Nuclear lineage simulations with and without transcriptional inheritance.

<p>Shown are simulated examples (A and B) and the H-function profiles (C and D) of the nuclear types with (B and D) or without (A and C) inheritance of transcriptional states. These depicted examples are for illustrative purposes by showing the simulated transcription state lineages with nuclei aligned in one dimension; see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060876#pone.0060876.s003" target="_blank">Figure S3</a> for simulated examples of 8-nuclei lineage clusters arranged in two-dimensional fields. For the initial conditions at cycle 11, the probability of <i>hb</i> busting is set at a high level as observed experimentally (see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060876#s2" target="_blank">Materials and Methods</a>). With an overall transcribing probability of 90%, the majority of nuclei are Type 2 (81%), with Type-1 being 18% and Type-0 being 1% (not shown in the diagrams that are for illustrative purposes only). At cycle 13, a binomial process is implemented in our simulation that randomly shuts off active <i>hb</i> copies so that the overall transcribing probability becomes 50% (with Types-0, -1 and -2 being 25%, 50% and 25%, respectively). The type of each nucleus in (A) is assigned by the binomial random number generator of MATLAB.</p

H-function analysis of experimental fields.

<p>Shown are the profiles of H-functions with respect of the distance <i>r</i> for Type-0 nuclei (A), Type-1 nuclei (B), Type-2 nuclei (C), Type-0/Type-2 bivariate (purple dots in D) and all nuclei combined (solid lines in D). The dashed line shows the theoretical expectation of complete spatial randomness (CSR; see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060876#s2" target="_blank">Materials and Methods</a>). Error bars show the standard deviations calculated from 14 experimental fields.</p

Distributions of different types of nuclei in relations to a Type-2 nucleus.

<p>Shown are the empirical cumulative distribution function plots of the distances from a Type-2 nucleus to another nucleus of any given type (A), and the proportions of nuclei of different types that immediately surround a Type-2 nucleus (B). Here the analysis was performed on the entire dataset pooled from 14 experimental fields; see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060876#pone.0060876.s002" target="_blank">Figure S2</a> for results performed on individual embryos as in panel (B).</p

Basic features of the nuclear monolayer.

<p>Shown are regularity indexes (RI) derived by the measurement of nearest-neighbor distances. Black: results from 14 experimental fields; white: results from 14 random simulations, each of which was constrained by the total nuclear number and the proportions nuclear types observed in the corresponding experimental field. The dashed line shows the theoretical expectation of 1.91 for randomly distributed points (see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060876#s2" target="_blank">Materials and Methods</a>). In simulations, nuclei of different types or all nuclei combined behave indistinguishable from each other or the theoretical expectation. Error bars show the standard deviations calculated from 14 experimental or simulated fields. <i>p</i>-values from paired Student’s t-tests to compare the means of experimental and simulated RI values were shown over the bars.</p

Spatial point pattern of nuclear transcriptional states.

<p>Shown is an embryo with nuclei masked according to <i>hb</i> transcriptional states, i.e., the number of <i>hb</i> intron dots detected. Blue: 0-dot nuclei; green: 1-dot nuclei; red: 2-dot nuclei; black: nuclei with over 2 dots. (B) is the cropped experimental field from the solid square in (A). See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060876#pone.0060876.s001" target="_blank">Figure S1</a> for locations of the experimental fields in all 14 embryos.</p

H-function analysis of simulated fields.

<p>Shown are results of an analysis that is identical to that of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060876#pone-0060876-g003" target="_blank">Figure 3</a>, but simulated fields are used here. Unlike simulations shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060876#pone-0060876-g002" target="_blank">Figure 2</a>, the simulations performed here were based on the molds derived from the experimental fields, with both the locations of the nuclei and the proportions of the nuclear types constrained by experimental observations. Note that the profiles of individual nuclear types are all below 0. This is expected because the nuclei of a given type are spatially mixed with the nuclei of other types when randomly distributed and thus the nuclei of a given type always exhibit a self-repelling SPP. Moreover, because the proportion of Type-0 nuclei is the smallest, the H-function profile of this type is the most negative among all three types. Also note that the profiles do not converge to zero at <i>r</i> = 100 µm, which is the boundary of the reference nuclei to compute distance, but not the limit of a complete SPP (see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060876#s2" target="_blank">Materials and Methods</a>).</p

Phytoremediation of cadmium-trichlorfon co-contaminated water by Indian mustard (<i>Brassica juncea</i>): growth and physiological responses

In this study, the morphological and physiological responses of Brassica juncea to the stresses of Cadmium (Cd) and trichlorfon (TCF), and the phytoremediation potential of B. juncea to Cd and TCF were investigated under hydroponics. Results showed that Cd exhibited strong inhibition on biomass and root morphology of B. juncea as Cd concentration increased. The chlorophyll a fluorescence intensity and chlorophyll content of B. juncea decreased with the increased Cd concentration, whereas the malondialdehyde and soluble protein contents and superoxide dismutase activity increased. TCF with different concentrations showed no significant influence on these morphological and physiological features of B. juncea. The biomass and physiological status of B. juncea were predominantly regulated by Cd level under the co-exposure of Cd and TCF. B. juncea could accumulate Cd in different plant parts, as well as showed efficient TCF degradation performance. A mutual inhibitory removal of Cd and TCF was observed under their co-system. The present study clearly signified the physiological responses and phytoremediation potential of B. juncea toward Cd and TCF, and these results suggest that B. juncea can be used as an effective phytoremediation agent for the Cd-TCF co-contamination in water. Combined pollution of heavy metals and pesticides in agricultural water systems is a common phenomenon. In previous phytoremediation studies, limited information is available on the co-contamination of heavy metals and pesticides. In this study, we aimed to investigate the concentration-dependent morphological and physiological characteristics of B. juncea under single and co-stress of Cd and trichlorfon (TCF), and the phytoremediation ability of B. juncea to remove Cd and TCF through hydroponic experiment. B. juncea exhibited efficient removal performance of Cd and TCF alone and simultaneous exposure of both pollutants, indicating that B. juncea is an effective phytoremediation agent for the Cd-TCF co-contaminated water.</p

Correction: Degradation of <i>YRA1</i> Pre-mRNA in the Cytoplasm Requires Translational Repression, Multiple Modular Intronic Elements, Edc3p, and Mex67p

Correction: Degradation of <i>YRA1</i> Pre-mRNA in the Cytoplasm Requires Translational Repression, Multiple Modular Intronic Elements, Edc3p, and Mex67

Parameters used in the NIDE for all numerical experiments.

<p>Parameters used in the NIDE for all numerical experiments.</p

Comparison of runtime of between NIDE and NDEMO of Electricity market with two players.

<p>Comparison of runtime of between NIDE and NDEMO of Electricity market with two players.</p