probe. When an in situ-grown bacterial biofilm is exposed to glucose, a reduction in extracellular pH near the bacterial biomass protonates the probe, leading to its increased concentration inside the bacteria. The disparity in emission wavelength between the prot...

Video: An Assay for Real-Time Monitoring of Extracellular pH in Dental Biofilms - Concept

Visualization of Biofilm Formation in Candida albicans Using an Automated Microfluidic Device

Candida albicans is the most common fungal pathogen of humans, causing about 15% of hospital-acquired sepsis cases. A major virulence attribute of C. albicans is its ability to form biofilms, structured communities of cells attached to biotic and abiotic surfaces. C. albicans biofilms can form on host tissues, such as mucosal layers, and on medical devices, such as catheters, pacemakers, dentures, and joint prostheses. Biofilms pose significant clinical challenges because they are highly resistant to physical and chemical perturbations, and can act as reservoirs to seed disseminated infections. Various in vitro assays have been utilized to study C. albicans biofilm formation, such as microtiter plate assays, dry weight measurements, cell viability assays, and confocal scanning laser microscopy. All of these assays are single end-point assays, where biofilm formation is assessed at a specific time point. Here, we describe a protocol to study biofilm formation in real-time using an automated microfluidic device under laminar flow conditions. This method allows for the observation of biofilm formation as the biofilm develops over time, using customizable conditions that mimic those of the host, such as those encountered in vascular catheters. This protocol can be used to assess the biofilm defects of genetic mutants as well as the inhibitory effects of antimicrobial agents on biofilm development in real-time.

Visualization of Biofilm Formation in Candida albicans Using an Automated Microfluidic Device

This protocol describes the use of a customizable automated microfluidic device to visualize biofilm formation in Candida albicans under host physiological conditions.

Candida albicans is the most common fungal pathogen of humans, causing about 15% of hospital-acquired sepsis cases. A major virulence attribute of C. ...

JoVE Journal

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Real-time Imaging and Quantification of Fungal Biofilm Development Using a Two-Phase Recirculating Flow System

In oropharyngeal candidiasis, members of the genus Candida must adhere to and grow on the oral mucosal surface while under the effects of salivary flow. While models for the growth under flow have been developed, many of these systems are expensive, or do not allow imaging while the cells are under flow. We have developed a novel apparatus that allows us to image the growth and development of Candida albicans cells under flow and in real-time. Here, we detail the protocol for the assembly and use of this flow apparatus, as well as the quantification of data that are generated. We are able to quantify the rates that the cells attach to and detach from the slide, as well as to determine a measure of the biomass on the slide over time. This system is both economical and versatile, working with many types of light microscopes, including inexpensive benchtop microscopes, and is capable of extended imaging times compared to other flow systems. Overall, this is a low-throughput system that can provide highly detailed real-time information on the biofilm growth of fungal species under flow.

We describe the assembly, operation, and cleaning of a flow apparatus designed to image fungal biofilm formation in real time while under flow. We also provide and discuss quantitative algorithms to be used on the acquired images.

In oropharyngeal candidiasis, members of the genus Candida must adhere to and grow on the oral mucosal surface while under the effects of salivary flow. ...

Monitoring Extracellular pH in Cross-Kingdom Biofilms using Confocal Microscopy

Cross-kingdom biofilms consisting of both fungal and bacterial cells are involved in a variety of oral diseases, such as endodontic infections, periodontitis, mucosal infections and, most notably, early childhood caries. In all of these conditions, the pH in the biofilm matrix impacts microbe-host interactions and thus the disease progression. The present protocol describes a confocal microscopy-based method to monitor pH dynamics inside cross-kingdom biofilms comprising Candida albicans and Streptococcus mutans. The pH-dependent dual-emission spectrum and the staining properties of the ratiometric probe C-SNARF-4 are exploited to determine drops in pH in extracellular areas of the biofilms. Use of pH ratiometry with the probe requires a meticulous choice of imaging parameters, a thorough calibration of the dye, and careful, threshold-based post-processing of the image data. When used correctly, the technique allows for the rapid assessment of extracellular pH in different areas of a biofilm and thus the monitoring of both horizontal and vertical pH gradients over time. While the use of confocal microscopy limits Z-profiling to thin biofilms of 75 &#181;m or less, the use of pH ratiometry is ideally suited for the noninvasive study of an important virulence factor in cross-kingdom biofilms.

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.

An Assay for Real-Time Monitoring of Extracellular pH in Dental Biofilms

Transcript

An Assay for Real-Time Monitoring of Extracellular pH in Dental Biofilms

Visualization of Biofilm Formation in Candida albicans Using an Automated Microfluidic Device

Real-time Imaging and Quantification of Fungal Biofilm Development Using a Two-Phase Recirculating Flow System

Monitoring Extracellular pH in Cross-Kingdom Biofilms using Confocal Microscopy