This study was supported in part by a grant-in-aid for scientific research from the Ministry of Education, Culture, Sports, and Technology of Japan (18K04843) to Y. Yawata, the JST ERATO (JPMJER1502) to N. Nomura.

1. Preparation of the sample
<ol>
	<li>Place a 1 mm thick silicone gasket with wells on a glass slide.</li>
	<li>Place a 1 mm thick 0.8% (w/v) agarose slab in the well of the silicone gasket.</li>
	<li>Dilute the cell density of an arbitrary microbial cell culture to an optical density at 600 nm (OD660) = 1.0.</li>
	<li>Place a 5 &#181;L aliquot of cell suspension on the agarose slab.</li>
	<li>Cover gently with a glass coverslip.</li>
</ol>
2. Setup of a microscope
<p class="jove_c...

<ol>
	<li>Monici, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cell+and+tissue+autofluorescence+research+and+diagnostic+applications.">Cell and tissue autofluorescence research and diagnostic applications.</a> Biotechnology Annual Review. 11, 227-256 (2005).</li><li>Tang, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microbial+metabolomics.">Microbial metabolomics.</a> Current Genomics. 12, 391-403 (2011).</li><li>Woo, P. C., Lau, S. K., Teng, J. L., Tse, H., Yuen, K. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Then+and+now:+use+of+16S+rDNA+gene+sequencing+for+bacterial+identification+and+discovery+of+novel+bacteria+in+clinical+microbiology+laboratories.">Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories.</a> Clinical Microbiology and Infection. 14, 908-934 (2008).</li><li>Amman, R., Fuchs, B. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-cell+identification+in+microbial+communities+by+improved+fluorescence+in+situ+hybridization+techniques.">Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques.</a> Nature Reviews Microbiology. 6, 339-348 (2008).</li><li>Giana, H. E., Silveira, L., Z&#226;ngaro, R. A., Pacheco, M. T. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+identification+of+bacterial+species+by+fluorescence+spectroscopy+and+classification+through+principal+components+analysis.">Rapid identification of bacterial species by fluorescence spectroscopy and classification through principal components analysis.</a> Journal of Fluorescence. 13 (6), 489-493 (2003).</li><li>Leblanc, L., Dufour, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Monitoring+the+identity+of+bacteria+using+their+intrinsic+fluorescence.">Monitoring the identity of bacteria using their intrinsic fluorescence.</a> FEMS Microbiology Letters. 211 (2), 147-153 (2002).</li><li>Hou, X., Liu, S., Feng, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+autofluorescence+characteristics+of+bacterial+intracellular+and+extracellular+substances+during+the+operation+of+anammox+reactor.">The autofluorescence characteristics of bacterial intracellular and extracellular substances during the operation of anammox reactor.</a> Scientific Reports. 7, 39289 (2017).</li><li>Ramanujam, 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=In+vivo+diagnosis+of+cervical+intraepithelial+neoplasia+using+337-nm-excited+laser-induced+fluorescence.">In vivo diagnosis of cervical intraepithelial neoplasia using 337-nm-excited laser-induced fluorescence.</a> Proceeding National Academy of Sciences of the United States of America. 91 (21), 10193-10197 (1994).</li><li>Zhang, J. 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=Innate+cellular+fluorescence+reflects+alterations+in+cellular+proliferation.">Innate cellular fluorescence reflects alterations in cellular proliferation.</a> Lasers in Surgery and Medicine. 20 (3), 319-331 (1997).</li><li>Gosnell, M. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+non-invasive+cell+characterisation+and+discrimination+based+on+multispectral+autofluorescence+features.">Quantitative non-invasive cell characterisation and discrimination based on multispectral autofluorescence features.</a> Scientific Reports. 6, 23453 (2016).</li><li>Yawata, Y., 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=Intra-+and+interspecies+variability+of+single-cell+innate+fluorescence+signature+of+microbial+cell.">Intra- and interspecies variability of single-cell innate fluorescence signature of microbial cell.</a> Applied and Environmental Microbiology. 85, 00608-00619 (2019).</li><li>Nelson, K. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Complete+genome+sequence+and+comparative+analysis+of+the+metabolically+versatile+Pseudomonas+putida+KT2440.">Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440.</a> Environmental Microbiology. 4 (12), 799-808 (2002).</li><li>Bagdasarian, 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=Specific-purpose+plasmid+cloning+vectors.+II.+Broad+host+range,+high+copy+number,+RSF1010-derived+vectors,+and+a+host-vector+system+for+gene+cloning+in+Pseudomonas.">Specific-purpose plasmid cloning vectors. II. Broad host range, high copy number, RSF1010-derived vectors, and a host-vector system for gene cloning in Pseudomonas.</a> Gene. 16 (1-3), 237-247 (1981).</li><li>Luo, Y., Vijaychander, S., Stile, J., Zhu, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cloning+and+analysis+of+DNA-binding+proteins+by+yeast+one-hybrid+and+one-two-hybrid+systems.">Cloning and analysis of DNA-binding proteins by yeast one-hybrid and one-two-hybrid systems.</a> Biotechniques. 20 (4), 564-568 (1996).</li><li>Yawata, Y., 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=Monitoring+biofilm+development+in+a+microfluidic+device+using+modified+confocal+reflection+microscopy.">Monitoring biofilm development in a microfluidic device using modified confocal reflection microscopy.</a> Journal of Bioscience and Bioengineering. 110 (3), 377-380 (2010).</li><li>Lakowicz, J. 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The authors have nothing to disclose.

