Regulation of zygotic gene activation in the preimplantation mouse embryo: Global activation and repression of gene expression

Superimposed on the activation of the embryonic genome in the preimplantation mouse embryo is the formation of a transcriptionally repressive state during the two-cell stage. This repression appears mediated at the level of chromatin structure, because it is reversed by inducing histone hyperacetylation or inhibiting the second round of DNA replication. We report that of more than 200 amplicons analyzed by mRNA differential display, about 45% of them are repressed between the two-cell and four-cell stages. This repression is scored as either a decrease in amplicon expression that occurs between the two-cell and four-cell stages or on the ability of either trichostatin A tan inhibitor of histone deacetylases) or aphidicolin tan inhibitor of replicative DNA polymerases) to increase the level of amplicon expression. Results of this study also indicate that about 16% of the amplicons analyzed likely are novel genes whose sequence doesn't correspond to sequences in the current databases, whereas about 20% of the sequences expressed during this transition likely are repetitive sequences. Lastly, inducing histone hyperacetylation in the two-cell embryos inhibits cleavage to the four-cell stage. These results suggest that genome activation is global and relatively promiscuous and that a function of the transcriptionally repressive state is to dictate the appropriate profile of gene expression that is compatible with further development.

Spatial correlation of heat release rate and sound emission from turbulent premixed flames

The two-point spatial correlation of the rate of change of fluctuating heat release rate is central to the sound emission from open turbulent flames, and a few attempts have been made to address this correlation in recent studies. In this paper, the two-point correlation and its role in combustion noise are studied by analysing direct numerical simulation (DNS) data of statistically multi-dimensional turbulent premixed flames. The results suggest that this correlation function depends on the separation distance and direction but, not on the positions inside the flame brush. This correlation can be modelled using a combination of Hermite-Gaussian functions of zero and second order, i.e. functions of the form (1-Ax2)e-Bx2 for constants A and B, to include its possible negative values. The integral correlation volume obtained using this model is about 0.2δL3 with the length scale obtained from its cube root being about 0.6δ L, where δ L is the laminar flame thermal thickness. Both of the values are slightly larger than the values reported in an earlier study because of the anisotropy observed for the correlation. This model together with the turbulence-dependent parameter K, the ratio of the root-mean-square (RMS) value of the rate of change of reaction rate to the mean reaction rate, derived from the DNS data is applied to predict the far-field sound emitted from open flames. The calculated noise levels agree well with recently reported measurements and show a sensitivity to K values. © 2012 The Combustion Institute.

Control of meiotic recombination frequency in plant genomes.

Sexual eukaryotes reproduce via the meiotic cell division, where ploidy is halved and homologous chromosomes undergo reciprocal genetic exchange, termed crossover (CO). CO frequency has a profound effect on patterns of genetic variation and species evolution. Relative CO rates vary extensively both within and between plant genomes. Plant genome size varies by over 1000-fold, largely due to differential expansion of repetitive sequences, and increased genome size is associated with reduced CO frequency. Gene versus repeat sequences associate with distinct chromatin modifications, and evidence from plant genomes indicates that this epigenetic information influences CO patterns. This is consistent with data from diverse eukaryotes that demonstrate the importance of chromatin structure for control of meiotic recombination. In this review I will discuss CO frequency patterns in plant genomes and recent advances in understanding recombination distributions.

Bayesian correlated clustering to integrate multiple datasets.

MOTIVATION: The integration of multiple datasets remains a key challenge in systems biology and genomic medicine. Modern high-throughput technologies generate a broad array of different data types, providing distinct-but often complementary-information. We present a Bayesian method for the unsupervised integrative modelling of multiple datasets, which we refer to as MDI (Multiple Dataset Integration). MDI can integrate information from a wide range of different datasets and data types simultaneously (including the ability to model time series data explicitly using Gaussian processes). Each dataset is modelled using a Dirichlet-multinomial allocation (DMA) mixture model, with dependencies between these models captured through parameters that describe the agreement among the datasets. RESULTS: Using a set of six artificially constructed time series datasets, we show that MDI is able to integrate a significant number of datasets simultaneously, and that it successfully captures the underlying structural similarity between the datasets. We also analyse a variety of real Saccharomyces cerevisiae datasets. In the two-dataset case, we show that MDI's performance is comparable with the present state-of-the-art. We then move beyond the capabilities of current approaches and integrate gene expression, chromatin immunoprecipitation-chip and protein-protein interaction data, to identify a set of protein complexes for which genes are co-regulated during the cell cycle. Comparisons to other unsupervised data integration techniques-as well as to non-integrative approaches-demonstrate that MDI is competitive, while also providing information that would be difficult or impossible to extract using other methods.

