The authors gratefully acknowledge the work of Dr Mohamad Navab, Alan Fogelman and Srinivasa Reddy for their key role in development of earlier iterations of this model. T.A.A. is supported by an RMIT University Vice-Chancellor&#39;s Postdoctoral Fellowship. AJ and AH are supported by NHMRC project grant 1108792. TK is supported by NIH grants NIH K08AI08272, NIH/NCATS Grant # &#181;L1TR000124.

All experiments using human biological samples were performed with ethics approval from the University of California Los Angeles, Los Angeles and the Alfred Hospital Human Ethics committee, Melbourne.
NOTE: There are many variations of the fluorochrome HDL function Assay (see discussion)32. Below we will describe the protocol that gives the most consistent and reproducible results. An overview of the assay is shown in Figure 2.
1. Specimen Processing
<ol>
	<li>Use fresh, non-hemolyzed serum (can be collected in serum separator tubes) or citrate plasma obtained after 12-14 hours fasting. If using cryopreserved samples, include appropriate control as described in this Protocol.</li>
</ol>
2. Day 0-Preparation for the assay
<ol>
	<li>Prepare working layout of experiment with the appropriate controls, samples and replicates. Run each sample at least in triplicates. A representative 96 well layout is shown in Figure 3.</li>
	<li>Calculate all volumes of reagents that will be used for the assay based on number of samples and replicates. 
	NOTE: Include an additional 10% volume in each working stock to make sure there is enough volume for each reagent for the specific experiment.</li>
	<li>Label all required tubes for all different steps of the assay e.g. for the separation of HDL, measurement of HDL-C (optional) and the fluorochromeassay.</li>
</ol>
3. Day 1-Preparation of controls
<ol>
	<li>Preparation of study-specific pooled control
	<ol>
		<li>Create a control sample from pooled plasma or serum of all study samples. If running 20 samples in each plate in triplicate, combine 10 &#181;L from each sample into a 200 &#181;L pooled control. Give a separate aliquot of this pooled control to the clinical laboratory to determine the HDL-C value of this control. 
		NOTE: Use this pooled control to standardize the assay and account for all possible known (e.g. type of matrix serum versus plasma, freeze-thaw cycles, cryopreservation) and unknown confounders that may affect experimental variability27,28.</li>
	</ol>
	</li>
	<li>Preparation of laboratory-specific quality control (QCs)
	<ol>
		<li>Prepare a large stock of HDL in each laboratory (for example HDL isolated from 5 mL of plasma from 10 healthy donors) and cryopreserve several aliquots of this stock to minimize freeze-thaw cycles.</li>
		<li>Use at least 10 different replicates from this stock to determine the average value of HDLox. An acceptable range of measured HDLox values for each QC sample included in each assay is within &#60;15% of the coefficient of variation of this average value.</li>
		<li>Give a separate aliquot of this pooled control to the clinical laboratory to determine the HDL-C value of this control (e.g. 40 mg/dL). 
		NOTE: A detailed approach how to use blood from blood banks to create these controls has previously been described 27,28,32. Use additional QCs as needed (e.g. one from a healthy donor known to have normal HDL function and one from a donor known to have largely abnormal HDL function.</li>
	</ol>
	</li>
	<li>Optimization of background signal and blank values (optional)
	<ol>
		<li>To minimize background, add the appropriate amount of catalase (1-4 U/mL) in the incubation medium to rapidly remove the formed H2O2 due to spontaneous air oxidation of the buffers. 
		NOTE: Since the values from the blank wells (no HDL) are being subtracted from the values of the HDL samples and the results are being reported relative to a pooled control (that is included in the same 96 well plate), we have found that this step does not practically affect the results. Thus, optimization of the background signal with catalase can be omitted, if needed.</li>
	</ol>
	</li>
</ol>
4. Day 1-Separation of HDL Cholesterol using HDL precipitation
NOTE: Use a commercially available standardized HDL Cholesterol precipitating reagent to isolate apoB depleted serum according to the manufacturer&#39;s instructions. These reagents are widely used in colorimetric assays to determine HDL cholesterol levels.
<ol>
	<li>Use fresh (or thaw) plasma or serum sample.</li>
	<li>Mix equal volumes (e.g. 80 &#181;L) of plasma and HDL Cholesterol Precipitating Reagent (20% w/v polyethylene glycol in glycine buffer at pH 10.0 (25 &#176;C)).</li>
	<li>Mix well by pipetting up and down.</li>
	<li>Centrifuge at 1000-2000 x g for 10 min.</li>
	<li>Aspirate the supernatant (HDL fraction).</li>
	<li>Ideally use immediately the isolated HDL for the fluorochromeassay of HDL lipid peroxidation. However, if several samples are run in the same day and other steps such as measurement of HDL-cholesterol concentration are also done, then store the isolated HDL at 4 &#176;C and use it the next day for the fluorochromeHDL function Assay.</li>
</ol>
5. Day 1-Determination of HDL-C in isolated HDL
NOTE: This is optional if the value of HDL-C from the clinical laboratory is used to normalize HDLox by HDL-C amount.
<ol>
	<li>Quantify the HDL-cholesterol from plasma, using standard colorimetric assays27. Add 50 &#181;L of Cholesterol Reagent in each well and determine cholesterol concentration using a colorimetric plate reader and a cholesterol standard provided in each kit.</li>
</ol>
6. Day 2-Preparation of reagents
<ol>
	<li>Prepare HRP and cholesterol solutions of HRP 5 U/mL solution (Range 1-10 U/mL).</li>
