We are very grateful to Victor G.J. Rodgers for valuable advice. We thank all of the members of the Liao group for very close collaborative work and for help with this study. This study was supported by the National Institutes of Health (Grant AI076504 to J.L.).

1. Plasmid Constructs
<ol>
 <li>Amplify the open reading frames of the genes by PCR, and clone the PCR products into PCRII-TOPO vector.</li>
 <li>Confirm the products by sequencing, and clone the cDNA encoding CyPet-(pre-SUMO1)-YPet, CyPet-SUMO1, YPet and catalytic domains of SENP1 into the pET28 (b) vector with an N-terminal hexahistidine tag.</li>
</ol>
2. Protein Expression and Purification
<ol>
 <li>Transform Escherichia coli cells of strain BL21 (DE3) with pET28 (b) vectors encoding CyPet-(pre-SUMO1)-YPet, CyPet-SUMO1, YPet and the catalytic domains of SENP1.</li>
 <li>Grown the transformed bacteria in 2xYT medium for 3 hr at 37 &deg;C (shaking at 250 rpm) to reach an optical density of 0.5 at 600 nm.</li>
 <li>Add 100 &mu;M isopropyl-&beta;-D-thiogalactoside (IPTG) (final concentration) to induce protein expression and shake for 16 hr at 25 &deg;C at 200 rpm.</li>
 <li>Harvest the bacteria by centrifugation at 10,000 rpm at 4 &deg;C for 5 min and resuspend them in a buffer of 20 mM Tris-HCl (pH 7.4), 50 mM NaCl, and 5 mM imidazole.</li>
 <li>Sonicate the cells for 10 min in 5-sec intervals at a power setting of 25 W using MiSonics 4,000 sonicator and collect them by centrifugation at 35,000 x g at 4 &deg;C for 30 min.</li>
 <li>Set up the column with 500 ml Ni-NTA beads for 1 L culture and transfer the supernatant into the column.</li>
 <li>Wash the resin with buffer of 20 mM Tris-HCl (pH 7.4), 500 mM NaCl, and 10 mM imidazole twice.</li>
 <li>Elute protein with buffer of 20 mM Tris-HCl (pH 7.4), 500 mM NaCl, and 500 mM imidazole and dialysis into a buffer of 20 mM Tris-HCl (pH 7.4), 50 mM NaCl and 1 mM dithiothreitol (DTT) at 4 &deg;C overnight.</li>
 <li>Determine the concentrations of the purified proteins by the Bradford assay. Alternative method for protein concentration measurements will be SDS-PAGE gel electrophoresis and then stained with Coomassie blue followed with imaging quantitative.</li>
</ol>
3. Quantitative FRET Spectrum Analysis
<ol>
 <li>The general strategy for the assay was based on FRET signaling (Figure 1). The FRET pair, CyPet and YPet, was tagged to the N- and C-termini, respectively, of pre-SUMO1. SENP1 cleaves the fusion protein CyPet-(pre-SUMO1)-YPet at the Gly-Gly site in SUMO1's C-terminus and, thus, releases the SUMO tail with YPet. The FRET signal is disrupted, resulting in an increase of the emission from CyPet and a dramatic decrease of YPet's emission at the CyPet excitation wavelength.</li>
 <li>When excited by light of wavelength 414 nm, the total fluorescence emission of CyPet-(pre-SUMO1)-YPet at 530 nm can be derived from three sources: the absolute FRET-induced YPet's emission, CyPet direct emission and YPet direct emission (Figure 2).</li>
</ol>
<img alt="Equation 1" src="/files/ftp_upload/4430/4430eq1.jpg" /> 
where FL530/414 is the total fluorescence emission at 530 nm when excited at 414 nm, FLFRET is the absolute FRET signal, FLCyPet(cont) is the CyPet direct emission when excited at 414 nm, and FLYPet (cont) is the YPet direct emission when excited at 414 nm. The subscript of (cont) stands for contribution.
<ol start="3">
 <li>The direct emission of CyPet at 530 nm was proportional to its emission at 475 nm when excited at 414 nm with a constant ratio of &alpha;. CyPet-SUMO1 was prepared at concentrations of 50, 100, 200, 500, and 750 nM and 1 mM, and emissions at 475 and 530 nm were measured after excitation at 414 nm to determine &alpha; (Figure 3-1).</li>
 <li>The direct emission of YPet at 530 nm under excitation at 414 nm was proportional to its emission at 530 nm when excited at 475 nm with a constant ratio of &beta;. YPet was prepared at concentrations of 50, 100, 200, 500, 750 and 1,000 nM, and the emission at 530 nm was measured when the samples were excited by wavelengths of 414 and 475 nm to determine &beta; (Figure 3-2).</li>
 <li>When CyPet-(pre-SUMO1)-YPet was digested by SENP1, the cleavage released CyPet-SUMO1 and the SUMO1 tail with YPet. When the compound was excited at 414 nm, the fluorescence emission at 530 nm (FL'530/414) was decreased but can still be divided into three parts as:</li>
</ol>
<img alt="Equation 2" src="/files/ftp_upload/4430/4430eq2.jpg" /> 
where FL'530/414 is the total fluorescence emission at 530 nm after digestion when excited at 414 nm, FL'FRET is the remaining absolute FRET signal, FL'CyPet(475/414)is the CyPet emission at 475 nm after digestion when excited at 414 nm (here the CyPet emission is from two parts: undigested CyPet-(pre-SUMO1)-YPet and digested CyPet-SUMO1), and FLYPet (530/475) is the YPet emission when excited at 475 nm, which is constant whether CyPet-(pre-SUMO1)-YPet is digested or not.
<ol start="6">
 <li>After digestion by SENP1, the remaining FRET emission (FL'FRET) is:</li>
</ol>
<img alt="Equation 3" src="/files/ftp_upload/4430/4430eq3.jpg" /> 
where C is the total concentration of CyPet-(pre-SUMO1)-YPet and x is the concentration of digested CyPet-(pre-SUMO1)-YPet.
<ol start="7">
