Twist/Writhe Partitioning in a Coarse-Grained DNA Minicircle Model

Here we present a systematic study of supercoil formation in DNA minicircles under varying linking number by using molecular dynamics simulations of a two-bead coarse-grained model. Our model is designed with the purpose of simulating long chains without sacrificing the characteristic structural properties of the DNA molecule, such as its helicity, backbone directionality and the presence of major and minor grooves. The model parameters are extracted directly from full-atomistic simulations of DNA oligomers via Boltzmann inversion, therefore our results can be interpreted as an extrapolation of those simulations to presently inaccessible chain lengths and simulation times. Using this model, we measure the twist/writhe partitioning in DNA minicircles, in particular its dependence on the chain length and excess linking number. We observe an asymmetric supercoiling transition consistent with experiments. Our results suggest that the fraction of the linking number absorbed as twist and writhe is nontrivially dependent on chain length and excess linking number. Beyond the supercoiling transition, chains of the order of one persistence length carry equal amounts of twist and writhe. For longer chains, an increasing fraction of the linking number is absorbed by the writhe.Comment: 21 pages, 7 figures, 1 tabl

An evaluation of perspectives on animal researches of Baskent University term II students in Faculties of Medicine and Law

INTRODUCTION[|]In this study, it was aimed to determine whether the view of medical students from animal experiments is different from those who did not receive medical education and if there is a difference, this difference should be evaluated statistically.[¤]METHODS[|]The survey conducted in the study of Joffie et al. was translated into Turkish. According to the preliminary study, a total of 88 participants, 29 of whom were 2nd grade students of the Faculty of Medicine and 59 of the second year students of the Law Faculty, were administered the questionnaire. After the participants had been informed, it was asked whether they were offered an argument (A) for animal experiments and whether or not they participated in the argument and also it is questioned whether the counter arguments (CA) make the argument less convincing. The percentage of those who were persuaded by counter arguments was compared.[¤]RESULTS[|]Twenty-nine of the participants (33,00%) were male and 59 (67,00%) were female. When the percentages of persuasion of the sections are examined, it is seen that the rate of convincing with CA1.1 and CA2.3 is low in both groups. The proportion of medical students convinced by CA1.1, CA1.2, CA2.2, CA3.1, CA3.2 is higher than that of Law students. In A5, A6 and A7, Medical students are less likely to respond "Yes" than Law students. The percentage of convincing with CA5 and CA6 seems to be low for both parts. The rate of convincing Medical students with CA5 and CA7 is lower than that of Law students, whereas it is higher in CA6. However, differences between all these ratios are not statistically significant.[¤]DISCUSSION AND CONCLUSION[|]In the study of Joffie et al., there is no information available on these differences are statistically significant, since they do not give a "p" for the percentage differences in their research. This comparison can only be made between the percentages obtained in our study. For exaple, in our study with CA1.1, the conviction rate of law students was 14.30%, while the rate of convincing non-medical participants in Joffie et al's study was 92%. In CA2.1, CA2.3, CA4, CA5, CA7, CA9.2, CA9.4 and CA11.1, it is seen that the Law students are more convinced than the Medical students. However, these differences between the ratios were not statistically significant, so our hypothesis was not confirmed. It is proposed to apply the survey to a larger sample size and a heterogeneous group of participants.[¤

Effect of Chromosome Tethering on Nuclear Organization in Yeast

<div><p>Interphase chromosomes in <i>Saccharomyces cerevisiae</i> are tethered to the nuclear envelope at their telomeres and to the spindle pole body (SPB) at their centromeres. Using a polymer model of yeast chromosomes that includes these interactions, we show theoretically that telomere attachment to the nuclear envelope is a major determinant of gene positioning within the nucleus only for genes within 10 kb of the telomeres. We test this prediction by measuring the distance between the SPB and the silent mating locus (<i>HML</i>) on chromosome III in wild–type and mutant yeast strains that contain altered chromosome-tethering interactions. In wild-type yeast cells we find that disruption of the telomere tether does not dramatically change the position of <i>HML</i> with respect to the SPB, in agreement with theoretical predictions. Alternatively, using a mutant strain with a synthetic tether that localizes an <i>HML</i>-proximal site to the nuclear envelope, we find a significant change in the SPB-<i>HML</i> distance, again as predicted by theory. Our study quantifies the importance of tethering at telomeres on the organization of interphase chromosomes in yeast, which has been shown to play a significant role in determining chromosome function such as gene expression and recombination.</p></div

Comparison of theoretical and experimental distributions.