	<li>Prepare 20 mM fluorochrome (e.g., Amplex Red) solutions: Thaw a vial of fluorochrome reagent and DMSO to room temperature. Prior to use, dissolve fluorochrome reagent (1 mg) in 200 &#181;L of DMSO. Store stock solution frozen at &#8804;-20 &#176;C, protected from light.</li>
	<li>Prepare positive and negative controls: Use 1X &#39;reaction buffer&#39; without cholesterol and 20 mM H2O2 working solution as a negative and positive control, respectively.</li>
</ol>
7. Day 2-Fluorochrome Assay
<ol>
	<li>Add 50 &#181;L of 1x Reaction buffer as blank (negative control).</li>
	<li>Optional: Add 20 mM working solution of H2O2 as positive control in each plate.</li>
	<li>To minimize experimental variability and ensure that addition of reagents and samples are done consistently and in a timely manner, perform all additions of samples in a separate 96 well round-bottom, clear, polystyrene or polypropylene plate (Plate 1). Then use a multichannel pipette to transfer specific volumes into 3 96-well plates (Plates 2-4: polypropylene, flat bottom, black) (that have identical layout) (Figure 2, Figure 3).
	<ol>
		<li>For example, first add 160 &#181;L of isolated HDL into each well/sample of plate 1 and then with the use of multichannel pipette transfer 50 &#181;L of HDL-cholesterol from each well/sample into the 96-well black plates. Change tips between each row/column and use non-filtered tips for all the transfers.</li>
	</ol>
	</li>
	<li>Leave samples in the wells. Do not discard. There are no wash steps between addition of reagents.</li>
	<li>Add 50 &#181;L of HRP solution 5 U/mL (0.25 U) to each well. 
	NOTE: Use HRP before the addition of the fluorochrome reagent.</li>
	<li>Incubate for 30 min at 37 &#176;C. Do not discard samples after incubation (no wash steps between additions of reagents).</li>
	<li>Add 50 &#181;L of fluorochromereagent for a final concentration of 300 &#181;M. At this point, total reaction volume is 150 &#181;L. Mix well and protect from light.</li>
	<li>Assess the fluorescent readout (in the dark) every minute over 120 min at 37 &#176;C with a fluorescent plate reader (530/590 nm filters). 
	NOTE: Use a shorter 60-minute interval with fresh samples. We have found that 120-minute assay gives more reproducible data with the use of cryopreserved samples.</li>
	<li>Record data using appropriate software.</li>
</ol>
8. Day 3-Data analysis
<ol>
	<li>Record fluorescence units (arbitrary units) at 120 minutes after addition of the fluorochrome Reagent for all the samples including blank wells and all controls.</li>
	<li>Calculate the mean value of fluorescence units (based on at least triplicates) (HDLox_sample). Do not take outliers (&#62; 2 SDs from the average value) into consideration.</li>
	<li>Subtract the background fluorescence by using the following equation: 
	<img alt="Equation 1" src="/files/ftp_upload/56325/56325eq1.jpg" /></li>
	<li>Normalization for HDL cholesterol amount (HDL-C): Normalize the HDLox lipid peroxidation value for each sample (including the pooled control) by the HDL-C) (mg/dl). Throughout the results section, HDLox is presented as n(HDL-C) HDLox measure to reflect the adjustment for HDL-C. Use the following equation: 
	<img alt="Equation 2" src="/files/ftp_upload/56325/56325eq2.jpg" /></li>
	<li>Standardize the expression of HDLox lipid peroxidation value of each sample against the value of a pooled control. Normalize the n(HDL-C) HDLox lipid peroxidation value for each sample (adjusted for HDL-C) by the n(HDL-C) HDLox lipid peroxidation value of the pooled control. Throughout the results section, HDLox is presented as nHDLox measure to reflect the adjustment for experimental variability and HDL-C. Use the following equation: 
	<img alt="Equation 3" src="/files/ftp_upload/56325/56325eq3.jpg" /> 
	NOTE: This approach is similar to other established experimental approaches to reduce experimental variability of measurements such as international normalized ratio (INR)44,45. This approach has been validated in clinical studies32,33,34,35,36,37,38,39.</li>
	<li>Perform quality control of experimental results using standard quality control samples. Each laboratory should establish their own quality controls (QCs). Ideally there is a QC for nHDLox from a sample with known dysfunctional HDL and a QC for nHDLox from a sample from healthy donors [e.g. use pooled sample from young adults who are established blood bank donors and have no known comorbidity and risk factors for cardiovascular disease including smoking]. The latter control standardizes results among different laboratories. The average values of these QCs are established based on at least 5 replicates (typically we use 10 replicates for this important step).
	<ol>
		<li>Check whether measured QCs in each assay have values within the expected range of values. Assuming an acceptable maximum experimental variability of 15%, all the measured experimental values should fall within 15% of the known average values of established QC. Use the following equations: 
		<img alt="Equation 4" src="/files/ftp_upload/56325/56325eq4.jpg" /> 
		<img alt="Equation 5" src="/files/ftp_upload/56325/56325eq5.jpg" /> 
		NOTE: If either of the included quality control samples (normal versus dysfunctional HDL) gives HDLox values outside expected range (established in each laboratory) then repeat the experiment.</li>
	</ol>
	</li>
	<li>Perform quality control of experimental results using the coefficient of variation (CV) to quantify experimental variability: Repeat all samples with CV% &#62; 15%. Use the following equation: 
	<img alt="Equation 6" src="/files/ftp_upload/56325/56325eq6.jpg" /> 
	NOTE: A typical intra-assay (within the same plate) and inter-assay (among different plates) experimental variability is &#60; 15%. 2) A typical intra-assay CV is between 1-7% and a typical interassay CV is between 3-10%.</li>
</ol>

This protocol and assay are relevant to the patent PCT/US2015/018147.