There are two critical points in this method that need to be closely followed to obtain reproducible results: 1) keep the laser power output under the microscope objective consistent through excitation wavelengths and experiments, and 2) perform accurate cell segmentation.
The first point is particularly important when comparing the innate fluorescence signature among different experiments. Avoid simply applying the same &#8220;percent output&#8221; settings to the excitation wavelengths (i.e....

Diverse biomolecules within a cell1 emit autofluorescence signals, and the innate fluorescence signature of a cell consists of the assembly of these signals. This signature fluorescence reflects various cellular properties and also differences in physiological status. Analysis of innate fluorescence is minimally invasive and can complement traditional, more invasive microbiological probes that leave a range of traces from mild metabolic modification to complete cell destruction. While traditional techniques such as DNA or cell content extraction2,3, fluorescent in situ hybridization4, and the introduction of fluorescent reporter genes to the genome are effective in determining cell type or physiological status, they commonly require either manipulation of the cells or invasive tagging.
Studies of the innate fluorescence of various live and intact microbial colonies, including bulk microbial culture suspensions5,6, active sludges7, mammalian tissues8,9, and mammalian cells1,10, have shown that innate fluorescence analysis facilitates tag-free analysis of cell types and physiological status. Innate fluorescence signatures have been traditionally analyzed at the population level and not at the single-cell level, and thus necessitate a clonal culture. In contrast, the confocal reflection microscopy-assisted single-cell innate fluorescence analysis (CRIF) technique11 described here reconstructs and catalogues the innate cellular fluorescence signature of each individual live microbial cell. Moreover, CRIF can systematically collate the innate fluorescence signature of a single microbial cell within a population that is distributed in a three-dimensional (3D) space.

