Journal: STAR Protocols

Article Title: Comparing Circadian Rhythmicity in the Human Gut Microbiome

doi: 10.1016/j.xpro.2020.100148

Figure Lengend Snippet: .OTU Table in GraphPad The Excel sheet is transferred in an XZ/Sheet in GraphPad Prism for further analysis.

Article Snippet: A nonlinear regression needs to be applied with the following equation ( ): y = b a s e l i n e + a m p l i t u d e ∗ cos ( 2 ∗ π ( x − p h a s e s h i f t 24 ) ) .OTU Nonlinear Regression Analysis in GraphPad or a double harmonic cosine wave equation: y = b a s e l i n e + ( a m p l i t u d e A ∗ cos ( 2 ∗ π ( x − p h a s e s h i f t A 24 ) ) ) + ( a m p l i t u d e B ∗ cos ( 4 ∗ π ( x − p h a s e s h i f t B 24 ) ) ) on alpha -diversity and relative abundance, with a fixed 24-h period. iv.

Techniques:

Journal: STAR Protocols

Article Title: Comparing Circadian Rhythmicity in the Human Gut Microbiome

doi: 10.1016/j.xpro.2020.100148

Figure Lengend Snippet: .OTU Nonlinear Regression Analysis in GraphPad

Article Snippet: A nonlinear regression needs to be applied with the following equation ( ): y = b a s e l i n e + a m p l i t u d e ∗ cos ( 2 ∗ π ( x − p h a s e s h i f t 24 ) ) .OTU Nonlinear Regression Analysis in GraphPad or a double harmonic cosine wave equation: y = b a s e l i n e + ( a m p l i t u d e A ∗ cos ( 2 ∗ π ( x − p h a s e s h i f t A 24 ) ) ) + ( a m p l i t u d e B ∗ cos ( 4 ∗ π ( x − p h a s e s h i f t B 24 ) ) ) on alpha -diversity and relative abundance, with a fixed 24-h period. iv.

Techniques:

Journal:

Article Title: Biochemical and Genetic Characterizations of a Novel Human Immunodeficiency Virus Type 1 Inhibitor That Blocks gp120-CD4 Interactions

doi: 10.1128/JVI.77.19.10528-10536.2003

Figure Lengend Snippet: Competitive inhibition of gp120-CD4 binding by BMS-378806 and binding affinity of BMS-378806 to gp120. (A) Saturation binding curve of BMS-378806. The levels of sCD4 bound to gp120 in the absence or presence of various concentrations of BMS-378806 and in escalating concentrations of sCD4 were measured by using the gp120-CD4 binding ELISA. BMS-378806 concentrations: ▪, 0 μM; ▴, 0.8 μM; ▾, 1.6 μM; ⧫, 3.2 μM. Data were analyzed according to the one-site binding model with GraphPad Prism. OD450, optical density at 450 nm. (B) Apparent binding constants for sCD4 in the absence and presence of BMS-378806. The Kd and Bmax values were derived by using nonlinear regression analysis with GraphPad Prism. Values were the means ± standard errors of the means, representing two independent experiments. (C) Binding affinity of BMS-378806 to gp120 by SPA. [3H]BMS-378806 binding to the gp120 protein was measured by employing gp120-coated SPA beads. The amount of gp120-bound [3H]BMS-378806 was determined by using a Packard TopCount scintillation counter. The results from Scatchard analysis of binding isotherm are shown in the insert. The x axis represents bound (corrected), and the y axis indicates bound/free.

Article Snippet: The curve represents the best fit to a saturation binding isotherm determined by using GraphPad Prism.

Techniques: Inhibition, Binding Assay, Enzyme-linked Immunosorbent Assay, Derivative Assay

Journal:

Article Title: Biochemical and Genetic Characterizations of a Novel Human Immunodeficiency Virus Type 1 Inhibitor That Blocks gp120-CD4 Interactions

doi: 10.1128/JVI.77.19.10528-10536.2003

Figure Lengend Snippet: Binding stoichiometry of BMS-378806 to gp120 protein. gp120JRFL (1.0 μM) was titrated with BMS-378806, and the observed percent reduction in fluorescence from each of four independent experiments was plotted first as a function of BMS-378806 concentration (data not shown). Each of these data sets was then normalized to the percent maximal fluorescence reduction observed for each experiment in order to analyze the four sets of data together. The individual, normalized data sets are depicted as open squares, closed squares, closed diamonds, and open triangles. The curve represents the best fit to a saturation binding isotherm determined by using GraphPad Prism.

Article Snippet: The curve represents the best fit to a saturation binding isotherm determined by using GraphPad Prism.

Techniques: Binding Assay, Fluorescence, Concentration Assay