Name: a simple and rapid protocol for measuring neutral lipids in algal cells using fluorescence
Uploaded: 2014-05-30T15:00:00
Description: Watch this Scientific Journal Video about A Simple and Rapid Protocol for Measuring Neutral Lipids in Algal Cells Using Fluorescence at JoVE.com

The authors would like to thank the Natural Sciences and Engineering Research Council of Canada for providing financial support for this project.

1. Isolation of Dry Algal Biomass to be Used as Standards for Fluorescence Readings
<ol>
	<li>Remove a sample volume from the growing algal culture that will provide at least 200 mg of dry biomass, 400-600 mg is preferable.</li>
	<li>Centrifuge sample at 4 &#176;C for 10 min at 10,000 x g. Discard the supernatant and wash the pellet with an equal volume of phosphate buffer formulated to the same pH as the growth media.</li>
	<li>Repeat step 1.2 for a total of 3 washing steps.</li>
	<li>Re-suspend the pellet in de-ioniz...

<ol>
	<li>Chisti, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biodiesel+from+microalgae.">Biodiesel from microalgae.</a> Biotechnol. Adv. 25, 294-306 (2007).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=National+Algal+Biofuels+Technology+Roadmap.+Energy+Efficiency+&amp;+Renewable+Energy.">National Algal Biofuels Technology Roadmap. Energy Efficiency &amp; Renewable Energy.</a> U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Biomass Program. , (2010).</li><li>de la Hoz Siegler, H., 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=Optimization+of+microalgal+productivity+using+an+adaptive,+non-linear+model+based+strategy.">Optimization of microalgal productivity using an adaptive, non-linear model based strategy.</a> Bioresour. Technol. 104, 537-546 (2012).</li><li>Bligh, E. G., Dyer, W. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Rapid+method+of+total+lipid+extraction+and+purification.">A Rapid method of total lipid extraction and purification.</a> Can. J. Biochem. Physiol. 37, 911-917 (1959).</li><li>Hara, A., Radin, N. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lipid+extraction+of+tissues+with+a+low-toxicity+solvent.">Lipid extraction of tissues with a low-toxicity solvent.</a> Anal. Biochem. 90, 420-426 (1978).</li><li>Han, 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=Review+of+methods+used+for+microalgal+lipid-content+analysis.">Review of methods used for microalgal lipid-content analysis.</a> Energ. Procedia. 12, 944-950 (2011).</li><li>Pino, E. 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=Biochemical+and+high+throughput+microscopic+assessment+of+fat+mass+in+Caenorhabditis+elegans.">Biochemical and high throughput microscopic assessment of fat mass in Caenorhabditis elegans.</a> J. Vis. Exp. (73), (2013).</li><li>Sitepu, I. 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=An+improved+high-throughput+Nile+red+fluorescence+assay+for+estimating+intracellular+lipids+in+a+variety+of+yeast+species.">An improved high-throughput Nile red fluorescence assay for estimating intracellular lipids in a variety of yeast species.</a> J. Microbiol. Meth. 91, 321-328 (2012).</li><li>Izard, J., Limberger, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+screening+method+for+quantitation+of+bacterial+cell+lipids+from+whole+cells.">Rapid screening method for quantitation of bacterial cell lipids from whole cells.</a> J. Microbiol. Meth. 55, 411-418 (2003).</li><li>Chen, 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=A+high+throughput+Nile+red+method+for+quantitative+measurement+of+neutral+lipids+in+microalgae.">A high throughput Nile red method for quantitative measurement of neutral lipids in microalgae.</a> J. Microbiol. Meth. 77, 41-47 (2009).</li><li>de la Hoz Siegler, H., 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=Improving+the+reliability+of+fluorescence-based+neutral+lipid+content+measurements+in+microalgal+cultures.">Improving the reliability of fluorescence-based neutral lipid content measurements in microalgal cultures.