 <li>By combining all of the items, the detected fluorescence emission at 530 nm under excitation of 414 nm (FL'530/414) is:</li>
</ol>
<img alt="Equation 4" src="/files/ftp_upload/4430/4430eq4.jpg" />
4. FRET-based Protease Assay for Enzyme Kinetic Study
<ol>
 <li>CyPet-(pre-SUMO1)-YPet was incubated with the catalytic domain of SENP1 at 37 &deg;C in a buffer of 20 mM Tris-HCl (pH 7.4), 50 mM NaCl, 0.1% (v/v) Tween-20 and 1 mM DTT to a total volume of 80 ml and transferred into 384-well plate.</li>
 <li>Runs were conducted by measuring the fluorescence emission at 475 and 530 nm after an excitation at 414 nm in a fluorescence multiwell plate reader for 5 min with 15-sec intervals.</li>
 <li>The reaction rate (v) was correlated with the change in the amount of substrate (S) as:</li>
</ol>
<img alt="Equation 5" src="/files/ftp_upload/4430/4430eq5.jpg" />
<ol start="4">
 <li>The concentration of product increased exponentially from 0 as [S]0 (original substrate concentration) when t=0:</li>
</ol>
<img alt="Equation 6" src="/files/ftp_upload/4430/4430eq6.jpg" />
<ol start="5">
 <li>When t=0, the original velocity (V0) is:</li>
</ol>
<img alt="Equation 7" src="/files/ftp_upload/4430/4430eq7.jpg" />
<ol start="6">
 <li>The concentration of SENP1 was fixed, and the concentration of CyPet-(pre-SUMO1)-YPet was increased from 100 times more than the concentration of enzyme, which is required by Michaelis-Menten equation.</li>
 <li>All of the fluorescent readings were analyzed by the quantitative FRET analysis method and plotted in GraphPad Prism V Software to fit the Michaelis-Menten equation. The nonlinear regression can also be performed with the aid of more common software packages like spreadsheet programs (such as Microsoft Excel).</li>
</ol>
5. Representative Results
Maturation of pre-SUMO1 by SENP1 can be determined by monitoring the changes in the fluorescence signal at 475 and 530 nm during the process. The result showed that the velocity of pre-SUMO1 digestion by SENP1 in a substrate-dose dependent manner (Figure 4). This suggests that the catalytic domain of SENP1 exhibits excellent activity for pre-SUMO1's maturation. The initial reaction velocities were calculated by the above analysis with different substrate concentrations (Table 1).
The kcat/KM ratio is generally used to compare the efficiencies of different enzymes with one substrate or a particular enzyme with different substrates. KM and Vmax can be obtained from the Michaelis-Menten equation by plotting the various initial velocities, corresponding to the different concentrations of CyPet-(pre-SUMO1)-YPet (Figure 5). kcat was obtained as:
<img alt="Equation 8" src="/files/ftp_upload/4430/4430eq8.jpg" /> 
According to the above analysis, the calculated KM was 0.21 &plusmn; 0.04 &mu;M, the kcat was 6.90 &plusmn; 0.28 s-1, and the kcat/KM ratio was (3.2 &plusmn; 0.55) x107 M-1s-1.
<img alt="Figure 1" src="/files/ftp_upload/4430/4430fig1.jpg" /> 
Figure 1. Graph of FRET-based protease assay for SENP's pre-SUMOs maturation.
<img alt="Figure 2" src="/files/ftp_upload/4430/4430fig2.jpg" /> 
Figure 2. Quantitative analysis of fluorescent signal as contributions by the donor, acceptor and FRET. Dissection of emission spectra from CyPet-(pre-SUMO1)-YPet under excitation at 414 nm. FLCyPet(530/414) is CyPet's emission at 530 nm under excitation of 414 nm, FLFRET is the FRET-induced YPet emission at 530 nm under excitation of 414 nm, and FLYPet(530/414) is YPet's emission at 530 nm under excitation of 414 nm.
<img alt="Figure 3" src="/files/ftp_upload/4430/4430fig3.jpg" /> 
Figure 3. Calculation of direction emission factor &alpha; and &beta;.
<img alt="Figure 4" src="/files/ftp_upload/4430/4430fig4.jpg" /> 
Figure 4. Quantitative analysis of CyPet-(pre-SUMO1)-YPet digested by different ratios of the catalytic domain of SENP1. Reactions were monitored within the first 5 min.
<img alt="Figure 5" src="/files/ftp_upload/4430/4430fig5.jpg" /> 
Figure 5. Michaelis-Menten graphical analysis of CyPet-(pre-SUMO1)-YPet's digestion by SENP1. Data were plotted and analyzed by GraphPad Prism V and nonlinear regression.
<table border="1">
 <tbody>
 <tr>
 <td>[S](&mu;M)</td>
 <td>V0(&mu;M/s)</td>
 </tr>
 <tr>
 <td>0.115</td>
 <td>0.0023&plusmn;0.00005</td>
 </tr>
 <tr>
 <td>0.214</td>
 <td>0.0028&plusmn;0.00004</td>
 </tr>
 <tr>
 <td>0.407</td>
 <td>0.0033&plusmn;0.00007</td>
 </tr>
 <tr>
 <td>0.594</td>
 <td>0.0037&plusmn;0.00013</td>
 </tr>
 <tr>
 <td>0.725</td>
 <td>0.0043&plusmn;0.00012</td>
 </tr>
 <tr>
 <td>1.471</td>
 <td>0.0051&plusmn;0.00036</td>
 </tr>
 <tr>
 <td>1.899</td>
 <td>0.0050&plusmn;0.00031</td>
 </tr>
 <tr>
 <td>2.300</td>
 <td>0.0050&plusmn;0.00062</td>
 </tr>
 </tbody>
</table>
Table 1. Initial velocities determination of pre-SUMO1's maturation by SENP1. In each substrate concentration, four samples were used to measure the digestion. The standard deviation came from the variations of these four samples.
<table border="1">
 <tbody>
 <tr>
 <td>KM(&mu;M)</td>
 <td>kcat(s-1)</td>
 <td>kcat/kM(M-1&bull;s-1)</td>
 </tr>
 <tr>
 <td>0.21&plusmn;0.04</td>
 <td>6.90&plusmn;0.28</td>
 <td>3.2&plusmn;0.55&times;107</td>
 </tr>
 </tbody>
</table>
Table 2. Kinetic parameters of pre-SUMO1's maturation by SENP1 by quantitative FRET analysis. The standard deviation came from the four samples in each substrate concentration.

