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Kaleidagraph 4

Manufactured by Synergy Software
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Sourced in United States, Panama, Japan, United Kingdom

KaleidaGraph 4.0 is a data analysis and visualization software tool. It provides functionality for importing, manipulating, and graphing data. The software can generate a variety of chart types to display data.

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Lab products found in correlation

Prism 7b, by GraphPad (8 mentions) Metamorph 7, by Molecular Devices (4 mentions) Statview 4, by Abacus (3 mentions) Prism 5, by GraphPad (3 mentions) Prism 8, by GraphPad (2 mentions) Fluoromax 4 spectrofluorometer, by Horiba (2 mentions) Vc 8 valve controller, by Warner Instruments (2 mentions) Spss statistics 26, by IBM (2 mentions) Cary 50 uv vis spectrophotometer, by Agilent Technologies (2 mentions) Model fp 8500, by Jasco (2 mentions) Pmod v3, by PMOD Technologies (2 mentions) Cell growth determination kit mtt based, by Merck Group (1 mentions) Infinite m1000 plate reader, by Tecan (1 mentions) Softmax pro 4, by Molecular Devices (1 mentions) Prism 7, by GraphPad (1 mentions) Fluostar omega, by BMG Labtech (1 mentions) Pti time master fluorometer, by Molecular Devices (1 mentions) Gemini xps microplate spectrofluorometer, by Molecular Devices (1 mentions) Matlab, by MathWorks (1 mentions) Chirascan cd spectrometer, by Applied Photophysics (1 mentions)

169 protocols using kaleidagraph 4

1

Statistical Analysis of Cell Treatments

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Statistical analysis was performed using KaleidaGraph 4.0 Synergy Software Inc (Reading, PA, USA). One-way ANOVA, followed by a Scheffe multiple range test, was used to determine the statistical significance in comparison to cells treated and untreated. F values of all statistical analysis are shown in the Tables S1–S3 of Supplemental Information. Data are expressed as the mean ± standard error of the mean. In all cases, values of p ≤ 0.05 were considered statistically significant.
Silva T.C., de Andrade P.B., Paiva-Martins F., Valentão P, & Pereira D.M. (2017). In Vitro Anti-Inflammatory and Cytotoxic Effects of Aqueous Extracts from the Edible Sea Anemones Anemonia sulcata and Actinia equina. International Journal of Molecular Sciences, 18(3), 653.
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2

Dose-Dependent Cell Survival Assay

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Cells were seeded at subconfluent levels (<50% confluence) in 96-well tissue culture plates and treated with increasing concentrations of MS-444 [21 (link)] for 48 hours at 37°C. Cell survival was assayed using the MTT-based cell growth determination kit (Sigma-Aldrich) as previously described [3 (link)]. Relative cell survival was calculated as percentage relative to DMSO vehicle-treated controls. A dose-response curve was fitted to the data using the software KaleidaGraph 4.0 (Synergy), from which the half-maximal inhibitory concentration (IC50) was derived and represented as a mean of 4 independent experiments ± standard error of the mean (SEM).
Blanco F.F., Preet R., Aguado A., Vishwakarma V., Stevens L.E., Vyas A., Padhye S., Xu L., Weir S.J., Anant S., Meisner-Kober N., Brody J.R, & Dixon D.A. (2016). Impact of HuR inhibition by the small molecule MS-444 on colorectal cancer cell tumorigenesis. Oncotarget, 7(45), 74043-74058.
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3

Fluorescence Anisotropy Assays for Protein-DNA Binding

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Fluorescence anisotropy assays were performed in assay buffer (50 mM Tris/HCl pH 8.0, 150 mM NaCl, 1 mM TCEP, 0.1 mg/ml BSA) using a TECAN infinite M1000 plate reader (Tecan Group Ltd., Männedorf, Switzerland) and 480 nm excitation/520 nm emission wavelengths. His6-tagged AvrBs3 and variants were purified under reducing conditions and used at concentrations sufficient to saturate dsDNA E1U20 fragment [6 (link)] binding at the highest concentration. A protein dilution series (factor 0.6) was titrated with 0.5 nM fluoresceine-labeled DNA. DNA and protein mixtures were incubated in a 96-well plate for 10 min at RT before readout. Values are the means of three independent measurements wherein each measured point was set up in duplicate. Binding data were analyzed using Kaleidagraph 4.0 (Synergy Software, Reading, USA) and corrected with a linear equation for unspecific binding and using a simple model assuming one binding site per DNA fragment and a 1:1 stoichiometry. For comparison, fluorescence polarization units were normalized; 100% represents saturated binding.
Schreiber T., Sorgatz A., List F., Blüher D., Thieme S., Wilmanns M, & Bonas U. (2015). Refined Requirements for Protein Regions Important for Activity of the TALE AvrBs3. PLoS ONE, 10(3), e0120214.
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4