A priori assessment of algebraic flame surface density models in the context of large eddy simulation for nonunity lewis number flames in the thin reaction zones regime

The performance of algebraic flame surface density (FSD) models has been assessed for flames with nonunity Lewis number (Le) in the thin reaction zones regime, using a direct numerical simulation (DNS) database of freely propagating turbulent premixed flames with Le ranging from 0.34 to 1.2. The focus is on algebraic FSD models based on a power-law approach, and the effects of Lewis number on the fractal dimension D and inner cut-off scale η i have been studied in detail. It has been found that D is strongly affected by Lewis number and increases significantly with decreasing Le. By contrast, η i remains close to the laminar flame thermal thickness for all values of Le considered here. A parameterisation of D is proposed such that the effects of Lewis number are explicitly accounted for. The new parameterisation is used to propose a new algebraic model for FSD. The performance of the new model is assessed with respect to results for the generalised FSD obtained from explicitly LES-filtered DNS data. It has been found that the performance of the most existing models deteriorates with decreasing Lewis number, while the newly proposed model is found to perform as well or better than the most existing algebraic models for FSD. © 2012 Mohit Katragadda et al.

Conditional Moment Closure for Turbulent Premixed Flames

The conditional moment closure (CMC) method has been successfully applied to various non-premixed combustion systems in the past, but its application to premixed flames is not fully tested and validated. The main difficulty is associated with the modeling of conditional scalar dissipation rate of the conditioning scalar, the progress variable. A simple algebraic model for the conditional dissipation rate is validated using DNS results of a V-flame. This model along with the standard k- turbulence modeling is used in computations of stoichiometric pilot stabilized Bunsen flames using the RANS-CMC method. A first-order closure is used for the conditional mean reaction rate. The computed non reacting and reacting scalars are in reasonable agreement with the experimental measurements and are consistent with earlier computations using flamelets and transported PDF methods. Sensitivity to chemical kinetic mechanism is also assessed. The results suggest that the CMC may be applied across the regimes of premixed combustion.

Geometry and interaction of structures in homogeneous isotropic turbulence

A strategy to extract turbulence structures from direct numerical simulation (DNS) data is described along with a systematic analysis of geometry and spatial distribution of the educed structures. A DNS dataset of decaying homogeneous isotropic turbulence at Reynolds number Reλ = 141 is considered. A bandpass filtering procedure is shown to be effective in extracting enstrophy and dissipation structures with their smallest scales matching the filter width, L. The geometry of these educed structures is characterized and classified through the use of two non-dimensional quantities, planarity' and filamentarity', obtained using the Minkowski functionals. The planarity increases gradually by a small amount as L is decreased, and its narrow variation suggests a nearly circular cross-section for the educed structures. The filamentarity increases significantly as L decreases demonstrating that the educed structures become progressively more tubular. An analysis of the preferential alignment between the filtered strain and vorticity fields reveals that vortical structures of a given scale L are most likely to align with the largest extensional strain at a scale 3-5 times larger than L. This is consistent with the classical energy cascade picture, in which vortices of a given scale are stretched by and absorb energy from structures of a somewhat larger scale. The spatial distribution of the educed structures shows that the enstrophy structures at the 5η scale (where η is the Kolmogorov scale) are more concentrated near the ones that are 3-5 times larger, which gives further support to the classical picture. Finally, it is shown by analysing the volume fraction of the educed enstrophy structures that there is a tendency for them to cluster around a larger structure or clusters of larger structures. Copyright © 2012 Cambridge University Press.