<p>Column (A): Telomere tethered – wild type; column (B): untethered - <i>yku80/esc1</i> double mutant; column (C): Telomere and <i>LacO</i> tethered – mutant carrying LacI-FFAT-GFP. Top row: a schematic diagram of the polymer models used for each strain. Bottom row: comparison of the experimental PDFs for wild type (red), <i>yku80/esc1</i> double mutant (blue), and mutant carrying LacI-FFAT-GFP (green) cells, and the corresponding theoretical PDFs (black curves in each graph). The parameters of the model are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102474#pone-0102474-t001" target="_blank">Table 1</a>. The p-values for the one-sample Kolmogorov-Smirnov test that compares the experimental and corresponding theoretical distributions, are 5.4×10⁻⁷ for the wild type, 4.9×10⁻³ for untethered telomere mutant, and 3.3×10⁻⁸ for the <i>HML</i>-bound mutant (these p-values are also shown in the plots).</p

Model Parameters.

<p>Model Parameters.</p

Quantitative fluorescent microscopy of the spindle pole body (SPB) and an <i>HML</i> proximal locus.

<p>A) Schematic view of budding yeast chromosome III (top line indicates the distance of each locus from the left telomere end in kb). 256 tandem repeats of Lac operators are inserted at a site 1.5 kb proximal to HML. Expression of GFP-fused to LacI or LacI-FFAT marks the locus in the proximity of HML. SPB component SPC29 is fused with RFP. B) Representative wide field microscopy images of yeast strain YDB271 are shown; top left: bright field, top right: green channel, bottom left: red channel and bottom right: merged and pseudo colored view of fluorescence channels red and green (scale bar 1 micrometer). Unbudded and G1 (cells with no duplicated SPB) – marked with boxes 1 to 4 – were selected to be analyzed for distance measurements. C) Experimental distributions of SPB-<i>HML</i> distances of 1,266 wild type (red bars) and 1,049 <i>yku80/esc1</i> double mutant (blue bars) cells. Error bars represent counting errors, which we estimated as twice the standard deviation of the number of measurements of distance that falls into each bin, calculated from the binomial distribution. The Kolmogorov-Smirnov test was used to check if these two data sets are indeed from a different distribution and it returned a p-value of 0.011. D) Experimental distributions of SPB-<i>HML</i> distances in case of 657 cells with <i>HML</i> tethering via LacI-FFAT-GFP bound to the <i>HML</i> proximal <i>LacO</i> array in addition to the wild type tethering of telomeres (green), and for 1049 <i>yku80</i>Δ <i>esc1</i>Δ double mutant cells (blue; same as in Figure 4C). Error bars are calculated as explained in C. The Kolmogorov-Smirnov test for these two data sets returns a p-value of 3.5×10⁻⁹, much lower than obtained by comparing the tethered and untethered distributions in Figure 4C.</p

Random walk model of yeast chromosomes.

<p>A single arm of the yeast interphase chromosome is modeled as a random-walk polymer confined to a sphere of radius <i>R</i> and tethered at its ends to the surface of the sphere. The spindle pole body (SPB) tether (gray circle) is positioned at the north pole while the telomere tether (gray circle) is allowed to take any position on the surface of the sphere. The random walk polymer is made up of rigid segments of equal length (Kuhn length) connected by flexible links. In addition to spherical confinement, an impenetrable sub volume (red spherical cap) representing the nucleolar region limits the space available for the chromosome.</p

The effect of telomere tethering on gene positioning.

<p>A) Heat maps of the probability distributions for the position of genetic loci within the nucleus. The genes are located along a 100 kb chromosome arm at distances 0 kb, 10 kb, 20 kb, 40 kb and 60 kb away from the telomere. The probability distribution is projected to a plane that contains the north-south direction defined by the SPB and the nucleolus position, respectively (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102474#pone-0102474-g001" target="_blank">Figure 1</a>). The relative probability density (normalized by the maximum) is shown for one half the nuclear sphere while the other half is equivalent by symmetry. For each gene, we show its spatial distribution when the telomere is attached to the nuclear envelope, and when the telomere is not attached. The “difference” heat maps were calculated by subtracting the “no tether” heat map from the “with tether” heat map – i.e. they show the change in the spatial distribution of the gene upon attachment of the telomere to the nuclear envelope. B) The root-mean-square of the probability difference (RMSDs) map quickly decays as the gene is moved away from the telomere. For all genetic loci, except the ones at 0 and 3 kb away from the telomere, the decay of the RMSD with increasing distance from the telomere is roughly exponential with a characteristic length of 20 kb. (The best fitting line shown in the figure is fit to all points except the point at 0 and 3 kb.) When calculating RMSDs, we do not apply the normalization mentioned above in which the maximum probability density of each “no tether” heat map is assigned a value of 1. Rather, we use the absolute probabilities for each pixel when subtracting the “no tether” heat maps from the “with tether” heat maps to obtain the “difference” heat maps.</p