The protocol described here offers a robust tool to answer important research questions regarding the role of HDL function in atherosclerosis and human disease. The assay quantifies the HDL lipid peroxide content per mg of HDL-C using enzymatic amplification (HRP). This approach avoids known limitations of prior HDL function assays (e.g. the cholesterol efflux assay) including significant heterogeneity with regards to types of cells used, type of readout reported, lack of standardization and confounding effects of trigly...

Atherosclerotic cardiovascular disease (CVD) is the leading cause of death worldwide1,2. Epidemiological studies have shown that low levels of high-density lipoprotein (HDL) cholesterol are generally inversely associated with the risk for the development of atherosclerosis1,2. Although several studies support an atheroprotective role for HDL1,2, the mechanism by which HDL attenuates the initiation and progression of atherosclerosis is complex 3,4. Thus, it has been suggested that the complex structure and function of HDL rather than absolute level may more accurately predict atherosclerosis 5,6,7,8. Several HDL protein and lipid compositional changes that impair HDL function occur in inflammatory states such as atherosclerosis. These i) reduce its cholesterol efflux potential 9, ii) decrease anti-inflammatory and increase HDL-associated pro-inflammatory proteins 6,7, iii) decrease antioxidant factor levels and activity and HDLs ability to inhibit oxidation of Low Density Lipoprotein (LDLox)10 and iv) increase lipid hydroperoxide content and redox activity (HDLox)9,11. Robust assays that evaluate the pleotropic functions of HDL (such as cholesterol efflux, antioxidant function) may complement determination of HDL-HDL-C in the clinic.
HDL function is usually assessed by cell-based methods such as the cholesterol efflux assay8,12,13,14. These methods have major limitations including significant heterogeneity with regards to types of cells used, type of readout reported, lack of standardization and confounding effects of triglycerides 7,15. These drawbacks pose difficulties for large clinical studies16. Cell-free assays may give more robust measures of HDL function compared to cell-based assays. The cholesterol efflux is one of the most important functions of HDL but it can only be determined by cell-based assays. Other approaches to determine HDL function such as proteomics17,18,19,20,21,22,23,24 and cell-based monocyte chemotaxis assays of HDL function 17,22,25 have not been standardized and cannot be used in large scale human studies.
HDL has significant antioxidant atheroprotective effect5,6,7,8. The antioxidant function of HDL has been determined in the presence of LDL in previous cell free fluorometric assays 26. These biochemical fluorometric methods of HDL antioxidant function were originally developed by Mohamad Navab and Alan Fogelman and their colleagues26. Although many human studies have used these methods to determine HDL function 17,18,19,20,21,22,23,24, lipid (HDL)-lipid (LDL) and lipid-fluorochrome interactions may limit reproducibility of these cell free non-enzymatic biochemical assays of HDL function27,28.
Recent interest has focused on the functional consequences of HDL oxidation that is the result of oxidation of both lipids and proteins within HDL 27,29,30. Prior studies have shown that oxidation of HDL impairs HDL function 27,29,30. HDL has a major role in lipid peroxide transport and high amount of lipid peroxides is related to abnormal HDL function. Thus HDL lipid peroxide content can be used to determine HDL function 9,17,20,31 and given the known limitations of prior assays of HDL function7,15,27,32, we developed an alternative fluorometric method that quantifies HDL lipid peroxide content (HDLox) 32. This method is based on the enzyme horseradish peroxidase (HRP) and the fluorochrome Amplex Red that can quantify (without cholesterol oxidase) the lipid peroxide content per mg of HDL-C 32. The biochemical principle of the assay is shown in Figure 1. We have shown that this fluorescence-based approach does not have the limitations of prior HDL function assays27,28. This assay has been further refined and standardized in our laboratory so that it can reliably be used in large scale human studies even with cryopreserved plasma 32,33,34,35,36,37,38,39,40,41,42. The readout of this assay is associated with readouts of validated cell-based assays, surrogate measures of cardiovascular disease, systemic inflammation, immune dysfunction and associated cardiovascular and metabolic risk phenotypes32,33,34,35,36,37,38,39. Here, we describe this simple, yet robust method to measure HDL lipid peroxide content (HDLox). This assay can be used as a tool to answer important research questions regarding the role of HDL function in human disease where systemic inflammation, oxidative stress and oxidized lipids have a key role (such as atherosclerosis)32.