Catechol Levels in Parkinson's Diseases

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Tissue catechol concentrations were expressed as fmol/mg wet weight. For statistical tests individual neurochemical data were log transformed. This is a commonly used and appropriate approach when compared groups differ substantially not only in mean values but also in standard deviations and the standard deviations vary directly with the mean values.
Most of the samples had been assayed previously, before we had developed methodology for simultaneous measurements of cysteinyl and parent catechols. Re-thawing of the samples decreased DOPAL contents. Therefore, DOPAL data from the first set of assays were used.
Catechol concentrations in PDA and MSA vs. control groups were compared by factorial analyses of variance with Fisher’s PLSD post-hoc test. Pearson correlation coefficients relating neurochemical values across subjects were calculated using Kaleidagraph 4.0 (Synergy Software).
Goldstein D.S., Sullivan P., Holmes C., Mash D.C., Kopin I.J, & Sharabi Y. (2016). Determinants of denervation-independent depletion of putamen dopamine in Parkinson’s disease and multiple system atrophy. Parkinsonism & related disorders, 35, 88-91.
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5

Statistical Analysis of Experimental Data

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Statistical analysis of data was performed using Softmax Pro 4.8 software (Molecular Devices, Sunnyvale, CA), KaleidaGraph 4.0 (Synergy Software, Reading, PA), and GraphPad Prism 7 statistical software (GraphPad Software, Inc. La Jolla, CA).
Akter T., Atanelishvili I., Noguchi A., Silver R.M, & Bogatkevich G.S. (2017). Establishment of an indirect ELISA for detection of the novel antifibrotic peptide M10. PLoS ONE, 12(11), e0188588.
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6

Aggregation Kinetics of WT and H50Q α-Synuclein

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Samples of recombinant WT and H50Q α-Syn, 100 μl at different concentrations (5, 10, 30, 50, 70, and 100 μm, respectively) in PBS, pH 7.4, containing 10 μm thioflavin T (ThT) (32 (link)), were incubated at 37 °C in Costar 96-well black wall plates sealed with sealing film (4titude Gas Permeable Moisture Barrier Seal) and subjected to 900 rpm double orbital shaking. Bottom fluorescence was recorded at 15-min intervals (FLUOstar Omega, BMG LABTECH). Time courses of aggregation were fitted to a sigmoidal model, as y = y0 + (ymax − y0)/(1 + exp[−kapp(t − t½)]) using KaleidaGraph 4.0 (Synergy Software, Reading, PA), where y0 and ymax are the initial and maximum ThT fluorescence, respectively; kapp is the apparent rate constant, and lag time was defined as t½ − 2/kapp (18 (link)). Experiments were conducted in triplicate in three independent experiments. Samples containing the ThT positive material were further analyzed by electron microscopy. Further aggregation time courses were performed using mixtures of WT/H50Q at 0:1, 1:5, 1:2, 1:1, 2:1, 5:1, and 1:0 molar ratios, respectively, keeping the total protein concentration at 70 μm.
Porcari R., Proukakis C., Waudby C.A., Bolognesi B., Mangione P.P., Paton J.F., Mullin S., Cabrita L.D., Penco A., Relini A., Verona G., Vendruscolo M., Stoppini M., Tartaglia G.G., Camilloni C., Christodoulou J., Schapira A.H, & Bellotti V. (2014). The H50Q Mutation Induces a 10-fold Decrease in the Solubility of α-Synuclein. The Journal of Biological Chemistry, 290(4), 2395-2404.
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7