</a> Algal Res. 1, 176-184 (2012).</li><li>de la Jara, A., 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=Flow+cytometric+determination+of+lipid+content+in+a+marine+dinoflagellate,+Crypthecodinium+cohnii.">Flow cytometric determination of lipid content in a marine dinoflagellate, Crypthecodinium cohnii.</a> J. Appl. Phycol. 15, 433-438 (2003).</li><li>Elsey, 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=Fluorescent+measurement+of+microalgal+neutral+lipids.">Fluorescent measurement of microalgal neutral lipids.</a> J. Microbiol. Meth. 68, 639-642 (2007).</li><li>Feng, G. -. 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=Evaluation+of+FT-IR+and+Nile+Red+methods+for+microalgal+lipid+characterization+and+biomass+composition+determination.">Evaluation of FT-IR and Nile Red methods for microalgal lipid characterization and biomass composition determination.</a> Bioresour. Technol. 128, 107-112 (2013).</li><li>Guzm&#225;n, H., 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=Estimate+by+means+of+flow+cytometry+of+variation+in+composition+of+fatty+acids+from+Tetraselmis+suecica+in+response+to+culture+conditions.">Estimate by means of flow cytometry of variation in composition of fatty acids from Tetraselmis suecica in response to culture conditions.</a> Aquacult. Int. 18, 189-199 (2010).</li><li>Huang, G. -. H., 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=Rapid+screening+method+for+lipid+production+in+alga+based+on+Nile+red+fluorescence.">Rapid screening method for lipid production in alga based on Nile red fluorescence.</a> Biomass Bioenerg. 33, 1386-1392 (2009).</li><li>Lee, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+method+for+the+determination+of+lipid+from+the+green+alga+Botryococcus+braunii.">Rapid method for the determination of lipid from the green alga Botryococcus braunii.</a> Biotechnol. Tech. 12, 553-556 (1998).</li><li>Montero, 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=Isolation+of+high-lipid+content+strains+of+the+marine+microalga+Tetraselmis+suecica+for+biodiesel+production+by+flow+cytometry+and+single-cell+sorting.">Isolation of high-lipid content strains of the marine microalga Tetraselmis suecica for biodiesel production by flow cytometry and single-cell sorting.</a> J. Appl. Phycol. 23, 1053-1057 (2011).</li><li>Vigeolas, H., 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+and+partial+characterization+of+mutants+with+elevated+lipid+content+in+Chlorella+sorokiniana+and+Scenedesmus+obliquus.">Isolation and partial characterization of mutants with elevated lipid content in Chlorella sorokiniana and Scenedesmus obliquus.</a> J. Biotechnol. 162, 3-12 (2012).</li><li>Bertozzini, 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=Application+of+the+standard+addition+method+for+the+absolute+quantification+of+neutral+lipids+in+microalgae+using+Nile+red.">Application of the standard addition method for the absolute quantification of neutral lipids in microalgae using Nile red.</a> J. Microbiol. Meth. 87, 17-23 (2011).</li><li>Kou, Z., 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=Fluorescent+measurement+of+lipid+content+in+the+model+organism+Chlamydomonas+reinhardtii.">Fluorescent measurement of lipid content in the model organism Chlamydomonas reinhardtii.</a> J. Appl. Phycol. , 1-9 (2013).</li></ol>

The algae used in the standard curve must be the same species cultivated under the same experimental conditions as those being measured. Significant changes in media composition, cultivation technique, and staining protocol can affect the intensity of the fluorescence reading. Hexane extraction (described in sections 1 and 2) was used to determine the neutral lipid content of samples used in the standard curve. For accurate fluorescence intensity measurements, all samples must be analyzed at the same biomass concentratio...