<table>
	<tbody>
		<tr>
			<td>Experimental Reagents</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>HDL PEG (Polyethylene Glycol) Precipitating Reagent</td>
			<td>Pointe Scientific</td>
			<td>H7511</td>
			<td></td>
		</tr>
		<tr>
			<td>Amplex Red reagent.</td>
			<td>Life Technologies, Grand Island, NY</td>
			<td>A12216</td>
			<td>Amplex Red Cholesterol Assay Kit. 
			&#8226; &#8804;&#8211;20&#176;C &#8226; Desiccate 
			&#8226; Protect from light</td>
		</tr>
		<tr>
			<td>DMSO.</td>
			<td>Life Technologies, Grand Island, NY</td>
			<td>A12216</td>
			<td>Amplex Red Cholesterol Assay Kit. 
			&#8226; &#8804;&#8211;20&#176;C &#8226; Desiccate 
			&#8226; Protect from light</td>
		</tr>
		<tr>
			<td>Horse Radish Peroxidase (HRP)</td>
			<td>Life Technologies, Grand Island, NY</td>
			<td>A12216</td>
			<td>Amplex Red Cholesterol Assay Kit. 
			&#8226; &#8804;&#8211;20&#176;C &#8226; Desiccate 
			&#8226; Protect from light</td>
		</tr>
		<tr>
			<td>Cholesterol Esterase.</td>
			<td>Life Technologies, Grand Island, NY</td>
			<td>A12216</td>
			<td>Amplex Red Cholesterol Assay Kit. 
			&#8226; &#8804;&#8211;20&#176;C &#8226; Desiccate 
			&#8226; Protect from light</td>
		</tr>
		<tr>
			<td>&#160;Cholesterol Reference standard</td>
			<td>Life Technologies, Grand Island, NY</td>
			<td>A12216</td>
			<td>Amplex Red Cholesterol Assay Kit. 
			&#8226; &#8804;&#8211;20&#176;C &#8226; Desiccate 
			&#8226; Protect from light</td>
		</tr>
		<tr>
			<td>&#160;Resorufin fluorescense Reference standard</td>
			<td>Life Technologies, Grand Island, NY</td>
			<td>A12216</td>
			<td>Amplex Red Cholesterol Assay Kit. 
			&#8226; &#8804;&#8211;20&#176;C &#8226; Desiccate 
			&#8226; Protect from light</td>
		</tr>
		<tr>
			<td>5x Reaction Buffer.</td>
			<td>Life Technologies, Grand Island, NY</td>
			<td>A12216</td>
			<td>Amplex Red Cholesterol Assay Kit. 
			&#8226; &#8804;&#8211;20&#176;C &#8226; Desiccate 
			&#8226; Protect from light</td>
		</tr>
		<tr>
			<td>HDL Cholesterol Automated Reagent</td>
			<td>ThermoFisher Scientific Co., San Jose, CA, USA.</td>
			<td>TR39601</td>
			<td></td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>Plasticware&#160;</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>96-well plates (polypropylene, flat bottom, clear).</td>
			<td>Sigma Aldrich</td>
			<td>M0687</td>
			<td></td>
		</tr>
		<tr>
			<td>96-well plates (polypropylene, flat bottom, black).</td>
			<td>Sigma Aldrich</td>
			<td>M9936</td>
			<td></td>
		</tr>
		<tr>
			<td>1.5 mL Eppendorf tubes</td>
			<td>Eppendorf</td>
			<td>0030 125.150</td>
			<td></td>
		</tr>
		<tr>
			<td>ClipTip 200, sterile</td>
			<td>ThermoFisher Scientific Co., San Jose, CA, USA.</td>
			<td>14-488-058</td>
			<td></td>
		</tr>
		<tr>
			<td>Thermo Scientific Multichannel Pipettes, 8-channel, 125&#160;</td>
			<td>ThermoFisher Scientific Co., San Jose, CA, USA.</td>
			<td>&#160;14-387--955</td>
			<td></td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>Software&#160;</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Gen5 2.01 software</td>
			<td>Biotek, Vermont, USA</td>
			<td>NA</td>
			<td></td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>Equipment</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Gen5 Plate reader</td>
			<td>Biotek, Vermont, USA</td>
			<td>NA</td>
			<td></td>
		</tr>
	</tbody>
</table>

cell-free biochemical fluorometric enzymatic assay for high-throughput measurement of lipid peroxidation in high density lipoprotein

Low high-density lipoprotein cholesterol (HDL-C) levels are one of the most powerful independent negative predictors of atherosclerotic cardiovascular disease (CVD). The structure and function of HDL rather than HDL-C may more accurately predict atherosclerosis. Several HDL protein and lipid compositional changes that impair HDL function occur in inflammatory states such as atherosclerosis. HDL function is usually determined by cell based assays such as cholesterol efflux assay but these assays have numerous drawbacks lack of standardization. Cell-free assays may give more robust measures of HDL function compared to cell-based assays. HDL oxidation impairs HDL function. HDL has a major role in lipid peroxide transport and high amount of lipid peroxides is related to abnormal HDL function. Lipid-probe interactions should be considered when interpreting the results of non-enzymatic fluorescence assays for measuring the lipid oxidative state. This motivated us to develop a cell-free biochemical enzymatic method to assess HDL lipid peroxide content (HDLox) that contributes to HDL dysfunction. This method is based on the enzyme horseradish peroxidase (HRP) and the fluorochrome Amplex Red that can quantify (without cholesterol oxidase) the lipid peroxide content per mg of HDL-C. Here a protocol is describedfor determination of HDL-lipid peroxidation using the fluorochrome reagent. Assay variability can be reduced by strict standardization of experimental conditions. Higher HDLox values are associated with reduced HDL antioxidant function. The readout of this assay is associated with readouts of validated cell-based assays, surrogate measures of cardiovascular disease, systemic inflammation, immune dysfunction, and associated cardiovascular and metabolic risk phenotypes. This technical approach is a robust method to assess HDL function in human disease where systemic inflammation, oxidative stress and oxidized lipids have a key role (such as atherosclerosis).