<ol>
	<li>Johnson, E. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+modification+By+SUMO.">Protein modification By SUMO.</a> Annual Review of Biochemistry. 73, 355-382 (2004).</li><li>Gill, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SUMO+and+ubiquitin+in+the+nucleus:+different+functions,+similar+mechanisms.">SUMO and ubiquitin in the nucleus: different functions, similar mechanisms.</a> Genes &amp; Development. 18, 2046-2059 (2004).</li><li>Hay, R. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SUMO:+a+history+of+modification.">SUMO: a history of modification.</a> Molecular Cell. 18, 1-12 (2005).</li><li>M&#252;ller, S., Hoege, C., Pyrowolakis, G., Jentsch, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SUMO,+ubiquitin's+mysterious+cousin.">SUMO, ubiquitin's mysterious cousin.</a> Nature. , 202-210 (2001).</li><li>Hochstrasser, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SP-RING+for+SUMO:+new+functions+bloom+for+a+ubiquitin-like+protein.">SP-RING for SUMO: new functions bloom for a ubiquitin-like protein.</a> Cell. , 5-8 (2001).</li><li>Drag, M., Salvesen, G. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DeSUMOylating+enzymes-SENPs.">DeSUMOylating enzymes-SENPs.</a> IUBMB Life. 60, 734-742 (2008).</li><li>Mukhopadhyay, D., Dasso, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modification+in+reverse:+the+SUMO+proteases.">Modification in reverse: the SUMO proteases.</a> Trends in Biochemical Sciences. 32, 286-295 (2007).</li><li>Reverter, D., Lima, C. 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No conflicts of interest declared.

FRET technology has been used to study pre-SUMO1's maturation by SENP19. CFP-YFP was used as the FRET pair and ratiometric analysis, which is the ratio of acceptor to donor emissions, was used to characterize the kinetic properties. However, there is no consideration of donor and acceptor self-fluorescence in the traditional ratiometric FRET analysis. The ratio does not directly correlate with the amount of digested substrate.
Here we report a developed highly sensitive FRET-based p...