Due to their ability to store lipid bodies under certain stress conditions, algae have received a great deal of attention in recent years as a potential renewable fuel source1,2. Neutral lipids can account for over 60% of the cell dry weight under appropriate growth conditions3. Yet the industry does not have a simple, clean, rapid, and reliable standardized protocol to quantitate lipid content of algal cells in order to properly monitor bioprocess performance, analyze cultures, and screen for new strains.
The Bligh-Dyer gravimetric method developed some 50 years ago remains among the most common techniques used today4,5. While this procedure is simple, reliable, and easy to carry out, it is time-consuming, necessitates large sample volumes, and makes use of toxic solvents. It is not practical for analyzing many samples from a fermentation run or screening for new oil-rich strains. Other methods have been developed, but usually require advanced equipment and have not been standardized6.
An alternative that has garnered a great deal of interest is the Nile Red stain. Nile Red, a dye that fluoresces preferentially in non-polar environments, has been used to identify or quantify lipid bodies in various organisms including nematodes7, yeast8, bacteria9, and algae10-19. Initial techniques involving Nile Red were mostly qualitative or semi-quantitative, combining the stain with single-cuvette spectrophotometry or flow cytometry. In addition, some classes of algae such as green algae have thick cell wells that are mostly impermeable to the dye, which limited the range of the technique10.
Recent improvements to the Nile Red staining method have been reported that bypass the initial shortcomings of the protocol10,11. Staining the cells in the presence of a carrier solvent such as DMSO10 or ethanol10,11 linearizes the relationship between oil content and absorbance, allowing for reliable quantitative measurements. The solvent helps permeabilize the cell membrane so that the Nile Red molecules can pass through. In addition, incorporating a spectrophotometer with micro-plate reading capabilities enables high throughput protocols suitable for quantitative analysis.
In this article we detail a simple method for measuring oil content of algal cells by staining cultures with Nile Red in the presence of ethanol, a mild solvent. In order to most accurately account for background noise in the measurements, a standard curve correlating fluorescence intensity to oil content is developed using algal cells of known oil composition. The method is adapted from previously published protocols10,11. By using a 96-well spectrophotometer, one is able to analyze the same amount of samples in an hour that would take days to monitor by gravimetric methods. Furthermore, by calibrating using representative samples of the desired algal species this method produces relatively precise measurements that are directly interpretable. There exist many protocols outlining methods of staining algae with Nile Red optimized for different strains and applications; the protocol presented here was originally developed by de la Hoz Siegler et al.11 for Auxenochlorella protothecoides, Chlorella vulgaris, Scenedesmus dimorphus, and Scenedesmus obliquus, although it is likely suitable for many more species and classes. It has been designed with the specific application of monitoring bioprocess performance and it works equally well for previously dried samples and wet samples from a growing culture.