50 &#181;L of each HDL sample are added into each well as in step 7.3. 50 &#181;L of HRP solution 5 U/mL (0.25 U) are then added into each well as in step 7.5. Samples are incubated for 30 min at 37 &#176;C as in step 7.6. 50 &#181;L of fluorochrome reagent are then added into each well as in step 7.7 (final concentration of 300 &#181;M). The fluorescent readout (in dark) is then assessed every minute over 120 minutes at 37 &#176;C with a fluorescent plate reader (530/590 nm filters). Rep...

Watch this Scientific Journal Video about Cell-free Biochemical Fluorometric Enzymatic Assay for High-throughput Measurement of Lipid Peroxidation in High Density Lipoprotein at JoVE.com

Cell-free Biochemical Fluorometric Enzymatic Assay for High-throughput Measurement of Lipid Peroxidation in High Density Lipoprotein

We describe here a fluorometric cell-free biochemical assay for determination of HDL-lipid peroxidation. This rapid and reproducible assay can be used to determine HDL function in large scale studies and can contribute to our understanding of HDL function in human disease.

Low high-density lipoprotein cholesterol (HDL-C) levels are one of the most powerful independent negative predictors of atherosclerotic cardiovascular ...

cell-free-biochemical-fluorometric-enzymatic-assay-for-high

Research

JoVE Journal

Immunology and Infection

9.2K Views.  University of California, Los Angeles. We describe here a fluorometric cell-free biochemical assay for determination of HDL-lipid peroxidation. This rapid and reproducible assay can be used to determine HDL function in large scale studies and can contribute to our understanding of HDL function in human disease.

Video: Cell-free Biochemical Fluorometric Enzymatic Assay for High-throughput Measurement of Lipid Peroxidation in High Density Lipoprotein

High-throughput Detection Method for Influenza Virus

Influenza virus is a respiratory pathogen that causes a high degree of morbidity and mortality every year in multiple parts of the world. Therefore, precise diagnosis of the infecting strain and rapid high-throughput screening of vast numbers of clinical samples is paramount to control the spread of pandemic infections. Current clinical diagnoses of influenza infections are based on serologic testing, polymerase chain reaction, direct specimen immunofluorescence and cell culture 1,2.
Here, we report the development of a novel diagnostic technique used to detect live influenza viruses. We used the mouse-adapted human A/PR/8/34 (PR8, H1N1) virus 3 to test the efficacy of this technique using MDCK cells 4. MDCK cells (104 or 5 x 103 per well) were cultured in 96- or 384-well plates, infected with PR8 and viral proteins were detected using anti-M2 followed by an IR dye-conjugated secondary antibody. M2 5 and hemagglutinin 1 are two major marker proteins used in many different diagnostic assays. Employing IR-dye-conjugated secondary antibodies minimized the autofluorescence associated with other fluorescent dyes. The use of anti-M2 antibody allowed us to use the antigen-specific fluorescence intensity as a direct metric of viral quantity. To enumerate the fluorescence intensity, we used the LI-COR Odyssey-based IR scanner. This system uses two channel laser-based IR detections to identify fluorophores and differentiate them from background noise. The first channel excites at 680 nm and emits at 700 nm to help quantify the background. The second channel detects fluorophores that excite at 780 nm and emit at 800 nm. Scanning of PR8-infected MDCK cells in the IR scanner indicated a viral titer-dependent bright fluorescence. A positive correlation of fluorescence intensity to virus titer starting from 102-105 PFU could be consistently observed. Minimal but detectable positivity consistently seen with 102-103 PFU PR8 viral titers demonstrated the high sensitivity of the near-IR dyes. The signal-to-noise ratio was determined by comparing the mock-infected or isotype antibody-treated MDCK cells.
Using the fluorescence intensities from 96- or 384-well plate formats, we constructed standard titration curves. In these calculations, the first variable is the viral titer while the second variable is the fluorescence intensity. Therefore, we used the exponential distribution to generate a curve-fit to determine the polynomial relationship between the viral titers and fluorescence intensities. Collectively, we conclude that IR dye-based protein detection system can help diagnose infecting viral strains and precisely enumerate the titer of the infecting pathogens.

This method describes the use of Infrared dye based imaging system for detection of H1N1 in bronchioalveolar lavage (BAL) fluid of infected mice at a high sensitivity. This methodology can be performed in a 96- or 384-well plate, requires &lt;10 &mu;l volume of test material and has the potential for concurrent screening of multiple pathogens.

Influenza virus is a respiratory pathogen that causes a high degree of morbidity and mortality every year in multiple parts of the world. Therefore, ...