<table border="1">
<tbody>
 <tr>
 <td>Name of the reagent</td>
 <td>Company</td>
 <td>Catalogue number</td>
 </tr>
 <tr>
 <td>PCR II TOPO Kit</td>
 <td>Invitrogen</td>
 <td>K466040</td>
 </tr>
 <tr>
 <td>2xYT</td>
 <td>Research Products Internationa.l Corp.</td>
 <td>X15600 </td>
 </tr>
 <tr>
 <td>Ni-NTA Agrose</td>
 <td>Thermo Scientific</td>
 <td>88222 </td>
 </tr>
 <tr>
 <td>Coomassie plus (Bradford) Assay Regent</td>
 <td>Thermo Scientific</td>
 <td>23238</td>
 </tr>
 <tr>
 <td>384-well plate (glass bottom)</td>
 <td>Greiner</td>
 <td>781892</td>
 </tr>
 <tr>
 <td>FlexStation II 384 plate reader</td>
 <td>Molecular Device</td>
 <td></td>
 </tr>
 </tbody>
</table>

quantitative fret (f&#246;rster resonance energy transfer) analysis for senp1 protease kinetics determination

Reversible posttranslational modifications of proteins with ubiquitin or ubiquitin-like proteins (Ubls) are widely used to dynamically regulate protein activity and have diverse roles in many biological processes. For example, SUMO covalently modifies a large number or proteins with important roles in many cellular processes, including cell-cycle regulation, cell survival and death, DNA damage response, and stress response 1-5. SENP, as SUMO-specific protease, functions as an endopeptidase in the maturation of SUMO precursors or as an isopeptidase to remove SUMO from its target proteins and refresh the SUMOylation cycle 1,3,6,7.
The catalytic efficiency or specificity of an enzyme is best characterized by the ratio of the kinetic constants, kcat/KM. In several studies, the kinetic parameters of SUMO-SENP pairs have been determined by various methods, including polyacrylamide gel-based western-blot, radioactive-labeled substrate, fluorescent compound or protein labeled substrate 8-13. However, the polyacrylamide-gel-based techniques, which used the "native" proteins but are laborious and technically demanding, that do not readily lend themselves to detailed quantitative analysis. The obtained kcat/KM from studies using tetrapeptides or proteins with an ACC (7-amino-4-carbamoylmetylcoumarin) or AMC (7-amino-4-methylcoumarin) fluorophore were either up to two orders of magnitude lower than the natural substrates or cannot clearly differentiate the iso- and endopeptidase activities of SENPs.
Recently, FRET-based protease assays were used to study the deubiquitinating enzymes (DUBs) or SENPs with the FRET pair of cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP) 9,10,14,15. The ratio of acceptor emission to donor emission was used as the quantitative parameter for FRET signal monitor for protease activity determination. However, this method ignored signal cross-contaminations at the acceptor and donor emission wavelengths by acceptor and donor self-fluorescence and thus was not accurate.
We developed a novel highly sensitive and quantitative FRET-based protease assay for determining the kinetic parameters of pre-SUMO1 maturation by SENP1. An engineered FRET pair CyPet and YPet with significantly improved FRET efficiency and fluorescence quantum yield, were used to generate the CyPet-(pre-SUMO1)-YPet substrate 16. We differentiated and quantified absolute fluorescence signals contributed by the donor and acceptor and FRET at the acceptor and emission wavelengths, respectively. The value of kcat/KM was obtained as (3.2 &plusmn; 0.55) x107 M-1s-1 of SENP1 toward pre-SUMO1, which is in agreement with general enzymatic kinetic parameters. Therefore, this methodology is valid and can be used as a general approach to characterize other proteases as well.

Watch this Scientific Journal Video about Quantitative FRET FÃ¶rster Resonance Energy Transfer Analysis for SENP1 Protease Kinetics Determination at JoVE.com

Quantitative FRET F&amp;#246;rster Resonance Energy Transfer Analysis for SENP1 Protease Kinetics Determination

A novel method involving quantitative analysis of FRET (F&ouml;rster Resonance Energy Transfer) signals is described for studying enzyme kinetics. KM and kcat were obtained for the hydrolysis of the catalytic domain of SENP1 (SUMO/Sentrin specific protease 1) to pre-SUMO1 (Small Ubiquitin-like MOdifier). The general principles of this quantitative-FRET-based protease kinetic study can be applied to other proteases.

Quantitative FRET (F&#246;rster Resonance Energy Transfer) Analysis for SENP1 Protease Kinetics Determination

Reversible posttranslational modifications of proteins with ubiquitin or ubiquitin-like proteins (Ubls) are widely used to dynamically regulate protein ...