<table border="0" cellpadding="0" cellspacing="0" width="817">
	<colgroup>
		<col />
		<col span="2" />
		<col />
	</colgroup>
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">Dry Weight</td>
			<td style="width:152px;"></td>
			<td style="width:152px;"></td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">25 ml disposable pipettes</td>
			<td style="width:152px;">Fisher</td>
			<td style="width:152px;">13-676-10K</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">Pipette Bulb</td>
			<td style="width:152px;">Fisher</td>
			<td style="width:152px;">13-681-51</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">40 ml Nalgene Teflon Centrifuge Tubes</td>
			<td style="width:152px;">Fisher</td>
			<td style="width:152px;">05-562-16A</td>
			<td>Teflon needed for hexane</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">Weigh Dishes (polypropylene)</td>
			<td style="width:152px;">Fisher</td>
			<td style="width:152px;">2-202B</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">1.5 ml micro-centrifuge tubes</td>
			<td style="width:152px;">Fisher</td>
			<td style="width:152px;">05-408-129</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">Centrifuge</td>
			<td style="width:152px;">Sorvall</td>
			<td style="width:152px;">RC6plus</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">Drying Oven (Fisher 625D)</td>
			<td style="width:152px;">Fisher</td>
			<td style="width:152px;">13-254-2</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">Storage vials</td>
			<td style="width:152px;">Fisher</td>
			<td style="width:152px;">0337-4</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">Bench-top microcentrifuge (Eppendorf 5415D)</td>
			<td style="width:152px;">Fisher</td>
			<td style="width:152px;">05-40-100</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;"></td>
			<td style="width:152px;"></td>
			<td style="width:152px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">Gravimetric Quantification</td>
			<td style="width:152px;"></td>
			<td style="width:152px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">Porcelain Mortar (Coorstek)</td>
			<td style="width:152px;">Fisher</td>
			<td style="width:152px;">12-961A</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">Porcelain Pestle (Coorstek)</td>
			<td style="width:152px;">Fisher</td>
			<td style="width:152px;">12-961-5A</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">40 ml Centrifugation tubes (FEP)</td>
			<td style="width:152px;">Fisher</td>
			<td style="width:152px;">05-562-16A</td>
			<td>Could also use glass tubes</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">Pasteur Glass Pipettes</td>
			<td style="width:152px;">Fisher</td>
			<td style="width:152px;">13-678-20C</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">Aluminum weigh dishes</td>
			<td style="width:152px;">Fisher</td>
			<td style="width:152px;">08-732-101</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">Hexanes</td>
			<td style="width:152px;">Fisher</td>
			<td style="width:152px;">H292-4</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;"></td>
			<td style="width:152px;"></td>
			<td style="width:152px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;"></td>
			<td style="width:152px;"></td>
			<td style="width:152px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;"></td>
			<td style="width:152px;"></td>
			<td style="width:152px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;"></td>
			<td style="width:152px;"></td>
			<td style="width:152px;"></td>
			<td></td>
		</tr>
		<tr height="18">
			<td height="18" style="height:18px;width:347px;">Fluorometric quantification of oil content</td>
			<td style="width:152px;"></td>
			<td style="width:152px;"></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:347px;">Fluorescence multi-well plate reader</td>
			<td style="width:152px;">Thermo Lab Systems</td>
			<td style="width:152px;">Fluoroskan Ascent</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">Fluorescence reader software</td>
			<td style="width:152px;">Thermo Lab Systems</td>
			<td style="width:152px;">Ascent Software 2.6</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">COSTAR 96 well plate with round bottom</td>
			<td style="width:152px;">Fisher</td>
			<td style="width:152px;">06-443-2</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">Nile Red&#160;</td>
			<td style="width:152px;">Sigma</td>
			<td style="width:152px;">N3013-100MG</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">Ethanol (Alcohol reagent grade)</td>
			<td style="width:152px;">Fisher</td>
			<td style="width:152px;">AC65109-0020</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;"></td>
			<td style="width:152px;"></td>
			<td style="width:152px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;"></td>
			<td style="width:152px;"></td>
			<td style="width:152px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">Imaging Fluorescent cells</td>
			<td style="width:152px;"></td>
			<td style="width:152px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">Leica DMRXA2 (or equivalent) microscope</td>
			<td style="width:152px;">Leica</td>
			<td style="width:152px;">DMRXA2</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">Microscope slides</td>
			<td style="width:152px;">Fisher</td>
			<td style="width:152px;">12-550-15</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">Microscope cover slips</td>
			<td style="width:152px;">Fisher</td>
			<td style="width:152px;">12-541B</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">Camera</td>
			<td style="width:152px;">Qimaging</td>
			<td style="width:152px;">Retiga Ex</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:347px;">Imaging software</td>
			<td style="width:152px;">Qimaging</td>
			<td style="width:152px;">QCapture v.1.1.8</td>
			<td></td>
		</tr>
	</tbody>
</table>

a simple and rapid protocol for measuring neutral lipids in algal cells using fluorescence

Algae are considered excellent candidates for renewable fuel sources due to their natural lipid storage capabilities. Robust monitoring of algal fermentation processes and screening for new oil-rich strains requires a fast and reliable protocol for determination of intracellular lipid content. Current practices rely largely on gravimetric methods to determine oil content, techniques developed decades ago that are time consuming and require large sample volumes. In this paper, Nile Red, a fluorescent dye that has been used to identify the presence of lipid bodies in numerous types of organisms, is incorporated into a simple, fast, and reliable protocol for measuring the neutral lipid content of Auxenochlorella protothecoides, a green alga. The method uses ethanol, a relatively mild solvent, to permeabilize the cell membrane before staining and a 96 well micro-plate to increase sample capacity during fluorescence intensity measurements. It has been designed with the specific application of monitoring bioprocess performance. Previously dried samples or live samples from a growing culture can be used in the assay.