A presumed joint pdf model for turbulent combustion with varying equivalence ratio

Modeling of the joint probability density function of the mixture fraction and progress variable with a given covariance value is studied. This modeling is validated using experimental and direct numerical simulation (DNS) data. A very good agreement with experimental data of turbulent stratified flames and DNS data of a lifted hydrogen jet flame is obtained. The effect of using this joint pdf modeling to calculate the mean reaction rate with a flamelet closure in Reynolds averaged Navier-Stokes (RANS) calculation of stratified flames is studied. The covariance effect is observed to be large within the flame brush. The results obtained from RANS calculations using this modeling for stratified jet- and rod-stabilized V-flames are discussed and compared to the measurements as a posteriori validation for the joint probability density function model with the flamelet closure. The agreement between the computed and measured values of flame and turbulence quantities is found to be good. © 2012 Copyright Taylor and Francis Group, LLC.

Effects of turbulent reynolds number on the performance of algebraic flame surface density models for large eddy simulation in the thin reaction zones regime: A direct numerical simulation analysis

A direct numerical simulation (DNS) database of freely propagating statistically planar turbulent premixed flames with a range of different turbulent Reynolds numbers has been used to assess the performance of algebraic flame surface density (FSD) models based on a fractal representation of the flame wrinkling factor. The turbulent Reynolds number Ret has been varied by modifying the Karlovitz number Ka and the Damköhler number Da independently of each other in such a way that the flames remain within the thin reaction zones regime. It has been found that the turbulent Reynolds number and the Karlovitz number both have a significant influence on the fractal dimension, which is found to increase with increasing Ret and Ka before reaching an asymptotic value for large values of Ret and Ka. A parameterisation of the fractal dimension is presented in which the effects of the Reynolds and the Karlovitz numbers are explicitly taken into account. By contrast, the inner cut-off scale normalised by the Zel'dovich flame thickness ηi/δz does not exhibit any significant dependence on Ret for the cases considered here. The performance of several algebraic FSD models has been assessed based on various criteria. Most of the algebraic models show a deterioration in performance with increasing the LES filter width. © 2012 Mohit Katragadda et al.

Reynolds number effects on scalar dissipation rate transport and its modeling in turbulent premixed combustion

The effects of turbulent Reynolds number, Ret, on the transport of scalar dissipation rate of reaction progress variable in the context of Reynolds averaged Navier-Stokes simulations have been analyzed using three-dimensional simplified chemistry-based direct numerical simulation (DNS) data of freely propagating turbulent premixed flames with different values of Ret. Scaling arguments have been used to explain the effects of Ret on the turbulent transport, scalar-turbulence interaction, and the combined reaction and molecular dissipation terms. Suitable modifications to the models for these terms have been proposed to account for Ret effects, and the model parameters include explicit Ret dependence. These expressions approach expected asymptotic limits for large values of Ret. However, turbulent Reynolds number Ret does not seem to have any major effects on the modeling of the term arising from density variation. Copyright © Taylor and Francis Group, LLC.

Off-wall boundary conditions for turbulent flows obtained from buffer-layer minimal flow units

There is strong evidence that the transport processes in the buffer region of wall-bounded turbulence are common across various flow configurations, even in the embryonic turbulence in transition (Park et al., Phys. Fl. 24). We use this premise to develop off-wall boundary conditions for turbulent simulations. Boundary conditions are constructed from DNS databases using periodic minimal flow units and reduced order modeling. The DNS data was taken from a channel at Reτ=400 and a zero-pressure gradient transitional boundary layer (Sayadi et al., submitted to J. Fluid Mech.). Both types of boundary conditions were first tested on a DNS of the core of the channel flow with the aim of extending their application to LES and to spatially evolving flows.