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비디오: Quantitative FRET F&#246;rster Resonance Energy Transfer Analysis for SENP1 Protease Kinetics Determination

Improved Visualization and Quantitative Analysis of Drug Effects Using Micropatterned Cells

To date, most HCA (High Content Analysis) studies are carried out with adherent cell lines grown on a homogenous substrate in tissue-culture treated micro-plates. Under these conditions, cells spread and divide in all directions resulting in an inherent variability in cell shape, morphology and behavior. The high cell-to-cell variance of the overall population impedes the success of HCA, especially for drug development. The ability of micropatterns to normalize the shape and internal polarity of every individual cell provides a tremendous opportunity for solving this critical bottleneck 1-2.
To facilitate access and use of the micropatterning technology, CYTOO has developed a range of ready to use micropatterns, available in coverslip and microwell formats. In this video article, we provide detailed protocols of all the procedures from cell seeding on CYTOOchip micropatterns, drug treatment, fixation and staining to automated acquisition, automated image processing and final data analysis. With this example, we illustrate how micropatterns can facilitate cell-based assays. Alterations of the cell cytoskeleton are difficult to quantify in cells cultured on homogenous substrates, but culturing cells on micropatterns results in a reproducible organization of the actin meshwork due to systematic positioning of the cell adhesion contacts in every cell. Such normalization of the intracellular architecture allows quantification of even small effects on the actin cytoskeleton as demonstrated in these set of protocols using blebbistatin, an inhibitor of the actin-myosin interaction.

Adhesive micropatterns that normalize cellular architecture can be used to increase sensitivity in the detection of drug effects, improve reproducibility and simplify automated image acquisition and analysis. Such technology will benefit drug/siRNA screening assays, performed on conventional cell culture supports and consequently suffering from excessive cell-to-cell variability.

To date, most HCA (High Content Analysis) studies are carried out with adherent cell lines grown on a homogenous substrate in tissue-culture treated ...

Adhesion Frequency Assay for In Situ Kinetics Analysis of Cross-Junctional Molecular Interactions at the Cell-Cell Interface

The micropipette adhesion assay was developed in 1998 to measure two-dimensional (2D) receptor-ligand binding kinetics1. The assay uses a human red blood cell (RBC) as adhesion sensor and presenting cell for one of the interacting molecules. It employs micromanipulation to bring the RBC into contact with another cell that expresses the other interacting molecule with precisely controlled area and time to enable bond formation. The adhesion event is detected as RBC elongation upon pulling the two cells apart. By controlling the density of the ligands immobilized on the RBC surface, the probability of adhesion is kept in mid-range between 0 and 1. The adhesion probability is estimated from the frequency of adhesion events in a sequence of repeated contact cycles between the two cells for a given contact time. Varying the contact time generates a binding curve. Fitting a probabilistic model for receptor-ligand reaction kinetics1 to the binding curve returns the 2D affinity and off-rate.
The assay has been validated using interactions of Fc&gamma; receptors with IgG Fc1-6, selectins with glycoconjugate ligands6-9, integrins with ligands10-13, homotypical cadherin binding14, T cell receptor and coreceptor with peptide-major histocompatibility complexes15-19.
The method has been used to quantify regulations of 2D kinetics by biophysical factors, such as the membrane microtopology5, membrane anchor2, molecular orientation and length6, carrier stiffness9, curvature20, and impingement force20, as well as biochemical factors, such as modulators of the cytoskeleton and membrane microenvironment where the interacting molecules reside and the surface organization of these molecules15,17,19.
The method has also been used to study the concurrent binding of dual receptor-ligand species3,4, and trimolecular interactions19 using a modified model21.
The major advantage of the method is that it allows study of receptors in their native membrane environment. The results could be very different from those obtained using purified receptors17. It also allows study of the receptor-ligand interactions in a sub-second timescale with temporal resolution well beyond the typical biochemical methods.
To illustrate the micropipette adhesion frequency method, we show kinetics measurement of intercellular adhesion molecule 1 (ICAM-1) functionalized on RBCs binding to integrin &alpha;L&beta;2 on neutrophils with dimeric E-selectin in the solution to activate &alpha;L&beta;2.

Adhesion Frequency Assay for In Situ Kinetics Analysis of Cross-Junctional Molecular Interactions at the Cell-Cell Interface

An adhesion frequency assay for measuring receptor-ligand interaction kinetics when both molecules are anchored on the surfaces of the interacting cells is described. This mechanically-based assay is exemplified using a micropipette-pressurized human red blood cell as adhesion sensor and integrin &alpha;L&beta;2 and intercellular adhesion molecule-1 as interacting receptors and ligands.

The micropipette adhesion assay was developed in 1998 to measure two-dimensional (2D) receptor-ligand binding kinetics1. The assay uses a human red blood ...