Representative algal cells stained with Nile Red dye are depicted in Figure 1. Parts A and B of Figure 1 display images of A. protothecoides grown in excess nitrogen, leading to very low intracellular lipid accumulation. In parts C and D, samples of A. protothecoides grown under nitrogen limitation are shown. Under transmission illumination, the lipid bodies of the cell can be visualized with careful in...

Watch this Scientific Journal Video about A Simple and Rapid Protocol for Measuring Neutral Lipids in Algal Cells Using Fluorescence at JoVE.com

A Simple and Rapid Protocol for Measuring Neutral Lipids in Algal Cells Using Fluorescence

A simple protocol to determine the neutral lipid content of algal cells using a Nile Red staining procedure is described. This time-saving technique offers an alternative to traditional gravimetric-based lipid quantification protocols. It has been designed for the specific application of monitoring bioprocess performance.

Algae are considered excellent candidates for renewable fuel sources due to their natural lipid storage capabilities. Robust monitoring of algal ...

a-simple-rapid-protocol-for-measuring-neutral-lipids-algal-cells

Research

JoVE Journal

Chemistry

Untargeted Metabolomics from Biological Sources Using Ultraperformance Liquid Chromatography-High Resolution Mass Spectrometry (UPLC-HRMS)

Here we present a workflow to analyze the metabolic profiles for biological samples of interest including; cells, serum, or tissue. The sample is first separated into polar and non-polar fractions by a liquid-liquid phase extraction, and partially purified to facilitate downstream analysis. Both aqueous (polar metabolites) and organic (non-polar metabolites) phases of the initial extraction are processed to survey a broad range of metabolites. Metabolites are separated by different liquid chromatography methods based upon their partition properties. In this method, we present microflow ultra-performance (UP)LC methods, but the protocol is scalable to higher flows and lower pressures. Introduction into the mass spectrometer can be through either general or compound optimized source conditions. Detection of a broad range of ions is carried out in full scan mode in both positive and negative mode over a broad m/z range using high resolution on a recently calibrated instrument. Label-free differential analysis is carried out on bioinformatics platforms. Applications of this approach include metabolic pathway screening, biomarker discovery, and drug development.

Untargeted Metabolomics from Biological Sources Using Ultraperformance Liquid Chromatography-High Resolution Mass Spectrometry UPLC-HRMS

Untargeted metabolomics provides a hypothesis generating snapshot of a metabolic profile. This protocol will demonstrate the extraction and analysis of metabolites from cells, serum, or tissue. A range of metabolites are surveyed using liquid-liquid phase extraction, microflow ultraperformance liquid chromatography/high-resolution mass spectrometry (UPLC-HRMS) coupled to differential analysis software.

Here we present a workflow to analyze the metabolic profiles for biological samples of interest including; cells, serum, or tissue. The sample is first ...

Preparing Adherent Cells for X-ray Fluorescence Imaging by Chemical Fixation

X-ray fluorescence imaging allows us to non-destructively measure the spatial distribution and concentration of multiple elements simultaneously over large or small sample areas. It has been applied in many areas of science, including materials science, geoscience, studying works of cultural heritage, and in chemical biology. In the case of chemical biology, for example, visualizing the metal distributions within cells allows us to study both naturally-occurring metal ions in the cells, as well as exogenously-introduced metals such as drugs and nanoparticles. Due to the fully hydrated nature of nearly all biological samples, cryo-fixation followed by imaging under cryogenic temperature represents the ideal imaging modality currently available. However, under the circumstances that such a combination is not easily accessible or practical, aldehyde based chemical fixation remains useful and sometimes inevitable. This article describes in as much detail as possible in the preparation of adherent mammalian cells by chemical fixation for X-ray fluorescent imaging.

