Electrophysiology data were analyzed using standard macros available with Igor Pro v8.0 (Wavemetrics). In situ hybridization was analyzed using the Anaconda v1.9.7 distribution of Python v3.4 with a Jupyter environment v6.0.1. Electrophysiology and gene expression data were further analyzed in Excel (Microsoft Office 2016), and statistical analyses were performed in Prism v8.3.0 (GraphPad). Songs were analyzed using Sound Analysis Pro (SAP) software v2011.087 (soundanaylsispro.com)123 (link) and Raven Lite v2.0.1 (ravensoundsoftware.com)124 . Means and SE are reported unless otherwise noted.
Igorpro v8
Manufactured by Wavemetrics
Sourced in United States
IgorPro v8.04 is a powerful data analysis and graphing software developed by Wavemetrics. It provides a comprehensive suite of tools for processing, analyzing, and visualizing scientific data. The software is designed to handle a wide range of data types and offers a user-friendly interface for efficient data management and manipulation.
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Lab products found in correlation
Mueller hinton broth (mhb), by Merck Group (3 mentions)
Dp 311, by Warner Instruments (3 mentions)
X pert highscore plus software, by Malvern Panalytical (2 mentions)
Prism v8, by GraphPad (1 mentions)
Originpro v2020, by OriginLab (1 mentions)
Illustrator v24, by Adobe (1 mentions)
Prism v9, by GraphPad (1 mentions)
Prism 8, by GraphPad (1 mentions)
Prism v6, by GraphPad (1 mentions)
15 protocols using igorpro v8
1
Multi-Modal Analysis of Neurophysiology Data
2
ROS Imaging Data Analysis Workflow
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ROS imaging data were analyzed with EasyRatioPro (PTI, HORIBA Scientific) software and further processed with Excel (Microsoft, Redmond, WA, USA) and Igor Pro v8.0 (Wavemetrics, Lake Oswego, OR, USA) software. Protoplast images were processed with ImageJ (NIH). Figures were prepared with Origin Pro v2020 (Originlab, Northampton, MA, USA) and Adobe Illustrator v24.1 (Adobe, San Jose, CA, USA). Averaged data are presented as means ± SEM (N = number of protoplasts from 3–5 independent measurements). For comparisons with two groups such as basal ROS levels and ROS levels from DF M. sexta OS and tomato PF M. sexta OS, we used the non-parametric Mann-Whitney U test. For comparison with three groups, as depicted in Figure 4 , for basal OS/tbH2O2 and NAC, we used a non-parametric Kruskal-Wallis test followed by Dunn’s pairwise post hoc comparisons. Non-parametric tests were used since data failed to meet normality assumptions after transformations. For all analyses, data from extractions were pooled to attain a sample size of 66–124 protoplasts and were repeated for at least three replications. All analyses were carried out using GraphPad Prism v9.0 (La Jolla, CA, USA).
3
Microbial Growth Kinetics Assay
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Cells expressing plasmids of interest were grown in Mueller-Hinton broth (Sigma, 100µg/mL ampicillin, pH 7.0) from a single colony to an OD of 0.2 at 37 °C. The cells were then diluted to a final OD of 0.01 in 384-well microplates containing concentration ranges of MV 2+ , harmane, 18-crown-6-ether, and chelerythrine chloride. The plates were incubated and shaken in a microplate reader (BMG-Labtech) at 37°C. OD600 was measured every 5 minutes for 20 hours. Experiments were performed with four biological replicates and data were analyzed using Igor Pro v8 (WaveMetrics Inc.).
4
Harmane Drug Sensitivity in E. coli EmrE
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MG1655 ∆emrE E. coli cells expressing either WT or E14Q-EmrE were grown overnight at 37 °C from a single colony. Harmane was serially diluted across a 96-well microplate in Mueller-Hinton broth (Sigma, 100µg/mL ampicillin, pH 7.0) from 0-0.4mM, with or without 25mM bicarbonate, and assayed with a starting OD600 of 0.01. Plates were then sealed and incubated with shaking for 18h at 37°C. OD600 endpoints were taken using a microplate reader (BMG-Labtech). Relative growth was calculated by dividing the measured OD600 from a given concentration by the OD600 for cells containing no drug. IC50 curves were performed in triplicate with three biological replicates per plate. Data was fit to a simple sigmoid equation using Igor Pro v8 (WaveMetrics Inc.). For symport (blue), the 16-fold drug gradient is oriented with the proton gradient. A third condition testing the presence of a drug without a gradient (black) acts as a control for drug-activated proton uniport.