Microfluidic-based Electrotaxis for On-demand Quantitative Analysis of Caenorhabditis elegans' Locomotion

The nematode Caenorhabditis elegans is a versatile model organism for biomedical research because of its conservation of disease-related genes and pathways as well as its ease of cultivation. Several C. elegans disease models have been reported, including neurodegenerative disorders such as Parkinson's disease (PD), which involves the degeneration of dopaminergic (DA) neurons 1. Both transgenes and neurotoxic chemicals have been used to induce DA neurodegeneration and consequent movement defects in worms, allowing for investigations into the basis of neurodegeneration and screens for neuroprotective genes and compounds 2,3.
Screens in lower eukaryotes like C. elegans provide an efficient and economical means to identify compounds and genes affecting neuronal signaling. Conventional screens are typically performed manually and scored by visual inspection; consequently, they are time-consuming and prone to human errors. Additionally, most focus on cellular level analysis while ignoring locomotion, which is an especially important parameter for movement disorders.
We have developed a novel microfluidic screening system (Figure 1) that controls and quantifies C. elegans' locomotion using electric field stimuli inside microchannels. We have shown that a Direct Current (DC) field can robustly induce on-demand locomotion towards the cathode ("electrotaxis") 4. Reversing the field's polarity causes the worm to quickly reverse its direction as well. We have also shown that defects in dopaminergic and other sensory neurons alter the swimming response 5. Therefore, abnormalities in neuronal signaling can be determined using locomotion as a read-out. The movement response can be accurately quantified using a range of parameters such as swimming speed, body bending frequency and reversal time.
Our work has revealed that the electrotactic response varies with age. Specifically, young adults respond to a lower range of electric fields and move faster compared to larvae 4. These findings led us to design a new microfluidic device to passively sort worms by age and phenotype 6.
We have also tested the response of worms to pulsed DC and Alternating Current (AC) electric fields. Pulsed DC fields of various duty cycles effectively generated electrotaxis in both C. elegans and its cousin C. briggsae 7. In another experiment, symmetrical AC fields with frequencies ranging from 1 Hz to 3 KHz immobilized worms inside the channel 8.
Implementation of the electric field in a microfluidic environment enables rapid and automated execution of the electrotaxis assay. This approach promises to facilitate high-throughput genetic and chemical screens for factors affecting neuronal function and viability.

Microfluidic-based Electrotaxis for On-demand Quantitative Analysis of Caenorhabditis elegans&#039; Locomotion

A semi-automated micro-electro-fluidic method to induce on-demand locomotion in Caenorhabditis elegans is described. This method is based on the neurophysiologic phenomenon of worms responding to mild electric fields (&#x201C;electrotaxis&#x201D;) inside microfluidic channels. Microfluidic electrotaxis serves as a rapid, sensitive, low-cost, and scalable technique to screen for factors affecting neuronal health.

The nematode Caenorhabditis elegans is a versatile model organism for biomedical research because of its conservation of disease-related genes and ...

Drug-induced Sensitization of Adenylyl Cyclase: Assay Streamlining and Miniaturization for Small Molecule and siRNA Screening Applications

Sensitization of adenylyl cyclase (AC) signaling has been implicated in a variety of neuropsychiatric and neurologic disorders including substance abuse and Parkinson&#39;s disease. Acute activation of G&#945;i/o-linked receptors inhibits AC activity, whereas persistent activation of these receptors results in heterologous sensitization of AC and increased levels of intracellular cAMP. Previous studies have demonstrated that this enhancement of AC responsiveness is observed both in vitro and in vivo following the chronic activation of several types of G&#945;i/o-linked receptors including D2 dopamine and &#956; opioid receptors. Although heterologous sensitization of AC was first reported four decades ago, the mechanism(s) that underlie this phenomenon remain largely unknown. The lack of mechanistic data presumably reflects the complexity involved with this adaptive response, suggesting that nonbiased approaches could aid in identifying the molecular pathways involved in heterologous sensitization of AC. Previous studies have implicated kinase and Gb&#947; signaling as overlapping components that regulate the heterologous sensitization of AC. To identify unique and additional overlapping targets associated with sensitization of AC, the development and validation of a scalable cAMP sensitization assay is required for greater throughput. Previous approaches to study sensitization are generally cumbersome involving continuous cell culture maintenance as well as a complex methodology for measuring cAMP accumulation that involves multiple wash steps. Thus, the development of a robust cell-based assay that can be used for high throughput screening (HTS) in a 384&#160;well format would facilitate future studies. Using two D2 dopamine receptor cellular models (i.e.&#160;CHO-D2L and HEK-AC6/D2L), we have converted our 48-well sensitization assay (&#62;20 steps 4-5 days) to a five-step, single day assay in 384-well format. This new format is amenable to small molecule screening, and we demonstrate that this assay design can also be readily used for reverse transfection of siRNA in anticipation of targeted siRNA library screening.

Persistent activation of inhibitory G protein-coupled receptors results in sensitization of adenylyl cyclase signaling. To identify the essential molecular pathways, nonbiased approaches are necessary; however, this strategy requires the development of a scalable cell-based cAMP sensitization assay. Herein, we describe a sensitization assay for small molecule and siRNA screening.

Sensitization of adenylyl cyclase (AC) signaling has been implicated in a variety of neuropsychiatric and neurologic disorders including substance abuse ...