Here, we present a protocol on how to determine the quantity and distribution of metals in a sample using synchrotron X-ray fluorescence. We focus on adherent cells, and describe the chemical fixation method to prepare this sample. We then describe how to mount and image the sample using synchrotron X-rays.

X-ray fluorescence imaging allows us to non-destructively measure the spatial distribution and concentration of multiple elements simultaneously over ...

Rapid High-throughput Species Identification of Botanical Material Using Direct Analysis in Real Time High Resolution Mass Spectrometry

We demonstrate that direct analysis in real time-high resolution mass spectrometry can be used to produce mass spectral profiles of botanical material, and that these chemical fingerprints can be used for plant species identification. The mass spectral data can be acquired rapidly and in a high throughput manner without the need for sample extraction, derivatization or pH adjustment steps. The use of this technique bypasses challenges presented by more conventional techniques including lengthy chromatography analysis times and resource intensive methods. The high throughput capabilities of the direct analysis in real time-high resolution mass spectrometry protocol, coupled with multivariate statistical analysis processing of the data, provide not only class characterization of plants, but also yield species and varietal information. Here, the technique is demonstrated with two psychoactive plant products, Mitragyna speciosa (Kratom) and Datura (Jimsonweed), which were subjected to direct analysis in real time-high resolution mass spectrometry followed by statistical analysis processing of the mass spectral data. The application of these tools in tandem enabled the plant materials to be rapidly identified at the level of variety and species.

A method for species identification of botanical material by direct analysis in real time-high resolution mass spectrometry and multivariate statistical analysis is presented.

We demonstrate that direct analysis in real time-high resolution mass spectrometry can be used to produce mass spectral profiles of botanical material, ...

A Simple and Efficient Protocol for the Catalytic Insertion Polymerization of Functional Norbornenes

Norbornene can be polymerized by a variety of mechanisms, including insertion polymerization whereby the double bond is polymerized and the bicyclic nature of the monomer is conserved. The resulting polymer, polynorbornene, has a very high glass transition temperature, Tg, and interesting optical and electrical properties. However, the polymerization of functional norbornenes by this mechanism is complicated by the fact that the endo substituted norbornene monomer has, in general, a very low reactivity. Furthermore, the separation of the endo substituted monomer from the exo monomer is a tedious task. Here, we present a simple protocol for the polymerization of substituted norbornenes (endo:exo ca. 80:20) bearing either a carboxylic acid or a pendant double bond. The process does not require that both isomers be separated, and proceeds with low catalyst loadings (0.01 to 0.02 mol%). The polymer bearing pendant double bonds can be further transformed in high yield, to afford a polymer bearing pendant epoxy groups. These simple procedures can be applied to prepare polynorbornenes with a variety of functional groups, such as esters, alcohols, imides, double bonds, carboxylic acids, bromo-alkyls, aldehydes and anhydrides.

We describe the catalytic insertion polymerization of 5-norbornene-2-carboxylic acid and 5-vinyl-2-norbornene to form functional polymers with a very high glass transition temperature.

Norbornene can be polymerized by a variety of mechanisms, including insertion polymerization whereby the double bond is polymerized and the bicyclic ...

A Protocol for Safe Lithiation Reactions Using Organolithium Reagents

Organolithium reagents are powerful tools in the synthetic chemist&#39;s toolbox. However, the extreme pyrophoric nature of the most reactive reagents warrants proper technique, thorough training, and proper personal protective equipment. To aid in the training of researchers using organolithium reagents, a thorough, step-by-step protocol for the safe and effective use of tert-butyllithium on an inert gas line or within a glovebox is described. As a model reaction, preparation of lithium tert-butyl amide by the reaction of tert-butyl amine with one equivalent of tert-butyl lithium is presented.

The safe and proper use of organolithium reagents is described.

Organolithium reagents are powerful tools in the synthetic chemist&#39;s toolbox. However, the extreme pyrophoric nature of the most reactive reagents ...

