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183 protocols using igor pro software

1

Single-Molecule FRET Kinetics Analysis

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All intensity versus time traces were corrected for background and smoothed using 3-point linear averaging. For single-color experiments, multiple A555 emission traces were compiled and used to construct composite intensity histograms, using Igor Pro software (WaveMetrics). Individual time traces were also fitted using Hidden Markov modeling (26 (link)) to determine dwell times spent in a given state prior to transition to another state. Histograms of these dwell times were compiled and fitted with a single-exponential function to determine the rate constant for transitions from one state to another, using Igor Pro software (WaveMetrics). In cases where a single-exponential fit was not adequate, based on the reduced chi-square value, the histogram was fitted with a bi-exponential function. The uncertainties in the fitted rate constants were also reported by the software. For FRET analysis, the apparent FRET efficiency at each time point, Eapp, was calculated according to Equation (2): where ID and IA are the donor and acceptor emission intensities at the corresponding time point, respectively. Composite histograms of apparent FRET efficiency were compiled from multiple time traces.
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2

Indentation Testing for Material Stiffness

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The Young's modulus E was extracted from the indentation part of the force curves by fitting the modified Hertz model for a pyramidal indenter [53] , which gives the force (F) as a function of the indentation depth (d):
The Poisson's ratio ν was set to 0.5 for incompressible materials [54] (link); α is the half opening angle to an edge of the tip, which was 17.5°for the used tips. All force curves were analyzed from the contact point up to an indentation depth of 1 μm, using the JPK Data Processing software (Version 6.1.42, JPK Instruments AG, Berlin, Germany). The Young's modulus values of all force-indentation curves were summarized in a stiffness distribution (histogram). To locate the maxima of these histograms, a Gaussian distribution was fitted to each histogram using the Igor Pro software (Version 6.3.4.0, WaveMetrics, Oregon, USA).
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3

Automated Patch-Clamp Characterization of nAChRs

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Electrophysiological responses were recorded using an automated patch-clamp Patchliner Octo® system (Nanion Technologies, Munich, Germany) equipped with two EPC-10 Quadro patch-clamp amplifiers (HEKA Elektronik, Lambrecht, Germany) as described previously [2 (link)]. Chinese hamster ovarian (CHO) cells stably expressing human α4β2 nAChRs (Charles River Laboratories, Wilmington, MA, USA) were used. All experiments were performed at room temperature (24 °C) and repeated at least three times. Data were analyzed using Patchmaster software (HEKA Elektronik). Offline data analysis was performed in Apache OpenOffice™ (v4.1.2; Microsoft, Redmond, WA, USA). Igor Pro software (v6.2.2.2; WaveMetrics, Lake Oswego, OR, USA) was used to determine EC50 values. The efficacy of the compounds was calculated by first normalizing the current induced by each compound by the internal acetylcholine control. These values were then expressed as a percentage of maximum receptor activation by nicotine. The average values were then fitted to the Hill equation:  I=Baseline+XnH(Imax-Baseline)/XnH+EC50nH, where I is the current response, Baseline is the minimal current response, X is the agonist concentration, nH is the Hill coefficient, Imax is the maximal current, and EC50 is the agonist concentration producing half-maximal activation. Data are presented as mean ± SD.
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4

Analyzing Retinal Ganglion Cell Firing

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RGC firing rate was calculated in 100 ms bins for individual retinas in light and in darkness. The Photoswitch Index was calculated in order to normalize light-elicited changes in firing rate of individual retinal ganglion cells and plotted as interquartile range (Boxplot). PI = (firing rate in the light − firing rate in darkness)/(firing rate in the light + firing rate in darkness). Data analysis was performed using custom routines in IgorPro software (Wavemetrics) or Matlab. In order to analyze oscillatory activity between 0 to 40 Hz we used the Chronux Matlab Package to calculate the multitaper spectrum over a moving window (mtspecgramc)20 ,21 (link). Raw data was converted to hdf5-files with no further preprocessing. Settings parameters were set to (‘tapers’, [5 9], ‘Fs’, 40000, ‘fpass’, [1 40], ‘pad’, 1, ‘trialave’, 1). Power is represented as µV2.
For analysis of ‘maximum frequency in power’ the peak of the highest frequency reaching a threshold of 4 SD was measured.
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5

In Vivo Bioluminescence Imaging in Mice

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For BLI of live animals, as previously described (35 (link)), mice were injected intraperitoneally with 150 μg/g d-luciferin (Biosynth Carbosynth) in PBS, anesthetized with 2.5% isoflurane, and imaged with a charge-coupled device camera-based BLI system (IVIS 100; Caliper Life Sciences; exposure time 1–60 seconds, binning 8, field of view 12, f/stop 1, open filter, anterior side). Signal was displayed as photons/s/cm2/steradian. ROIs were defined manually around the legs using Living Image (PerkinElmer) and Igor Pro Software (Version 2.50, WaveMetrics).
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6