Quantitative High-throughput Single-cell Cytotoxicity Assay For T Cells

Cancer immunotherapy can harness the specificity of immune response to target and eliminate tumors. Adoptive cell therapy (ACT) based on the adoptive transfer of T cells genetically modified to express a chimeric antigen receptor (CAR) has shown considerable promise in clinical trials1-4. There are several advantages to using CAR+ T cells for the treatment of cancers including the ability to target non-MHC restricted antigens and to functionalize the T cells for optimal survival, homing and persistence within the host; and finally to induce apoptosis of CAR+ T cells in the event of host toxicity5.
Delineating the optimal functions of CAR+ T cells associated with clinical benefit is essential for designing the next generation of clinical trials. Recent advances in live animal imaging like multiphoton microscopy have revolutionized the study of immune cell function in vivo6,7. While these studies have advanced our understanding of T-cell functions in vivo, T-cell based ACT in clinical trials requires the need to link molecular and functional features of T-cell preparations pre-infusion with clinical efficacy post-infusion, by utilizing in vitro assays monitoring T-cell functions like, cytotoxicity and cytokine secretion. Standard flow-cytometry based assays have been developed that determine the overall functioning of populations of T cells at the single-cell level but these are not suitable for monitoring conjugate formation and lifetimes or the ability of the same cell to kill multiple targets8.
Microfabricated arrays designed in biocompatible polymers like polydimethylsiloxane (PDMS) are a particularly attractive method to spatially confine effectors and targets in small volumes9. In combination with automated time-lapse fluorescence microscopy, thousands of effector-target interactions can be monitored simultaneously by imaging individual wells of a nanowell array. We present here a high-throughput methodology for monitoring T-cell mediated cytotoxicity at the single-cell level that can be broadly applied to studying the cytolytic functionality of T cells.

We describe a single-cell high-throughput assay to measure cytotoxicity of T cells when incubated with tumor target cells. This method employs a dense, elastomeric array of sub-nanoliter wells (~100,000 wells/array) to spatially confine the T cells and target cells at defined ratios and is coupled to fluorescence microscopy to monitor effector-target conjugation and subsequent apoptosis.

Cancer immunotherapy can harness the specificity of  immune response to target and eliminate tumors. Adoptive cell therapy (ACT)  based on the adoptive ...

A Microscopic Phenotypic Assay for the Quantification of Intracellular Mycobacteria Adapted for High-throughput/High-content Screening

Despite the availability of therapy and vaccine, tuberculosis (TB) remains one of the most deadly and widespread bacterial infections in the world. Since several decades, the sudden burst of multi- and extensively-drug resistant strains is a serious threat for the control of tuberculosis. Therefore, it is essential to identify new targets and pathways critical for the causative agent of the tuberculosis, Mycobacterium tuberculosis (Mtb) and to search for novel chemicals that could become TB drugs. One approach is to set&#160;up methods suitable for the genetic and chemical screens of large scale libraries enabling the search of a needle in a haystack. To this end, we developed a phenotypic assay relying on the detection of fluorescently labeled Mtb within fluorescently labeled host&#160;cells using automated confocal microscopy. This in vitro assay allows an image based quantification of the colonization process of Mtb&#160;into the host and was optimized for the 384-well microplate format, which is proper for screens of siRNA-, chemical compound- or Mtb mutant-libraries. The images are then processed for multiparametric analysis, which provides read&#160;out inferring on the pathogenesis of Mtb&#160;within host cells.

Here, we describe a phenotypic assay applicable to the High-throughput/High-content screens of small-interfering synthetic RNA (siRNA), chemical compound, and Mycobacterium tuberculosis mutant libraries. This method relies on the detection of fluorescently labeled Mycobacterium tuberculosis within fluorescently labeled host&#160;cell using automated confocal microscopy.

Despite the availability of therapy and vaccine, tuberculosis (TB) remains one of the most deadly and widespread bacterial infections in the world. Since ...

High-throughput Screening for Broad-spectrum Chemical Inhibitors of RNA Viruses

RNA viruses are responsible for major human diseases such as flu, bronchitis, dengue, Hepatitis C or measles. They also represent an emerging threat because of increased worldwide exchanges and human populations penetrating more and more natural ecosystems. A good example of such an emerging situation is chikungunya virus epidemics of 2005-2006 in the Indian Ocean. Recent progresses in our understanding of cellular pathways controlling viral replication suggest that compounds targeting host cell functions, rather than the virus itself, could inhibit a large panel of RNA viruses. Some broad-spectrum antiviral compounds have been identified with host target-oriented assays. However, measuring the inhibition of viral replication in cell cultures using reduction of cytopathic effects as a readout still represents a paramount screening strategy. Such functional screens have been greatly improved by the development of recombinant viruses expressing reporter enzymes capable of bioluminescence such as luciferase. In the present report, we detail a high-throughput screening pipeline, which combines recombinant measles and chikungunya viruses with cellular viability assays, to identify compounds with a broad-spectrum antiviral profile.

In vitro assays to measure virus replication have been greatly improved by the development of recombinant RNA viruses expressing luciferase or other enzymes capable of bioluminescence. Here we detail a high-throughput screening pipeline that combines such recombinant strains of measles and chikungunya viruses to isolate broad-spectrum antivirals from chemical libraries.

RNA viruses are responsible for major human diseases such as flu, bronchitis, dengue, Hepatitis C or measles. They also represent an emerging threat ...