An Optimized Protocol for the Efficient Radiolabeling of Gold Nanoparticles by Using a 125I-labeled Azide Prosthetic Group

Here, we demonstrate a detailed protocol for the radiosynthesis of a 125I-labeled azide prosthetic group and its application to the efficient radiolabeling of DBCO-group-functionalized gold nanoparticles using a copper-free click reaction. Radioiodination of the stannylated precursor (2) was carried out by using [125I]NaI and chloramine T as an oxidant at room temperature for 15 min. After HPLC purification of the crude product, the purified 125I-labeled azide (1) was obtained with high radiochemical yield (75 &plusmn; 10%, n = 8) and excellent radiochemical purity (&gt;99%). For the synthesis of radiolabeled 13-nm-sized gold nanoparticles, the DBCO-functionalized gold nanoparticles (3) were prepared by using a thiolated polyethylene glycol polymer. A copper-free click reaction between 1 and 3 gave the 125I-labeled gold nanoparticles (4) with more than 95% of radiochemical yield as determined by radio-thin-layer chromatography (radio-TLC). These results clearly indicate that the present radiolabeling method using a strain-promoted copper-free click reaction will be useful for the efficient and convenient radiolabeling of DBCO-group-containing nanomaterials.

An Optimized Protocol for the Efficient Radiolabeling of Gold Nanoparticles by Using a 125I-labeled Azide Prosthetic Group

A detailed procedure for the synthesis of a 125I-labeled azide and the radiolabeling of dibenzocyclooctyne (DBCO)-group-conjugated, 13-nm-sized gold nanoparticles using a copper-free click reaction is described.

Here, we demonstrate a detailed protocol for the radiosynthesis of a 125I-labeled azide prosthetic group and its application to the efficient ...

Simultaneous Measurement of HDAC1 and HDAC6 Activity in HeLa Cells Using UHPLC-MS

The search for new histone deacetylase (HDAC) inhibitors is of increasing interest in drug discovery. Isoform selectivity has been in the spotlight since the approval of romidepsin, a class I HDAC inhibitor for cancer therapy, and the clinical investigation of HDAC6-specific inhibitors for multiple myeloma. The present method is used to determine the inhibitory activity of test compounds on HDAC1 and HDAC6 in cells. The isoform activity is measured using the ultra-high-performance liquid chromatography &#8211; mass spectrometry (UHPLC-MS) analysis of specific substrates incubated with treated and untreated HeLa cells. The method has the advantage of reflecting the endogenous HDAC activity within the cell environment, in contrast to cell-free biochemical assays conducted on isolated isoforms. Moreover, because it is based on the quantification of synthetic substrates, the method does not require the antibody recognition of endogenous acetylated proteins. It is easily adaptable to several cell lines and an automated process. The method has already proved useful in finding HDAC6-selective compounds in neuroblasts. Representative results are shown here with the standard HDAC inhibitors trichostatin A (non-specific), MS275 (HDAC1-specific), and tubastatin A (HDAC6-specific) using HeLa cells.

The present method serves to identify isoform-specific inhibitors of histone deacetylases (HDAC) in HeLa cells by the UHPLC-MS analysis of multiple substrates. This is an antibody-free method developed to reflect HDAC1 and HDAC6 activity in the living cell environment, in contrast to single-isoform cell-free assays.

The search for new histone deacetylase (HDAC) inhibitors is of increasing interest in drug discovery. Isoform selectivity has been in the spotlight since ...

Quantifying X-Ray Fluorescence Data Using MAPS

The quantification of X-ray fluorescence (XRF) microscopy maps by fitting the raw spectra to a known standard is crucial for evaluating chemical composition and elemental distribution within a material. Synchrotron-based XRF has become an integral characterization technique for a variety of research topics, particularly due to its non-destructive nature and its high sensitivity. Today, synchrotrons can acquire fluorescence data at spatial resolutions well below a micron, allowing for the evaluation of compositional variations at the nanoscale. Through proper quantification, it is then possible to obtain an in-depth, high-resolution understanding of elemental segregation, stoichiometric relationships, and clustering behavior.
This article explains how to use the MAPS fitting software developed by Argonne National Laboratory for the quantification of full 2-D XRF maps. We use as an example results from a Cu(In,Ga)Se2 solar cell, taken at the Advanced Photon Source beamline 2-ID-D at Argonne National Laboratory. We show the standard procedure for fitting raw data, demonstrate how to evaluate the quality of a fit and present the typical outputs generated by the program. In addition, we discuss in this manuscript certain software limitations and offer suggestions for how to further correct the data to be numerically accurate and representative of spatially resolved, elemental concentrations.

