An improved map of conserved regulatory sites for Saccharomyces cerevisiae

BACKGROUND: The regulatory map of a genome consists of the binding sites for proteins that determine the transcription of nearby genes. An initial regulatory map for S. cerevisiae was recently published using six motif discovery programs to analyze genome-wide chromatin immunoprecipitation data for 203 transcription factors. The programs were used to identify sequence motifs that were likely to correspond to the DNA-binding specificity of the immunoprecipitated proteins. We report improved versions of two conservation-based motif discovery algorithms, PhyloCon and Converge. Using these programs, we create a refined regulatory map for S. cerevisiae by reanalyzing the same chromatin immunoprecipitation data. RESULTS: Applying the same conservative criteria that were applied in the original study, we find that PhyloCon and Converge each separately discover more known specificities than the combination of all six programs in the previous study. Combining the results of PhyloCon and Converge, we discover significant sequence motifs for 36 transcription factors that were previously missed. The new set of motifs identifies 636 more regulatory interactions than the previous one. The new network contains 28% more regulatory interactions among transcription factors, evidence of greater cross-talk between regulators. CONCLUSION: Combining two complementary computational strategies for conservation-based motif discovery improves the ability to identify the specificity of transcriptional regulators from genome-wide chromatin immunoprecipitation data. The increased sensitivity of these methods significantly expands the map of yeast regulatory sites without the need to alter any of the thresholds for statistical significance. The new map of regulatory sites reveals a more elaborate and complex view of the yeast genetic regulatory network than was observed previously

Natural Variation in Maternal Care and Cross-Tissue Patterns of Oxytocin Receptor Gene Methylation in Rats

Since the first report of maternal care effects on DNA methylation in rats, epigenetic modifications of the genome in response to life experience have become the subject of intense focus across many disciplines. Oxytocin receptor expression varies in response to early experience, and both oxytocin signaling and methylation status of the oxytocin receptor gene (Oxtr) in blood have been related to disordered social behavior. It is unknown whether Oxtr methylation varies in response to early life experience, and whether currently employed peripheral measures of Oxtr methylation reflect variation in the brain. We examined the effects of early life rearing experience via natural variation in maternal licking and grooming during the first week of life on behavior, physiology, gene expression, and epigenetic regulation of Oxtr across blood and brain tissues (mononucleocytes, hippocampus, striatum, and hypothalamus). Rats reared by “high” licking-grooming (HL) and “low” licking-grooming (LL) rat dams exhibited differences across study outcomes: LL offspring were more active in behavioral arenas, exhibited lower body mass in adulthood, and showed reduced corticosterone responsivity to a stressor. Oxtr methylation was significantly lower at multiple CpGs in the blood of LL versus HL rats, but no differences were found in the brain. Across groups, Oxtr transcript levels in the hypothalamus were associated with reduced corticosterone secretion in response to stress, congruent with the role of oxytocin signaling in this region. Methylation of specific CpGs at a high or low level was consistent across tissues, especially within the brain. However, individual variation in methylation relative to these global patterns was not consistent across tissues. These results suggest that blood Oxtr methylation may reflect early experience of maternal care, and that Oxtr methylation across tissues is highly concordant for specific CpGs, but that inferences across tissues are not supported for individual variation in Oxtr methylation

Reorientation transition of ultrathin ferromagnetic films

We demonstrate that the reorientation transition from out-of-plane to in-plane magnetization with decreasing temperature as observed experimentally in Ni-films on Cu(001) can be explained on a microscopic basis. Using a combination of mean field theory and perturbation theory, we derive an analytic expression for the temperature dependent anisotropy. The reduced magnetization in the film surface at finite temperatures plays a crucial role for this transition as with increasing temperature the influence of the uniaxial anisotropies is reduced at the surface and is enhanced inside the film.Comment: 4 pages(RevTeX), 3 figures (EPS

Magnetic Properties of 2-Dimensional Dipolar Squares: Boundary Geometry Dependence

By means of the molecular dynamics simulation on gradual cooling processes, we investigate magnetic properties of classical spin systems only with the magnetic dipole-dipole interaction, which we call dipolar systems. Focusing on their finite-size effect, particularly their boundary geometry dependence, we study two finite dipolar squares cut out from a square lattice with $\Phi=0$ and $\pi/4$, where $\Phi$ is an angle between the direction of the lattice axis and that of the square boundary. Distinctly different results are obtained in the two dipolar squares. In the $\Phi=0$ square, the ``from-edge-to-interior freezing'' of spins is observed. Its ground state has a multi-domain structure whose domains consist of the two among infinitely (continuously) degenerated Luttinger-Tisza (LT) ground-state orders on a bulk square lattice, i.e., the two antiferromagnetically aligned ferromagnetic chains (af-FMC) orders directed in parallel to the two lattice axes. In the $\Phi=\pi/4$ square, on the other hand, the freezing starts from the interior of the square, and its ground state is nearly in a single domain with one of the two af-FMC orders. These geometry effects are argued to originate from the anisotropic nature of the dipole-dipole interaction which depends on the relative direction of sites in a real space of the interacting spins.Comment: 21 pages, 13 figures, submitted to Journal of Physical Society Japa

Attenuation and modification of the ballast water microbial community during voyages into the Canadian Arctic