High-throughput Assay to Phenotype Salmonella enterica Typhimurium Association, Invasion, and Replication in Macrophages

Salmonella species are zoonotic pathogens and leading causes of food borne illnesses in humans and livestock1. Understanding the mechanisms underlying Salmonella-host interactions are&#160;important to elucidate the molecular pathogenesis of Salmonella infection. The Gentamicin protection assay to phenotype Salmonella association, invasion and replication in phagocytic cells was adapted to allow high-throughput screening to define the roles of deletion mutants of Salmonella enterica serotype Typhimurium in host interactions using RAW 264.7 murine macrophages. Under this protocol, the variance in measurements is significantly reduced compared to the standard protocol, because wild-type and multiple mutant strains can be tested in the same culture dish and at the same time. The use of multichannel pipettes increases the throughput and enhances precision. Furthermore, concerns related to using less host cells per well in 96-well culture dish were addressed. Here, the protocol of the modified in vitro Salmonella invasion assay using phagocytic cells was successfully employed to phenotype 38 individual Salmonella deletion mutants for association, invasion and intracellular replication. The in vitro phenotypes are presented, some of which were subsequently confirmed to have in vivo phenotypes in an animal model. Thus, the modified, standardized assay to phenotype Salmonella association, invasion and replication in macrophages with high-throughput capacity could be utilized more broadly to study bacterial-host interactions.

High-throughput Assay to Phenotype Salmonella enterica Typhimurium Association, Invasion, and Replication in Macrophages

A high-throughput assay to in vitro phenotype Salmonella or other bacterial association, invasion, and replication in phagocytic cells with high-throughput capacity was developed. The method was employed to evaluate Salmonella gene knockout mutant strains for their involvements in host-pathogen interactions.

Salmonella species are zoonotic pathogens and leading causes of food borne illnesses in humans and livestock1. Understanding the mechanisms underlying ...

High Throughput Fluorometric Technique for Assessment of Macrophage Phagocytosis and Actin Polymerization

The goal of fluorometric analysis is to serve as an efficient, cost effective, high throughput method of analyzing phagocytosis and other cellular processes. This technique can be used on a variety of cell types, both adherent and non-adherent, to examine a variety of cellular properties. When studying phagocytosis, fluorometric technique utilizes phagocytic cell types such as macrophages, and fluorescently labeled opsonized particles whose fluorescence can be extinguished in the presence of trypan blue. Following plating of adherent macrophages in 96-well plates, fluorescent particles (green or red) are administered and cells are allowed to phagocytose for varied amounts of time. Following internalization of fluorescent particles, cells are washed with trypan blue, which facilitates extinction of fluorescent signal from bacteria which are not internalized, or are merely adhering to the cell surface. Following the trypan wash, cells are washed with PBS, fixed, and stained with DAPI (nuclear blue fluorescent label), which serves to label nuclei of cells. By a simple fluorometric quantification through plate reading of nuclear (blue) or particle (red/green) fluorescence we can examine the ratio of relative fluorescence units of green:blue and determine a phagocytic index indicative of amount of fluorescent bacteria internalized per cell. The duration of assay using a 96-well method and multichannel pipettes for washing, from end of phagocytosis to end of data acquisition, is less than 45 min. Flow cytometry could be used in a similar manner but the advantage of fluorometry is its high throughput, rapid method of assessment with minimal manipulation of samples and quick quantification of fluorescent intensity per cell. Similar strategies can be applied to non adherent cells, live labeled bacteria, actin polymerization, and essentially any process utilizing fluorescence. Therefore, fluorometry is a promising method for its low cost, high throughput capabilities in the study of cellular processes.

Here we present a protocol to quantify phagocytosis of fluorescent particles by adherent macrophage cell line using a fluorometric method. This method facilitates a high throughput quantification of particle internalization as well as the resulting actin polymerization.

The goal of fluorometric analysis is to serve as an efficient, cost effective, high throughput method of analyzing phagocytosis and other cellular ...

High Throughput Measurement of Extracellular DNA Release and Quantitative NET Formation in Human Neutrophils In Vitro

Neutrophil granulocytes are the most abundant leukocytes in the human blood. Neutrophils are the first to arrive at the site of infection. Neutrophils developed several antimicrobial mechanisms including phagocytosis, degranulation and formation of neutrophil extracellular traps (NETs). NETs consist of a DNA scaffold decorated with histones and several granule markers including myeloperoxidase (MPO) and human neutrophil elastase (HNE). NET release is an active process involving characteristic morphological changes of neutrophils leading to expulsion of their DNA into the extracellular space. NETs are essential to fight microbes, but uncontrolled release of NETs has been associated with several disorders. To learn more about the clinical relevance and the mechanism of NET formation, there is a need to have reliable tools capable of NET quantitation. 
Here three methods are presented that can assess NET release from human neutrophils in vitro. The first one is a high throughput assay to measure extracellular DNA release from human neutrophils using a membrane impermeable DNA-binding dye. In addition, two other methods are described capable of quantitating NET formation by measuring levels of NET-specific MPO-DNA and HNE-DNA complexes. These microplate-based methods in combination provide great tools to efficiently study the mechanism and regulation of NET formation of human neutrophils.