Here, we demonstrate the use of the X-ray fluorescence fitting software, MAPS, created by Argonne National Laboratory for the quantification of fluorescence microscopy data. The quantified data that results is useful for understanding the elemental distribution and stoichiometric ratios within a sample of interest.

The quantification of X-ray fluorescence (XRF) microscopy maps by fitting the raw spectra to a known standard is crucial for evaluating chemical ...

Fabrication and Testing of Catalytic Aerogels Prepared Via Rapid Supercritical Extraction

Protocols for preparing and testing catalytic aerogels by incorporating metal species into silica and alumina aerogel platforms are presented. Three preparation methods are described: (a) the incorporation of metal salts into silica or alumina wet gels using an impregnation method; (b) the incorporation of metal salts into alumina wet gels using a co-precursor method; and (c) the addition of metal nanoparticles directly into a silica aerogel precursor mixture. The methods utilize a hydraulic hot press, which allows for rapid (&#60;6 h) supercritical extraction and results in aerogels of low density (0.10 g/mL) and high surface area (200-800 m2/g). While the work presented here focuses on the use of copper salts and copper nanoparticles, the approach can be implemented using other metal salts and nanoparticles. A protocol for testing the three-way catalytic ability of these aerogels for automotive pollution mitigation is also presented. This technique uses custom-built equipment, the Union Catalytic Testbed (UCAT), in which a simulated exhaust mixture is passed over an aerogel sample at a controlled temperature and flow rate. The system is capable of measuring the ability of the catalytic aerogels, under both oxidizing and reducing conditions, to convert CO, NO and unburned hydrocarbons (HCs) to less harmful species (CO2, H2O and N2). Example catalytic results are presented for the aerogels described.

Here we present protocols for preparing and testing catalytic aerogels by incorporating metal species into silica and alumina aerogel platforms. Methods for preparing materials using copper salts and copper-containing nanoparticles are featured. Catalytic testing protocols demonstrate the effectiveness of these aerogels for three-way catalysis applications.

Protocols for preparing and testing catalytic aerogels by incorporating metal species into silica and alumina aerogel platforms are presented. Three ...

Separation of Aldehydes and Reactive Ketones from Mixtures Using a Bisulfite Extraction Protocol

The purification of organic compounds is an essential component of routine synthetic operations. The ability to remove contaminants into an aqueous layer by generating a charged structure provides an opportunity to use extraction as a simple purification technique. By combining the use of a miscible organic solvent with saturated sodium bisulfite, aldehydes and reactive ketones can be successfully transformed into charged bisulfite adducts that can then be separated from other organic components of a mixture by the introduction of an immiscible organic layer. Here, we describe a simple protocol for the removal of aldehydes, including sterically-hindered neopentyl aldehydes and some ketones, from chemical mixtures. Ketones can be separated if they are sterically unhindered cyclic or methyl ketones. For aliphatic aldehydes and ketones, dimethylformamide is used as the miscible solvent to improve removal rates. The bisulfite addition reaction can be reversed by basification of the aqueous layer, allowing for the re-isolation of the reactive carbonyl component of a mixture.

Here, we present a protocol to remove aldehydes and reactive ketones from mixtures by a liquid-liquid extraction protocol directly with saturated sodium bisulfite in a miscible solvent. This combined protocol is rapid and facile to perform. The aldehyde or ketone can be re-isolated by the basification of the aqueous layer.

The purification of organic compounds is an essential component of routine synthetic operations. The ability to remove contaminants into an aqueous layer ...