RADseq-derived SNP genotype data: 14,031 loci, 48 individuals, species = Leiopotherapon unicolor.

Data is R S4 class ‘genind’ object (adegenet R package): “unicolor_data.RData”. The data are RADseq-derived SNP genotypes scored for 14,031 loci in 48 individuals. Individual sample codes in this file include population identifier and individual identifier. Please see Readme.txt file

Mean COP Total excursions in the ML direction for all subjects, intervals and measurement sessions (1_1, …, 2_2).

<p>Mean COP Total excursions in the ML direction for all subjects, intervals and measurement sessions (1_1, …, 2_2).</p

Bland-Altman plots for the AP (top) and ML (bottom) perturbation directions, showing examples for intervals 1 (left plots) and 2 (right plots).

<p>Bland-Altman plots for the AP (top) and ML (bottom) perturbation directions, showing examples for intervals 1 (left plots) and 2 (right plots).</p

COP Total excursions in both perturbation directions: AP (top), ML (bottom) from six randomly chosen subjects, showing all individual trials (12) for each of the four measurement sessions (1_1, …, 2_2).

<p>COP Total excursions in both perturbation directions: AP (top), ML (bottom) from six randomly chosen subjects, showing all individual trials (12) for each of the four measurement sessions (1_1, …, 2_2).</p

COP Total excursions (mean±SD) for both perturbation directions (AP, ML), all four measurement sessions and all analyzed intervals.

<p>Significant differences</p><p>*p˂0.001</p><p>^#p = 0.001</p><p>^Φp = 0.003</p><p>^Ψp = 0.003</p><p>^Χp = 0.002.</p><p>Significant differences between the four measurement sessions are marked with superscripted symbols; see below (α = 0.0125).</p

Visualization of the Magnetic Structure of Sculpted Three-Dimensional Cobalt Nanospirals

In this work, we report on the direct visualization of magnetic structure in sculpted three-dimensional cobalt (Co) nanospirals with a wire diameter of 20 nm and outer spiral diameter of 115 nm and on the magnetic interactions between the nanospirals, using aberration-corrected Lorentz transmission electron microscopy. By analyzing the magnetic domains in three dimensions at the nanoscale, we show that magnetic domain formation in the Co nanospirals is a result of the shape anisotropy dominating over the magnetocrystalline anisotropy of the system. We also show that the strong dipolar magnetic interactions between adjacent closely packed nanospirals leads to their magnetization directions adopting alternating directions to minimize the total magnetostatic energy of the system. Deviations from such magnetization structure can only be explained by analyzing the complex three-dimensional structure of the nanospirals. These nanostructures possess an inherent chirality due to their growth conditions and are of significant importance as nanoscale building blocks in magneto-optical devices

Template position dependence of misincorporation rates.

<p>(A) Template position dependence of Dpo4 misincorporation rates on the original template at varying Mn²⁺ (left) and Mg²⁺ concentration (right). (B) Template position dependence of Dpo4 misincorporation rates on the swapped template at varying Mn²⁺ (left) and Mg²⁺ concentration (right). (C) Template position dependence of Klenow exo⁻ misincorporation rates on the original template at varying Mn²⁺ (left) and Mg²⁺ concentration (right). Letters above each data point denote the identity of the template base at that position. Grey shaded areas indicate the noise floor, defined as the maximum over positions of the misincorporation rate (plus SEM) observed in an identical experiment with Pfusion HF DNA polymerase (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043876#pone.0043876.s001" target="_blank">Figure S1</a>). Red (blue) shaded areas in (A) and (B) correspond to shared sub-sequences between the original and the swapped template.</p

Statistical analysis of misincorporation by Dpo4.

<p>(A) Spatial dependence (un-normalized) of Dpo4 error rate at 800 µM Mn²⁺ on the original template (blue curve), and generalized linear model fits of this data set with respect to itself (green curve), and with respect to the swapped template data set (red curve). (B) Spatial dependence (un-normalized) of Dpo4 error rate at 800 µM Mn²⁺ on the swapped template (blue curve), and generalized linear model fits of this data set with respect to itself (green curve), and with respect to the original template data set (red curve). (C) Feature weights for generalized linear model fit to Dpo4 original template data. (D) Feature weights for generalized linear model fit to Dpo4 swapped template data. (E) Information gain per base as a function of template position, for discrimination between high (800 µM) and low (75 µM) Mn²⁺ by Dpo4. (F) Information gain per base as a function of template position, for discrimination between high (7000 µM) and low (1000 µM) Mg²⁺ by Dpo4.</p

Ion-dependent misincorporation rates of Dpo4 and Klenow exo⁻ polymerases.

<p>(A, B, C, D) Mean (top) and template-base-specific (bottom) misincorporation rates as a function of Mn²⁺ (A, C) and Mg²⁺ (B, D) concentrations. (E, F, G, H) Normalized distributions of misincorporated dNTPs for each template base. (I, J, K, L) Mean (top) and template-base-specific (bottom) misincorporation rates as a function of Ca²⁺ concentration at 200 µM background Mn²⁺ (I, K) and 7000 µM background Mg²⁺ (J, L) concentrations. Errors are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043876#pone.0043876.s005" target="_blank">Tables S1</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043876#pone.0043876.s006" target="_blank">2</a>, and are shown as error bars in the line graphs when they are larger than the data symbol.</p

DNA polymerase (DNAP) as a molecular signal recorder.

<p>(A) Overview of a strategy for using DNA polymerases as signal recording devices. Signals (top) are coupled to intracellular or extracellular cation concentration through direct or indirect modulation of an ion channel activity. Cation concentration is in turn coupled to DNA polymerase fidelity on a known template according to a known transfer function (orange curve), generating a DNA recording, in which data is represented by the density of misincorporated bases, and which can be read by DNA sequencing (bottom). (B) Modulation of Taq polymerase by Ca²⁺ concentration, measured by a traditional blue-white colony counting assay <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043876#pone.0043876-Bebenek1" target="_blank">[25]</a>. (C) Biochemical steps of the multiplex deep sequencing assay for measuring the transfer functions of error-prone DNAPs.</p