High Throughput Measurement of Extracellular DNA Release and Quantitative NET Formation in Human Neutrophils In Vitro

High throughput assays are presented that in combination provide excellent tools to quantitate NET release from human neutrophils.

Neutrophil granulocytes are the most abundant leukocytes in the human blood. Neutrophils are the first to arrive at the site of infection. Neutrophils ...

High-throughput Gene Tagging in Trypanosoma brucei

Improvements in mass spectrometry, sequencing and bioinformatics have generated large datasets of potentially interesting genes. Tagging these proteins can give insights into their function by determining their localization within the cell and enabling interaction partner identification. We recently published a fast and scalable method to generate Trypanosoma brucei cell lines that express a tagged protein from the endogenous locus. The method was based on a plasmid we generated that, when coupled with long primer PCR, can be used to modify a gene to encode a protein tagged at either terminus. This allows the tagging of dozens of trypanosome proteins in parallel, facilitating the large-scale validation of candidate genes of interest. This system can be used to tag proteins for localization (using a fluorescent protein, epitope tag or electron microscopy tag) or biochemistry (using tags for purification, such as the TAP (tandem affinity purification) tag). Here, we describe a protocol to perform the long primer PCR and the electroporation in 96-well plates, with the recovery and selection of transgenic trypanosomes occurring in 24-well plates. With this workflow, hundreds of proteins can be tagged in parallel; this is an order of magnitude improvement to our previous protocol and genome scale tagging is now possible.

High-throughput Gene Tagging in Trypanosoma brucei

Addition of a tag to a protein is a powerful way of gaining insight into its function. Here, we describe a protocol to endogenously tag hundreds of Trypanosoma brucei proteins in parallel such that genome scale tagging is achievable.

Improvements in mass spectrometry, sequencing and bioinformatics have generated large datasets of potentially interesting genes. Tagging these proteins ...

A Fluorescence-based Lymphocyte Assay Suitable for High-throughput Screening of Small Molecules

High-throughput screening (HTS) is currently the mainstay for the identification of chemical entities capable of modulating biochemical reactions or cellular processes. With the advancement of biotechnologies and the high translational potential of small molecules, a number of innovative approaches in drug discovery have evolved, which explains the resurgent interest in the use of HTS. The oncology field is currently the most active research area for drug screening, with no major breakthrough made for the identification of new immunomodulatory compounds targeting transplantation-related complications or autoimmune ailments. Here, we present a novel in vitro murine fluorescent-based lymphocyte assay easily adapted for the identification of new immunomodulatory compounds. This assay uses T or B cells derived from a transgenic mouse, in which the Nur77 promoter drives GFP expression upon T- or B-cell receptor stimulation. As the GFP intensity reflects the activation/transcriptional activity of the target cell, our assay defines a novel tool to study the effect of given compound(s) on cellular/biological responses. For instance, a primary screening was performed using 4,398 compounds in the absence of a &#34;target hypothesis&#34;, which led to the identification of 160 potential hits displaying immunomodulatory activities. Thus, the use of this assay is suitable for drug discovery programs exploring large chemical libraries prior to further in vitro/in vivo validation studies.

We present in the current study a novel fluorescence-based assay using lymphocytes derived from a transgenic mouse. This assay is suitable for high-throughput screening (HTS) of small molecules endowed with the capacity of either inhibiting or promoting lymphocyte activation.

High-throughput screening (HTS) is currently the mainstay for the identification of chemical entities capable of modulating biochemical reactions or ...

A High-throughput, High-content, Liquid-based C. elegans Pathosystem

The number of new drugs identified by traditional, in vitro screens has waned, reducing the success of this approach in the search for new weapons to combat multiple drug resistance. This has led to the conclusion that researchers do not only need to find new drugs, but also need to develop new ways of finding them. Amongst the most promising candidate methods are whole-organism, in vivo assays that use high-throughput, phenotypic readouts and hosts that range from Caenorhabditis elegans to Danio rerio. These hosts have several powerful advantages, including dramatic reductions in false positive hits, as compounds that are toxic to the host and/or biounavailable are typically dropped in the initial screen, prior to costly follow up.
Here we show how our assay has been used to interrogate host variation in the well-documented C. elegans&#8212;Pseudomonas aeruginosa liquid killing pathosystem. We also demonstrate several extensions of this well-worked out technique. For example, we are able to carry out high-throughput genetic screens using RNAi in 24- or 96-well plate formats to query host factors in this host-pathogen interaction. Using this assay, whole genome screens can be completed in only a few months, which can dramatically simplify the task of identifying drug targets, potentially without the need for laborious biochemical purification approaches.
We also report here a variation of our method that substitutes the gram-positive bacterium Enterococcus faecalis for the gram-negative pathogen P. aeruginosa. Much as is the case for P. aeruginosa, killing by E. faecalis is time-dependent. Unlike previous C. elegans&#8212;E. faecalis assays, our assay for E. faecalis does not require preinfection, improving its safety profile and reducing the chances of contaminating liquid-handling equipment. The assay is highly robust, showing ~95% death rates 96 h post infection.

A High-throughput, High-content, Liquid-based C. elegans Pathosystem

Here we describe a protocol that is an adaptable, whole host, high-content screening tool that can be utilized to study host-pathogen interactions and be used for drug discovery.

The number of new drugs identified by traditional, in vitro screens has waned, reducing the success of this approach in the search for new weapons to ...