<table border="0" cellpadding="0" cellspacing="0" style="width:720px;" width="720">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:215px;">Agarose</td>
			<td style="width:220px;">Wako Chemicals</td>
			<td style="width:119px;">312-01193</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="105">
			<td height="105" style="height:105px;width:215px;">Beam splitters</td>
			<td style="width:220px;">Carl Zeiss, Nikon</td>
			<td style="width:119px;"></td>
			<td style="width:167px;">MBSInVis405, MBS458, MBS488, MBS458/514, MBS488/543, or MBS 488/543/633 beam splitters (Carl Zeiss)</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:215px;">Confocal microscope</td>
			<td style="width:220px;">Carl Zeiss, Nikon</td>
			<td style="width:119px;"></td>
			<td style="width:167px;">Model LSM 880 (Carl Zeiss), Model A1R (Nikon)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:215px;">Cover slips</td>
			<td style="width:220px;">Matsunami Glass</td>
			<td style="width:119px;">C024601</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:215px;">Glass slides</td>
			<td style="width:220px;">Matsunami Glass</td>
			<td style="width:119px;">S011120</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:215px;">Half-reflection mirror</td>
			<td style="width:220px;">Carl Zeiss, Nikon</td>
			<td style="width:119px;"></td>
			<td style="width:167px;">NT80/20</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:215px;">Laser power meter</td>
			<td style="width:220px;">Thorlabs</td>
			<td style="width:119px;"></td>
			<td style="width:167px;">PM400 (power meter console) and S175C (sensor)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:215px;">LB Broth</td>
			<td style="width:220px;">Nacalai tesque</td>
			<td style="width:119px;">20066-95</td>
			<td>For bacteria culture</td>
		</tr>
		<tr height="84">
			<td height="84" style="height:84px;width:215px;">Image analysis software</td>
			<td style="width:220px;">The MathWorks</td>
			<td style="width:119px;"></td>
			<td style="width:167px;">MATLAB version 2019a or later, Image Processing Toolbox is needed</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:215px;">Microscope objective</td>
			<td style="width:220px;">Carl Zeiss, Nikon</td>
			<td style="width:119px;">440762-9904</td>
			<td style="width:167px;">e.g. 63x plan Apochomat NA = 1.4 (Carl Zeiss)</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:215px;">Microscope software</td>
			<td style="width:220px;">Carl Zeiss, Nikon</td>
			<td style="width:119px;"></td>
			<td style="width:167px;">ZEN (Carl Zeiss),NIS-elements (Nikon)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:215px;">PBS(-)</td>
			<td style="width:220px;">Wako Chemicals</td>
			<td style="width:119px;">166-23555</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="147">
			<td height="147" style="height:147px;width:215px;">Programming language</td>
			<td style="width:220px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">Python and libraries, modules (numpy, scikit-learn, scikit-image, os, glob, matplotlib, tkinter) are rquired to run the supplied PCA script.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:215px;">Silicone gasket</td>
			<td style="width:220px;">ThermoFisher Scientific</td>
			<td style="width:119px;">P24744</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="84">
			<td height="84" style="height:84px;width:215px;">Workstation</td>
			<td style="width:220px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">A high-performance workstation with discrete GPUs is recommended.</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:215px;">Yeast extract-peptone-dextrose (YPD) agar medium</td>
			<td style="width:220px;">Sigma-Aldrich</td>
			<td style="width:119px;">Y1500-250G</td>
			<td>For yeast culture</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:215px;">YPD medium</td>
			<td style="width:220px;">Sigma-Aldrich</td>
			<td style="width:119px;">Y1375-250G</td>
			<td></td>
		</tr>
	</tbody>
</table>

reconstruction of single-cell innate fluorescence signatures by confocal microscopy

Described here is confocal reflection microscopy-assisted single-cell innate fluorescence analysis (CRIF), a minimally invasive method for reconstructing the innate cellular fluorescence signature from each individual live cell in a population distributed in a three-dimensional (3D) space. The innate fluorescence signature of a cell is a collection of fluorescence signals emitted by various biomolecules within the cell. Previous studies established that innate fluorescence signatures reflect various cellular properties and differences in physiological status and are a rich source of information for cell characterization and identification. Innate fluorescence signatures have been traditionally analyzed at the population level, necessitating a clonal culture, but not at the single-cell level. CRIF is particularly suitable for studies that require 3D resolution and/or selective extraction of fluorescence signals from individual cells. Because the fluorescence signature is an innate property of a cell, CRIF is also suitable for tag-free prediction of the type and/or physiological status of intact and single cells. This method may be a powerful tool for streamlined cell analysis, where the phenotype of each single cell in a heterogenous population can be directly assessed by its autofluorescence signature under a microscope without cell tagging.

Figure 1A shows the typical single-cell fluorescence signature of a bacterial cell presented as a traditional spectrum plot (top) and as a heatmap (middle). Figure 1B shows the result of an accurate 2D cell segmentation superimposed over the original CRM image of a population of soil bacteria (Pseudomonas putida KT2440)12. The resulting innate fluorescence signatures for the population are presented as a heatmap in <strong class=...

Watch this Scientific Journal Video about Reconstruction of Single-Cell Innate Fluorescence Signatures by Confocal Microscopy at JoVE.com

Reconstruction of Single-Cell Innate Fluorescence Signatures by Confocal Microscopy

Here, a protocol is presented for optically extracting and cataloging innate cellular fluorescence signatures (i.e., cellular autofluorescence) from every individual live cell distributed in a three-dimensional space. This method is suitable for studying the innate fluorescence signature of diverse biological systems at a single-cell resolution, including cells from bacteria, fungi, yeasts, plants, and animals.

Described here is confocal reflection microscopy-assisted single-cell innate fluorescence analysis (CRIF), a minimally invasive method for reconstructing ...

