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46 protocols using sigmaplot 9

1

Electrophysiological Characterization of Cells

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Current-clamp experiments were carried out using an Axopatch 200A (Axon Instruments, Union City, CA). Data were digitized using a Digidata 1332a (Axon Instruments). Data capture and voltage control were performed using Clampex (pClamp9.0; Axon Instruments). Data were analyzed with Clampfit10.6.2.2 (Molecular Devices, San Jose, CA).
For analyses, mean, SD, SE, and t test calculations were carried out using Excel (Microsoft, Redmond, WA). All calculated data are means ± SE. Plots were constructed using Excel (Microsoft) and SigmaPlot 9 (Systat Software, San Jose, CA).
Capacitance and input resistance were calculated by fitting the discharging phase of voltage traces using the following double-exponential decay equation: y=aexpt/τa+mexpt/τm, where y is membrane potential (Vm), a and m are amplitudes, τ − a and τ − m are decaying time constants, t is time, and τ = RC, where R is membrane resistance and C is cell capacitance.
Double-exponential fit was necessary because discharging voltage traces consist of the access resistance (Racc, number of transmembrane conductive nanoparticles) and the membrane input resistance (Rm). Contributions of Racc and Rm were determined as a and m, and contributions of decay time constant were τ − a and τ − m, respectively.
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2

Quantitative Protein Expression Analysis

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All experiments were repeated at least three times and results were expressed as mean ± SE. One Way analysis of variance (ANOVA) was calculated with SigmaPlot 9 (Systat Software, San Jose, CA). A one-tailed t-test was used to compare any significant difference between control and treated groups. The criterion for statistical significance was p<0.05. For western blotting results, the band intensities were measured by using the ImageJ and normalized with GAPDH.
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3

Statistical Analysis of Experimental Data

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Experimental data were analyzed using statistical software Statistix 8.1 (Analytical Software, Tallahassee, Florida, USA) while differences among means were separated using the least significant difference (LSD) test at the 5% probability level. Correlation analyses were computed and represented using SigmaPlot 9.0 (Systat Software Inc., San Jose, California, USA).
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4

Statistical Analysis of Experimental Data

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All the obtained data were subjected to a one-way analysis of variance (ANOVA) using Statistix 8.1 (Analytical Software, Tallahassee, FL, United States). Statistix 8.1 was also used to perform correlation analysis, and the heatmap for the investigated parameters was established with Microsoft Excel. The differences among means were separated using the least significant (LSD) test at the 5% probability level. Sigma Plot 9.0 (Systat Software Inc., San Jose, CA, United States) was used to make figures.
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5

Patch-Clamp Analysis of Ca2+ Channel Properties

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The patch pipettes and micropipettes used for injection of Ca 2+ were prepared from borosilicate glass capillary tubes with an outer diameter of 1.5 mm (Kwik-Fil, TW150-4, World Precision Instruments), pulled by a universal puller (DMZ). The patch pipette tip had an inside diameter of approx. 2 µm. An Ag-AgCl reference electrode filled with 100 mM KCl was connected with the bath solution via a ceramic porous bridge. The recordings were made by a patch-clamp amplifier EPC-10 (Heka Electronik) coupled with the Patchmaster software (Heka Elektronik). The signals were recorded with a frequency of 10 kHz and filtered at 2 kHz. The recordings, which lasted 10 s or more (Fig. 5), were drawn by taking into account every tenth measuring point. Elaboration of the current/voltage characteristics (I/V) and column diagrams showing dependence of the open probability on the voltage applied was made in SigmaPlot 9.0 (Systat Software Inc.). The slope of the I/V curve allowed calculation of the unitary conductance of the channels. Open probability of the channels was calculated in Fitmaster (Heka Elektronik).
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6

Statistical Analysis of Experimental Data

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Data were analyzed and plotted by using the pCLAMP8.1 Clampfit 8.1 software (Axon Instruments, Foster City, CA, USA) and SigmaPlot 9.0 (Systat Software, Richmond, CA, USA). Results were presented as the mean ± SD. Statistical significance was determined using the Student’s t test to compare the means between two groups, and one-way analysis of variance (ANOVA) to compare the means among more than two groups. Differences were considered to be significant if p < 0.05; all the differences listed were statistically significant, unless stated otherwise.
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7

Simulation Visualization in SigmaPlot

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All simulation plots are presented as mean ± SD, using SigmaPlot 9.0 from Systat Software, Inc., San Jose, CA, USA (www.sigmaplot.com).
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8

Automated Quantification of Retinal Cones

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Total numbers of remaining L- and S-cones were counted automatically on retinal wholemounts using recently developed routines that count labelled cone outer-segments [1] (link)–[3] , [42] (link), and the data were translated into isodensity maps (Sigmaplot 9.0, Systat Software Inc., Richmond, CA) as reported [1] (link)–[3] to allow the visualization of detailed topological distribution. The light exposed retinas showed a damaged region of circular shape, with diminished densities of L- and S-cones and an almost absence of these in its centre. Thus, an additional macro was designed to count remaining L- or S-opsin immunoreactive cones within predetermined fixed-size circular areas (PCA) of the retina that comprised the light-damaged region, which was larger for S- than for L-cones, and thus PCA were larger for S- (radius of 1.3 mm) than for L- (radius of 1 mm) cones (Fig. 2). For each experimental animal, these counts were obtained from the left retina and from a corresponding region in their right-fellow retina (Fig. 2). An additional macro enabled representation of the number of L- or S-opsin immunoreactive cone outer-segments within these PCA in both retinas.
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9

Kinetic Analysis of Competitive Inhibition

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The initial rates of O2 consumption by PHM were measured at eight different concentrations of the oxidizable substrate in the absence and presence of three different inhibitor concentrations. N-Acetylglycine served as the oxidizable substrate at concentrations of 1.0–45.0 mM. The initial velocities from the inhibition experiments were fit to the equations for competitive, noncompetitive and uncompetitive inhibition, respectively, using SigmaPlot 9.0 (Systat Software, San Jose, CA). All the inhibition data contained herein were the best fit to the one-site competitive inhibition model for the calculation of KI,obs.
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10

Randomized Pot Experiment with LSD

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Pots were arranged in a completely randomized design with 10 pots per treatment, whereas the dataset was analyzed by “Statistix 8” (Analytical Software, Tallahassee, Florida, USA) while the least significant difference (LSD) (P0.05) was used to calculate the difference among treatment means. SigmaPlot 9.0 (Systat Software Inc., San Jose, CA, USA) was used to generate graphs.
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