Aim: Ballast water is a major vector of non-indigenous species introductions world-wide. Our understanding of population dynamics of organisms entrained in ballast is largely limited to studies of zooplankton and phytoplankton. Bacteria are more numerous and diverse than zooplankton or phytoplankton, yet remain comparatively understudied. We apply a metagenomics approach to characterize changes in the microbial ballast water community over the course of three voyages on one ship, and assess the effects of ballast water exchange (BWE), spring/summer sampling month and time since voyage start. Location: Quebec City and Deception Bay, Quebec, and the coastal marine region offshore of eastern Canada. Methods: We used universal primers to Ion Torrent sequence a fragment of the bacterial 16S ribosomal DNA for samples collected over three voyages of one ship between Quebec City and Deception Bay in June, July and August 2015. We compared richness (total number of species in the community) and diversity (accounts for both species abundance and evenness) using linear mixed-effects analysis and compared community composition using non-metric multidimensional scaling and permutational multivariate analysis of variance. Initial comparisons were between months. Subsequent analyses focused on each month separately. Results: Ion Torrent sequencing returned c. 2.9 million reads and revealed monthly differences in diversity and richness, and in community structure in ballast water. June had higher richness and diversity than either July or August, and showed most clearly the effect of BWE on the microbial community. Main conclusions: Our results suggest that environmental conditions associated with different spring/summer sampling months drive differences in microbial diversity in ballast water. This study showed that BWE removes some components of the freshwater starting microbial community and replaces them with other taxa. BWE also changed proportional representation of some microbes without removing them completely. It appears that some taxa are resident in ballast tanks and are not removed by BWE. © 2017 John Wiley & Sons Lt

Dipolar interaction between two-dimensional magnetic particles

We determine the effective dipolar interaction between single domain two-dimensional ferromagnetic particles (islands or dots), taking into account their finite size. The first correction term decays as 1/D^5, where D is the distance between particles. If the particles are arranged in a regular two-dimensional array and are magnetized in plane, we show that the correction term reinforces the antiferromagnetic character of the ground state in a square lattice, and the ferromagnetic one in a triangular lattice. We also determine the dipolar spin-wave spectrum and evaluate how the Curie temperature of an ensemble of magnetic particles scales with the parameters defining the particle array: height and size of each particle, and interparticle distance. Our results show that dipolar coupling between particles might induce ferromagnetic long range order at experimentally relevant temperatures. However, depending on the size of the particles, such a collective phenomenon may be disguised by superparamagnetism.Comment: 11 pages, 5 figure

Ferromagnetism and Temperature-Driven Reorientation Transition in Thin Itinerant-Electron Films

The temperature-driven reorientation transition which, up to now, has been studied by use of Heisenberg-type models only, is investigated within an itinerant-electron model. We consider the Hubbard model for a thin fcc(100) film together with the dipole interaction and a layer-dependent anisotropy field. The isotropic part of the model is treated by use of a generalization of the spectral-density approach to the film geometry. The magnetic properties of the film are investigated as a function of temperature and film thickness and are analyzed in detail with help of the spin- and layer-dependent quasiparticle density of states. By calculating the temperature dependence of the second-order anisotropy constants we find that both types of reorientation transitions, from out-of-plane to in-plane (``Fe-type'') and from in-plane to out-of-plane (``Ni-type'') magnetization are possible within our model. In the latter case the inclusion of a positive volume anisotropy is vital. The reorientation transition is mediated by a strong reduction of the surface magnetization with respect to the inner layers as a function of temperature and is found to depend significantly on the total band occupation.Comment: 10 pages, 8 figures included (eps), Phys Rev B in pres

A Monte Carlo study of the three-dimensional Coulomb frustrated Ising ferromagnet

We have investigated by Monte-Carlo simulation the phase diagram of a three-dimensional Ising model with nearest-neighbor ferromagnetic interactions and small, but long-range (Coulombic) antiferromagnetic interactions. We have developed an efficient cluster algorithm and used different lattice sizes and geometries, which allows us to obtain the main characteristics of the temperature-frustration phase diagram. Our finite-size scaling analysis confirms that the melting of the lamellar phases into the paramgnetic phase is driven first-order by the fluctuations. Transitions between ordered phases with different modulation patterns is observed in some regions of the diagram, in agreement with a recent mean-field analysis.Comment: 14 pages, 10 figures, submitted to Phys. Rev.

Bayesian Centroid Estimation for Motif Discovery

Biological sequences may contain patterns that are signal important biomolecular functions; a classical example is regulation of gene expression by transcription factors that bind to specific patterns in genomic promoter regions. In motif discovery we are given a set of sequences that share a common motif and aim to identify not only the motif composition, but also the binding sites in each sequence of the set. We present a Bayesian model that is an extended version of the model adopted by the Gibbs motif sampler, and propose a new centroid estimator that arises from a refined and meaningful loss function for binding site inference. We discuss the main advantages of centroid estimation for motif discovery, including computational convenience, and how its principled derivation offers further insights about the posterior distribution of binding site configurations. We also illustrate, using simulated and real datasets, that the centroid estimator can differ from the maximum a posteriori estimator.Comment: 24 pages, 9 figure

New Dynamic Monte Carlo Renormalization Group Method

The dynamical critical exponent of the two-dimensional spin-flip Ising model is evaluated by a Monte Carlo renormalization group method involving a transformation in time. The results agree very well with a finite-size scaling analysis performed on the same data. The value of $z = 2.13 \pm 0.01$ is obtained, which is consistent with most recent estimates