This technique offers a unique research to for proving your cell's identity or physiological characteristics at the single-cell level without the need for invasive tagging. The main advantages of this technique are that it facilitates single-cell level spatial resolution for your analysis, and that it allows the distinction between and background process. So this technique can potentially contribute to the identification and the phenotypic analysis of pathogenic microbes.This technique can also be applied to the study of the phenotypic heterogeneity, or the monitoring of the physiological status of microbial population of interests. Demonstrating the procedure will be Kyosuke Takabe, an assistant professor from my laboratory. The confocal reflection microscopy and multichannel confocal microspectroscopy setup.Connect the confocal microscope with descanned spectral channels to a photomultiplier tube. Equip the microscope with a high numerical aperture objective, with an adequate magnification. And equip the microscope with a half-reflection mirror to accommodate confocal reflection microscopy, which relies on the cellular scatter of incident light to visualize cell morphology.For multichannel confocal microspectroscopy, equip the microscope with dichroic mirrors and use a laser power meter to adjust the illumination intensity for each excitation wavelength. Then set the output under the microscope to be constant through the excitation wavelengths. To image the bacteria through the microscope, set the pinhole size to 1.0 area unit in the microscope software and set the pixel dwell time for each excitation wavelength.Set the scanning resolution. For small cells such as bacteria, use a scanning area of 1024 by 1024. Set the Z-Scanning range so that the region of interest is covered.And using a spectral window of eight to 10 nanometers, set the D-Scan detector to capture the visible wavelength range. Then acquire multichannel confocal microspectroscopy images in a sequence from longest to shortest excitation wavelengths to create Z-Stacks of fluorescence images and confocal reflection microscopy images, and save the images in 16-bit tiff format. To perform cell segmentation and the reconstruction of single cell innate fluorescent signatures, open an appropriate image analysis software program and double click to open one of the provided scripts.Under the editor tab, click run. A folder selection window will appear. Select the directory in which the Z-Stack images were saved and click open.A dialogue box prompting the input of the segmentation parameter will automatically appear. Set the threshold of image binarization to 0-1, the image binarization to 0.45, the upper threshold for a cell region to 200, the lower threshold for a cell region to 10, and the number of detectors to 32. A dialogue box requesting input for the number of excitation wavelengths will appear.Input the number of wavelengths used for the image acquisition and click okay. A dialogue box that is requesting input for the excitation wavelengths will appear. Enter the excitation wavelengths in sequence from shortest to longest and click okay.A new image window presenting a confocal reflection microscopy image will appear. Select an arbitrary background region to use for the background subtraction and draw a rectangle within the confocal reflection microscopy image. Double click within the selected region to confirm the selection and locate a new directory named, signature.To perform dimensional reduction techniques, create an empty directory and name the directory, parent_directory. Store the fluorescent signatures of each of the two cell populations into two separate directories and open the command line interface of the workstation. Enter the command.When select target directory is displayed, select the parent_directory. Then in the parent_directory folder, locate the PCA. png file, which will contain the resulting principle component analysis plot.Here, a typical single cell fluorescent signature of a bacterial cell presented as a traditional spectrum plot and as a heat map is shown. In this figure, inaccurate 2D cell segmentation superimposed over the original confocal reflection microscopy image of a population of soil bacteria can be observed. With the resulting innate fluorescent signatures for the population presented as a heat map.Note that the intra population variability was relatively minor following successful cell segmentation. Here, an example of inaccurate cell segmentation is shown super imposed onto the same population of P.putida as previously shown. The impact of the inaccurate cell segmentation on the innate fluorescent signatures of the population is readily apparent from the considerable number of outliers observed in the corresponding heat map.Inaccurate cell segmentation results in a looser cluster after principle component analysis, compared to the type cluster obtained following accurate cell segmentation. Despite the minor variabilities of innate fluorescent signature observed within individual bacterial strains, each population forms a distinct cluster on the principle component analysis plot. In this figure, inaccurate 3D cell segmentation superimposed over the original confocal reflection microscopy image of a population of budding yeast Saccharomyces cerevisiae YM4271, can be observed.Note the lack of outliers and the resulting innate fluorescent signatures for the population. It is essential to acquire as clean as possible, an image by confocal microscopy and to avoid a signal intensity saturation as noise can spoil accuracy of subsequent analysis. You can train machine learning models with the innate Western signature dataset for use in classification or prediction tasks, offering a tag-free population analysis and phenotypic prediction.

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2.6K Views.  University of Tsukuba. This technique offers a unique research to for proving your cell's identity or physiological characteristics at the single-cell level without the need for invasive tagging. The main advantages of this technique are that it facilitates single-cell level spatial resolution for your analysis, and that it allows the distinction between and background process. So this technique can potentially contribute to the identification and the phenotypic analysis of pathogenic microbes.This technique...