Kinetic Analysis of Aptamer-Conjugated ALPs

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The kinetic parameters, including affinity of the substrate to the active site of the enzyme (Km), maximum rate of reaction (Vmax), and rate constant for the catalytic conversion of substrate into product (kcat), of ALPs conjugated with the RBD-1C aptamer [36 (link)] were determined for four types of substrates: pNPP, BCIP, 4-MUP, and CDP-Star®. Briefly, 1 nM of the RBD-1C aptamer-ALP conjugates were incubated at 37 °C for 15 min in a solution containing 0.1 M Na2CO3/NaHCO3 buffer (pH 9.6) and 1 mM MgCl2, with the final concentration of each substrate ranging from 0.23 mM to 2.50 mM. After the enzymatic reaction was terminated, the concentration of inorganic phosphate ions liberated from each solution was quantified using the conventional colorimetric molybdenum blue method [42 (link)]. Finally, the approximate Km and Vmax values were determined using KaleidaGraph 4.0 (Synergy Software, Reading, PA, USA).
Nukazuka A., Asai S., Hayakawa K., Nakagawa K., Kanazashi M., Kakizoe H., Hayashi K., Kawahara T., Sawada K., Kuno H, & Kano K. (2023). Electrical biosensing system utilizing ion-producing enzymes conjugated with aptamers for the sensing of severe acute respiratory syndrome coronavirus 2. Sensing and Bio-Sensing Research, 39, 100549.
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8

Steady-State Kinetics of GTPase Inhibition

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Steady-state kinetic measurements were conducted under initial velocity conditions with varying concentrations of GTP (3-50 μM) as substrate. Assays were carried out in 100 mM HEPES (pH 8.0), 100 mM KCl, 0.5 mM MnCl2, 1 mM DTT and 0.5 μM of protein in a final volume of 100 μL at 37 oC. Reactions were terminated at various time points and analyzed by fluorescence with either a PTI Time-Master fluorometer or a Gemini XPS microplate spectrofluorometer (Molecular Devices) as described above. Kinetic parameters were calculated from the average of minimally 4 triplicates with the Michaelis-Menten equation using the software Kaleidagraph 4.0 (Synergy Software, Reading, PA).
Inhibition analysis was conducted by assessing enzyme activity in the presence of various fixed concentrations of 2′-deoxy-GTP (0, 50, 100, 200 μM), 7-deaza-GTP (0, 15, 30, 60 μM), or 8-oxo-GTP (0.1, 0.25, 0.5 μM). Reactions were carried out as described above in the presence of 1 mM DTT, 0.5 μM protein, 0.5 mM MnCl2, variable GTP concentration (3-50 μM), and analyzed by fluorescence. The data (average of minimally 4 triplicates) were fitted to the equation for competitive inhibition (eq. 1)
where ν is the initial rate of reaction, S is the varied substrate concentration, I is the inhibitor concentration, Ki is the inhibition constant, and V is the maximum reaction velocity.
Paranagama N., Bonnett S.A., Alvarez J., Luthra A., Stec B., Gustafson A., Iwata-Reuyl D, & Swairjo M.A. (2017). Mechanism and catalytic strategy of the prokaryotic specific GTP cyclohydrolase IB. The Biochemical journal, 474(6), 1017-1039.
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9

Statistical Analysis of Group Differences

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Differences between two groups were examined with the Student’s t-test. Differences among more than two groups were analyzed with a one-way analysis of variance followed by Dunnett’s post-hoc test and Tukey’s test. p values < 0.05 were considered significantly different. All statistics were performed using KaleidaGraph 4.0 (Synergy Software, Tokyo, Japan).
Hamano M., Tomonaga S., Osaki Y., Oda H., Kato H, & Furuya S. (2020). Transcriptional Activation of Chac1 and Other Atf4-Target Genes Induced by Extracellular l-Serine Depletion is negated with Glycine Consumption in Hepa1-6 Hepatocarcinoma Cells. Nutrients, 12(10), 3018.
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10

Statistical Analysis of Experimental Data

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Data are presented as mean ± SD or as frequency. Statistical analyses on means were performed using the Student's t test. Statistical analyses on frequencies were performed using the χ2 test. All analyses were performed using Excel 2010 (Microsoft, Redmond, WA). All plots were created using KaleidaGraph 4.0 (Synergy Software, Reading, PA). Dot-and-box plots show all individual data points, and the plots enclose 50% of the data in the box, with the median value displayed as a line. The lines extending from the top and bottom of each box mark the minimum and maximum values within the data set that fall within an acceptable range. Outliers are displayed as individual points.
Costa J., Fu C., Khare V.M, & Tran P.T. (2014). csi2p modulates microtubule dynamics and organizes the bipolar spindle for chromosome segregation. Molecular Biology of the Cell, 25(24), 3900-3908.
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