Atomic Force Microscopy of Articular Cartilage

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Knees from 14-week-old WT and ERp57 cKO mice were dissected, embedded in O.C.T. compound mounting medium (00411243, VWR chemicals, Darmstadt, Germany), and frozen in liquid nitrogen. A Leica CM1950 cryostat (Leica Biosystems, Wetzlar, Germany) was used to generate 20 µm-thick frozen tissue sections. Sections were thawed, submerged in PBS buffer, and analyzed with a NanoWizard I AFM (JPK Instruments, Berlin, Germany) in combination with an inverse optical microscope (Axiovert 200, Zeiss, Göttingen, Germany) as described before [23 (link),54 (link),55 (link)]. Briefly, silicon nitride cantilevers (0.1 N/m, MLCT, Bruker) were used to record 625 indentation curves in an area of 3 × 3 µm2. For each sample, 9 areas were measured. The sample stiffness was determined by fitting a modified Hertz model to the force-indentation curves using the JPK Data Processing software (V5.0.96, JPK Instruments, Berlin, Germany). Histograms of the Youngs Moduli were generated and a linear combination of two Gaussian functions was fitted to the histograms utilizing Igor Pro software (Version 6.3.7.2, WaveMetrics).
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7

Intercellular Calcium Wave Induction

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Intercellular calcium waves were induced as previously described by deformation of the cell membrane via a light mechanical stimulus using a glass micropipette electrode [28 (link)–30 (link)]. Glass micropipette electrodes were pulled from thick-walled borosilicate glass tubing, filled with imaging buffer, and mounted on a piezoelectric micromanipulator. With constant monitoring of the resistance, the electrode was slowly lowered toward the cell layer, briefly contacting the cell surface followed by immediate withdrawal. This mechanical stimulus reliably induced intercellular calcium waves in the astrocyte cultures. Movies were imported into Igor Pro software (Wavemetrics). All fluorescent data were normalized to the global maximum value and plotted as a percentage of this value. The radial distribution of intensities was calculated based on the manually-identified wave center initiation point. Distance and time measures were based on a threshold intensity of 50%.
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8

Artificial Lesion Removal Imaging Analysis

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Images were acquired before and after artificial lesion removal using three different modalities: Digital microscopy (DCDM), PS-OCT, and PLM. The volume of the lesions was measured using CP-OCT before and after removal by the laser. Statistical calculations were carried out using Prism (Graphpad Software, La Jolla, CA). Teeth were sectioned after lesion removal and the 200-μm thick sections were examined using polarized light microscopy (PLM). Images were then compared to their respective CP-OCT images to confirm existence of artificial lesions. All image analysis was carried out using Igor pro software (Wavemetrics, Lake Oswego, OR). A repeated measures one-way analysis of variance (ANOVA) followed by the Tukey-Kramer post-hoc multiple comparison test was used to compare groups employing Prism software (GraphPad, San Diego, CA).
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9

Surface Plasmon Resonance Analysis of Hsp90 Binding

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All SPR experiments were performed using a Reichert (Depew, NY) SR7000 SPR refractometer at 37°C with a flow rate of 41 μL/min. Full-length CtxA1, full-length PtxS1 (List Biologicals, Campbell, CA), or peptide (Peptide 2.0, Chantilly, VA) was amide-coupled to an SPR sensor slide with a mixed-assembled monolayer as previously described (Massey et al., 2009 (link)). The slide was then washed with phosphate-buffered saline with 0.1% Tween 20 (Medicago AB, Uppsala, Sweden) until a stable baseline signal was achieved. Hsp90 with 1 mM ATP was then added to the perfusion buffer for 100–180 sec. After the removal of Hsp90/ATP, the slide was washed with phosphate-buffered saline with 0.1% Tween 20. Hsp90 without ATP was used as a negative control for all experiments. For competition assays, Hsp90 was first incubated with the indicated peptide in the presence of ATP for 10 min at room temperature before addition to the perfusion buffer. SPR traces were processed using Reichert software, BioLogic (Campbell, Australia) Scrubber2 software, and WaveMetrics (Lake Oswego, OR) Igor Pro software.
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10

Screening STIM1 Residues Involved in Cholesterol Interaction

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To screen important residues in cholesterol interact within SOAR we used a modified version of lg-TIRFM (TIRF Labs, Inc., Cary, NC.) as previously described48 (link)49 (link). Briefly, 30 length aminoacids covering from 350 to 380 of STIM1 were synthetized. All peptides were purchased from JPT Peptide Technologies (Berlin, Germany). Peptide spots were printed manually by means of a TIRF MicroArrayer (TIRF Labs, Cary, NC.) on conventional microarray slides coated with poly-L-lysine (Sigma, St. Louis, MO.). Lg-TIRFM-1000 system in combination with an iXon electron-multiplying charge-coupled device (EMCCD) camera (Andor Technology, South Windsor, CT.) were used to monitor fluorescence of peptide arrays incubated with 10 μM of Dehydroergosterol (DHE). Image analysis was conducted with Igor pro software (wavemetrics, Portland, OR.).
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