Luminescence Resonance Energy Transfer to Study Conformational Changes in Membrane Proteins Expressed in Mammalian Cells

Luminescence Resonance Energy Transfer, or LRET, is a powerful technique used to measure distances between two sites in proteins within the distance range of 10-100 &#197;. By measuring the distances under various ligated conditions, conformational changes of the protein can be easily assessed. With LRET, a lanthanide, most often chelated terbium, is used as the donor fluorophore, affording advantages such as a longer donor-only emission lifetime, the flexibility to use multiple acceptor fluorophores, and the opportunity to detect sensitized acceptor emission as an easy way to measure energy transfer without the risk of also detecting donor-only signal. Here, we describe a method to use LRET on membrane proteins expressed and assayed on the surface of intact mammalian cells. We introduce a protease cleavage site between the LRET fluorophore pair. After obtaining the original LRET signal, cleavage at that site removes the specific LRET signal from the protein of interest allowing us to quantitatively subtract the background signal that remains after cleavage. This method allows for more physiologically relevant measurements to be made without the need for purification of protein.

We describe here an improved Luminescence Resonance Energy Transfer (LRET) method where we introduce a protease cleavage site between the donor and acceptor fluorophore sites. This modification allows us to obtain specific LRET signals arising from membrane proteins of interest, allowing for the study of membrane proteins without protein purification.

Luminescence Resonance Energy Transfer, or LRET, is a powerful technique used to measure distances between two sites in proteins within the distance range ...

Measuring TCR-pMHC Binding In Situ using a FRET-based Microscopy Assay

T-cells are remarkably specific and effective when recognizing antigens in the form of peptides embedded in MHC molecules (pMHC) on the surface of Antigen Presenting Cells (APCs). This is despite T-cell antigen receptors (TCRs) exerting usually a moderate affinity (&#181;M range) to antigen when binding is measured in vitro1. In view of the molecular and cellular parameters contributing to T-cell antigen sensitivity, a microscopy-based methodology has been developed as a means to monitor TCR-pMHC binding in situ, as it occurs within the synapse of a live T-cell and an artificial and functionalized glass-supported planar lipid bilayer (SLB), which mimics the cell membrane of an Antigen presenting Cell (APC) 2. Measurements are based on F&#246;rster Resonance Energy Transfer (FRET) between a blue- and red-shifted fluorescent dye attached to the TCR and the pMHC. Because the efficiency of FRET is inversely proportional to the sixth power of the inter-dye distance, one can employ FRET signals to visualize synaptic TCR-pMHC binding. The sensitive of the microscopy approach supports detection of single molecule FRET events. This allows to determine the affinity and off-rate of synaptic TCR-pMHC interactions and in turn to interpolate the on-rate of binding. Analogous assays could be applied to measure other receptor-ligand interactions in their native environment.

Measuring TCR-pMHC Binding In Situ using a FRET-based Microscopy Assay

This manuscript describes how to conduct (single molecule) F&#246;rster Resonance Energy Transfer (FRET)- based assays to measure the binding dynamics between T-cell antigen receptor (TCR) and antigenic peptide-loaded MHC molecules as they occur within the immunological synapse of a T-cell in contact with a functionalized planar supported lipid bilayer.

T-cells are remarkably specific and effective when recognizing antigens in the form of peptides embedded in MHC molecules (pMHC) on the surface of Antigen ...

Sensitive Detection of Proteopathic Seeding Activity with FRET Flow Cytometry

Increasing evidence supports transcellular propagation of toxic protein aggregates, or proteopathic seeds, as a mechanism for the initiation and progression of pathology in several neurodegenerative diseases, including Alzheimer's disease and the related tauopathies. The potentially critical role of tau seeds in disease progression strongly supports the need for a sensitive assay that readily detects seeding activity in biological samples. 
By combining the specificity of fluorescence resonance energy transfer (FRET), the sensitivity of flow cytometry, and the stability of a monoclonal cell line, an ultra-sensitive seeding assay has been engineered and is compatible with seed detection from recombinant or biological samples, including human and mouse brain homogenates. The assay employs monoclonal HEK 293T cells that stably express the aggregation-prone repeat domain (RD) of tau harboring the disease-associated P301S mutation fused to either CFP or YFP, which produce a FRET signal upon protein aggregation. The uptake of proteopathic tau seeds (but not other proteins) into the biosensor cells stimulates aggregation of RD-CFP and RD-YFP, and flow cytometry sensitively and quantitatively monitors this aggregation-induced FRET. The assay detects femtomolar concentrations (monomer equivalent) of recombinant tau seeds, has a dynamic range spanning three orders of magnitude, and is compatible with brain homogenates from tauopathy transgenic mice and human tauopathy subjects. With slight modifications, the assay can also detect seeding activity of other proteopathic seeds, such as &#945;-synuclein, and is also compatible with primary neuronal cultures. The ease, sensitivity, and broad applicability of FRET flow cytometry makes it useful to study a wide range of protein aggregation disorders.