5
Ethidium and harmane resistance assay
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MG1655 ∆emrE E. coli cells expressing either WT or E14Q-EmrE were grown overnight at 37 °C from a single colony. Concentration ranges of ethidium bromide (0-5 mM) and harmane (0-0.4mM) were assayed in microplates with a starting OD600 of 0.1. Plates were then incubated with shaking for 18 hours with shaking at 37 °C. OD600 endpoints were taken using a BMG plate reader. Relative growth was calculated by dividing the measured OD600 from a given concentration by the OD600 for cells containing no s. Experiments were performed in triplicate and fit a simple sigmoid equation using Igor Pro v8 (WaveMetrics Inc.).
6
Evaluating EmrE Efflux Pump Inhibition
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MG1655 ∆emrE E. coli cells expressing either WT or E14Q-EmrE were grown overnight at 37 °C from a single colony. Harmane was serially diluted across a 96-well microplate in Mueller-Hinton broth (Sigma, 100 µg/mL ampicillin, pH 7.0) from 0–0.4 mM, with or without 25 mM bicarbonate (pH 7.4), and assayed with a starting OD600 of 0.01. Plates were then sealed and incubated with shaking for 18 h at 37 °C. OD600 endpoints were taken using a microplate reader (BMG-Labtech). Relative growth was calculated by dividing the measured OD600 from a given concentration by the OD600 for cells containing no drug. IC50 curves were performed in triplicate with three biological replicates per plate. Data were fit to a simple sigmoid equation using Igor Pro v8 (WaveMetrics Inc.).
7
Ultrafast Transient Absorption Spectroscopy
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A Helios pump-probe spectrometer (Ultrafast Systems, LLC, Florida, USA) was used in a transmission mode. 800-nm pulses (≥ 35 fs, 4.0 mJ per pulse, at 1 kHz) were generated by a SpitFire Pro 35F regenerative amplifier (Spectra Physics, Newport, CA, USA). The amplifier was pumped with an Empower 30 Q-switched laser ran at 20 W. A MaiTai SP oscillator provided the seed pulses with 55-nm bandwidth. The wavelength of the pump was tuned using an optical parametric amplifier, OPA-800CU (Newport Corporation, Newport, CA, USA), equipped with harmonic generators. Responses from pure solvents were used for the chirp correction of the transient-absorption data. The data analysis was carried out using Surface Xplorer (Ultrafast Systems, LLC, Florida, USA) and IgorPro v. 8 (WaveMetrics, Inc., Lake Oswego, OR, USA) (Purc et al. 2016 (link); Bao et al. 2014 (link); Upadhyayula et al. 2015 (link); Gray et al. 2017 (link); Guo et al. 2013 (link)).
8
Acute Cortical Slice Excitotoxicity
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Acute brain slices were placed in an interface chamber (32–34°C) and perfused with aCSF saturated with 95% O2 and 5% CO2. Glass electrodes filled with aCSF were placed in the neocortex (layers IV and V of somatosensory regions) identified using a stereomicroscope (AmScope). Extracellular field potentials were recorded using a low-noise differential amplifier (DP-311, Warner Instruments, 100x gain) and digitized at 2 kHz (IX/408, iWorx Systems Incorporated). NMDA was briefly applied to the slices (30µM, 10 minutes) to induce an acute excitotoxic injury. Field potentials at baseline, during NMDA treatment, and washout were analyzed using a custom-written macro in IgorPro v8.04 (WaveMetrics).
9
Statistical Analysis of Gaussian Data
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We tested the Gaussian distribution of data with the Shapiro–Wilk and Kolmogorov–Smirnov tests. Paired t-tests were used for parametric comparisons, and the Mann–Whitney test was used for unpaired non-parametric data. For non-parametric analysis, a Friedman test was performed with Dunn’s multiple comparison test for post-hoc analysis. Estimation statistics were performed and used to compute 95% confidence intervals of the mean differences27 (link),28 (link). Statistical significance was set to p < 0.05. IgorPro v8.04 (WaveMetrics), Prism 8 (GraphPad Software, LLC), and the python package DABEST28 (link) were used for data analysis.
10
Inducing Epileptiform Activity in Cortical Slices
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