Kelvin-Helmholtz-like instability of turbulent flows over riblets

The turbulent drag reduction due to riblets is a function of their size and, for different configurations, collapses well with a length scale l+g=(A+g)1/2, based in the groove cross-section Ag. The initially linear drag reduction breaks down for l+g≈11, which agrees in our DNS with the previously reported appearance of quasi-two-dimensional spanwise rollers immediately above the riblets. They are similar to those found over porous surfaces and plant canopies, and can be traced to a Kelvin-Helmholtz-like instability associated with the relaxation of the impermeability condition for the wall-normal velocity. The extra Reynolds stress associated with them accounts quantitatively for the drag degradation. An inviscid model for the instability confirms its nature, agreeing well with the observed perturbation wavelengths and shapes. The onset of the instability is determined by a length scale L+w that, for conventional riblet geometries, is proportional to l+g. The instability onset, L+w≥4, corresponds to the empirical breakdown point l+g≈11.

Nonlinear thermoacoustics of ducted premixed flames: The influence of perturbation convection speed

When a premixed flame is placed within a duct, acoustic waves induce velocity perturbations at the flame's base. These travel down the flame, distorting its surface and modulating its heat release. This can induce self-sustained thermoacoustic oscillations. Although the phase speed of these perturbations is often assumed to equal the mean flow speed, experiments conducted in other studies and Direct Numerical Simulation (DNS) conducted in this study show that it varies with the acoustic frequency. In this paper, we examine how these variations affect the nonlinear thermoacoustic behaviour. We model the heat release with a nonlinear kinematic G-equation, in which the velocity perturbation is modelled on DNS results. The acoustics are governed by linearised momentum and energy equations. We calculate the flame describing function (FDF) using harmonic forcing at several frequencies and amplitudes. Then we calculate thermoacoustic limit cycles and explain their existence and stability by examining the amplitude-dependence of the gain and phase of the FDF. We find that, when the phase speed equals the mean flow speed, the system has only one stable state. When the phase speed does not equal the mean flow speed, however, the system supports multiple limit cycles because the phase of the FDF changes significantly with oscillation amplitude. This shows that the phase speed of velocity perturbations has a strong influence on the nonlinear thermoacoustic behaviour of ducted premixed flames. © 2013 The Combustion Institute.

Morphological and ultrastructural changes in tobacco BY-2 cells exposed to microcystin-RR

Tobacco BY-2 cells were exposed to microcystin-RR (MC-RR) at two concentrations, 60 mu g mL(-1) and 120 mu g mL(-1), to study the changes in morphology and ultrastructure of cells as a result of the exposure. Exposure to the lower concentration for 5 d led to typical apoptotic morphological changes including condensation of nuclear chromatin, creation of a characteristic 'half moon' structure, and cytoplasm shrinkage and decreased cell volume, as revealed through light microscopy. fluorescence microscopy, and transmission electron microscopy, respectively. Exposure to the higher concentration, on the other hand, led to morphological and ultrastructural changes typical of necrosis, such as rupture of the plasma membrane and the nuclear membrane and a marked swelling of cells. The presence of many vacuoles containing unusual deposits points to the involvement of vacuoles in detoxifying MC-RR. Results of the present study indicate that exposure of tobacco BY-2 cells to MC-RR at a lower concentration (60 mu g mL(-1)) results in apoptosis and that to a higher concentration (120 mu g mL(-1)), in necrosis. (C) 2009 Elsevier Ltd. All rights reserved.

Histone H2A Has a Novel Variant in Fish Oocytes

Histone variants and their modification have significant roles in many cellular processes. In this study, we identified and characterized the histone H2A variant h2af1o in fish and revealed its oocyte-specific expression pattern during oogenesis and embryogenesis. Moreover, posttranslational modification of H2af1o was observed that results from phosphorylation during oocyte maturation. To understand the binding dynamics of the novel core histone variant H2af1o in nucleosomes, we cloned ubiquitous gibel carp h2afx as a conventional histone control and investigated the dynamic exchange difference in chromatin by fluorescence recovery after photobleaching. H2af1o has significantly higher mobility in nucleosomes than ubiquitous H2afx. Compared with ubiquitous H2afx, H2af1o has a tightly binding C-terminal and a weakly binding N-terminal. These data indicate that fish oocytes have a novel H2A variant that destabilizes nucleosomes by protruding its N-terminal tail and stabilizes core particles by contracting its C-terminal tail. Our findings suggest that H2af1o may have intrinsic ability to modify chromatin properties during fish oogenesis, oocyte maturation, and early cleavage.