Cell-to-cell transfer of protein aggregates, or proteopathic seeds, may underlie the progression of pathology in neurodegenerative diseases. Here, a novel FRET flow cytometry assay is described that enables specific and sensitive detection of seeding activity from recombinant or biological samples.

Increasing evidence supports transcellular propagation of toxic protein aggregates, or proteopathic seeds, as a mechanism for the initiation and ...

Multicolor Fluorescence Detection for Droplet Microfluidics Using Optical Fibers

Fluorescence assays are the most common readouts used in droplet microfluidics due to their bright signals and fast time response. Applications such as multiplex assays, enzyme evolution, and molecular biology enhanced cell sorting require the detection of two or more colors of fluorescence. Standard multicolor detection systems that couple free space lasers to epifluorescence microscopes are bulky, expensive, and difficult to maintain. In this paper, we describe a scheme to perform multicolor detection by exciting discrete regions of a microfluidic channel with lasers coupled to optical fibers. Emitted light is collected by an optical fiber coupled to a single photodetector. Because the excitation occurs at different spatial locations, the identity of emitted light can be encoded as a temporal shift, eliminating the need for more complicated light filtering schemes. The system has been used to detect droplet populations containing four unique combinations of dyes and to detect sub-nanomolar concentrations of fluorescein.

Multicolor fluorescence detection in droplet microfluidics typically involves bulky and complex epifluorescence microscope-based detection systems. Here we describe a compact and modular multicolor detection scheme that utilizes an array of optical fibers to temporally encode multicolor data collected by a single photodetector.

Fluorescence assays are the most common readouts used in droplet microfluidics due to their bright signals and fast time response. Applications such as ...

A Protocol for Using F&#246;rster Resonance Energy Transfer (FRET)-force Biosensors to Measure Mechanical Forces across the Nuclear LINC Complex

The LINC complex has been hypothesized to be the critical structure that mediates the transfer of mechanical forces from the cytoskeleton to the nucleus. Nesprin-2G is a key component of the LINC complex that connects the actin cytoskeleton to membrane proteins (SUN domain proteins) in the perinuclear space. These membrane proteins connect to lamins inside the nucleus. Recently, a F&#246;rster Resonance Energy Transfer (FRET)-force probe was cloned into mini-Nesprin-2G (Nesprin-TS (tension sensor)) and used to measure tension across Nesprin-2G in live NIH3T3 fibroblasts. This paper describes the process of using Nesprin-TS to measure LINC complex forces in NIH3T3 fibroblasts. To extract FRET information from Nesprin-TS, an outline of how to spectrally unmix raw spectral images into acceptor and donor fluorescent channels is also presented. Using open-source software (ImageJ), images are pre-processed and transformed into ratiometric images. Finally, FRET data of Nesprin-TS is presented, along with strategies for how to compare data across different experimental groups.

A Protocol for Using F&amp;#246;rster Resonance Energy Transfer (FRET)-force Biosensors to Measure Mechanical Forces across the Nuclear LINC Complex

A number of FRET-based force biosensors have recently been developed, enabling the protein-specific resolution of intracellular force. In this protocol, we demonstrate how one of these sensors, designed for the linker of the nucleoskeleton-cytoskeleton (LINC) complex protein Nesprin-2G can be used to measure actomyosin forces on the nuclear LINC complex.

The LINC complex has been hypothesized to be the critical structure that mediates the transfer of mechanical forces from the cytoskeleton to the nucleus. ...

Engineering Molecular Recognition with Bio-mimetic Polymers on Single Walled Carbon Nanotubes

Semiconducting single-wall carbon nanotubes (SWNTs) are a class of optically active nanomaterial that fluoresce in the near infrared, coinciding with the optical window where biological samples are most transparent. Here, we outline techniques to adsorb amphiphilic polymers and polynucleic acids onto the surface of SWNTs to engineer their corona phases and create novel molecular sensors for small molecules and proteins. These functionalized SWNT sensors are both biocompatible and stable. Polymers are adsorbed onto the nanotube surface either by direct sonication of SWNTs and polymer or by suspending SWNTs using a surfactant followed by dialysis with polymer. The fluorescence emission, stability, and response of these sensors to target analytes are confirmed using absorbance and near-infrared fluorescence spectroscopy. Furthermore, we demonstrate surface immobilization of the sensors onto glass slides to enable single-molecule fluorescence microscopy to characterize polymer adsorption and analyte binding kinetics.

We present a protocol for engineering the corona phase of near infrared fluorescent single walled carbon nanotubes (SWNTs) using amphiphilic polymers and DNA to develop sensors for molecular targets without known recognition elements.

Semiconducting single-wall carbon nanotubes (SWNTs) are a class of optically active nanomaterial that fluoresce in the near infrared, coinciding with the ...