Epigenetic inheritance in plants.

The function of plant genomes depends on chromatin marks such as the methylation of DNA and the post-translational modification of histones. Techniques for studying model plants such as Arabidopsis thaliana have enabled researchers to begin to uncover the pathways that establish and maintain chromatin modifications, and genomic studies are allowing the mapping of modifications such as DNA methylation on a genome-wide scale. Small RNAs seem to be important in determining the distribution of chromatin modifications, and RNA might also underlie the complex epigenetic interactions that occur between homologous sequences. Plants use these epigenetic silencing mechanisms extensively to control development and parent-of-origin imprinted gene expression.

RNAi, DRD1, and histone methylation actively target developmentally important Non-CG DNA methylation in Arabidopsis

Cytosine DNA methylation protects eukaryotic genomes by silencing transposons and harmful DNAs, but also regulates gene expression during normal development. Loss of CG methylation in the Arabidopsis thaliana met1 and ddm1 mutants causes varied and stochastic developmental defects that are often inherited independently of the original met1 or ddm1 mutation. Loss of non-CG methylation in plants with combined mutations in the DRM and CMT3 genes also causes a suite of developmental defects. We show here that the pleiotropic developmental defects of drm1 drm2 cmt3 triple mutant plants are fully recessive, and unlike phenotypes caused by met1 and ddm1, are not inherited independently of the drm and cmt3 mutations. Developmental phenotypes are also reversed when drm1 drm2 cmt3 plants are transformed with DRM2 or CMT3, implying that non-CG DNA methylation is efficiently re-established by sequence-specific signals. We provide evidence that these signals include RNA silencing though the 24-nucleotide short interfering RNA (siRNA) pathway as well as histone H3K9 methylation, both of which converge on the putative chromatin-remodeling protein DRD1. These signals act in at least three partially intersecting pathways that control the locus-specific patterning of non-CG methylation by the DRM2 and CMT3 methyltransferases. Our results suggest that non-CG DNA methylation that is inherited via a network of persistent targeting signals has been co-opted to regulate developmentally important genes. © 2006 Chan et al.

Geometrical properties and turbulent flame speed measurements in stationary premixed V-flames using direct numerical simulation

Three dimensional, fully compressible direct numerical simulations (DNS) of premixed turbulent flames are carried out in a V-flame configuration. The governing equations and the numerical implementation are described in detail, including modifications made to the Navier-Stokes Characteristic Boundary Conditions (NSCBC) to accommodate the steep transverse velocity and composition gradients generated when the flame crosses the boundary. Three cases, at turbulence intensities, u′/sL, of 1, 2, and 6 are considered. The influence of the flame holder on downstream flame properties is assessed through the distributions of the surface-conditioned displacement speed, curvature and tangential strain rates, and compared to data from similarly processed planar flames. The distributions are found to be indistinguishable from planar flames for distances greater than about 17δth downstream of the flame holder, where δth is the laminar flame thermal thickness. Favre mean fields are constructed, and the growth of the mean flame brush is found to be well described by simple Taylor type diffusion. The turbulent flame speed, sT is evaluated from an expression describing the propagation speed of an isosurface of the mean reaction progress variable c̃ in terms of the imbalance between the mean reactive, diffusive, and turbulent fluxes within the flame brush. The results are compared to the consumption speed, sC, calculated from the integral of the mean reaction rate, and to the predictions of a recently developed flame speed model (Kolla et al., Combust Sci Technol 181(3):518-535, 2009). The model predictions are improved in all cases by including the effects of mean molecular diffusion, and the overall agreement is good for the higher turbulence intensity cases once the tangential convective flux of c̃ is taken into account. © 2010 Springer Science+Business Media B.V.

Effects of Lewis number on scalar variance transport in premixed flames

The influences of differential diffusion rates of heat and mass on the transport of the variances of Favre fluctuations of reaction progress variable and non-dimensional temperature have been studied using three-dimensional simplified chemistry based Direct Numerical Simulation (DNS) data of statistically planar turbulent premixed flames with global Lewis number ranging from Le = 0.34 to 1.2. The Lewis number effects on the statistical behaviours of the various terms of the transport equations of variances of Favre fluctuations of reaction progress variable and non-dimensional temperature have been analysed in the context of Reynolds Averaged Navier Stokes (RANS) simulations. It has been found that the turbulent fluxes of the progress variable and temperature variances exhibit counter-gradient transport for the flames with Lewis number significantly smaller than unity whereas the extent of this counter-gradient transport is found to decrease with increasing Lewis number. The Lewis number is also shown to have significant influences on the magnitudes of the chemical reaction and scalar dissipation rate contributions to the scalar variance transport. The modelling of the unclosed terms in the scalar variance equations for the non-unity Lewis number flames have been discussed in detail. The performances of the existing models for the unclosed terms are assessed based on a-priori analysis of DNS data. Based on the present analysis, new models for the unclosed terms of the active scalar variance transport equations are proposed, whenever necessary, which are shown to satisfactorily capture the behaviours of unclosed terms for all the flames considered in this study. © 2010 Springer Science+Business Media B.V.

Statistics and modelling of turbulent kinetic energy transport in different regimes of premixed combustion

The statistical behaviour of turbulent kinetic energy transport in turbulent premixed flames is analysed using data from three-dimensional Direct Numerical Simulation (DNS) of freely propagating turbulent premixed flames under decaying turbulence. For flames within the corrugated flamelets regime, it is observed that turbulent kinetic energy is generated within the flame brush. By contrast, for flames within the thin reaction zones regime it has been found that the turbulent kinetic energy decays monotonically through the flame brush. Similar trends are observed also for the dissipation rate of turbulent kinetic energy. Within the corrugated flamelets regime, it is demonstrated that the effects of the mean pressure gradient and pressure dilatation within the flame are sufficient to overcome the effects of viscous dissipation and are responsible for the observed augmentation of turbulent kinetic energy in the flame brush. In the thin reaction zones regime, the effects of the mean pressure gradient and pressure dilatation terms are relatively much weaker than those of viscous dissipation, resulting in a monotonic decay of turbulent kinetic energy across the flame brush. The modelling of the various unclosed terms of the turbulent kinetic energy transport equation has been analysed in detail. The predictions of existing models are compared with corresponding quantities extracted from DNS data. Based on this a-priori DNS assessment, either appropriate models are identified or new models are proposed where necessary. It is shown that the turbulent flux of turbulent kinetic energy exhibits counter-gradient (gradient) transport wherever the turbulent scalar flux is counter-gradient (gradient) in nature. A new model has been proposed for the turbulent flux of turbulent kinetic energy, and is found to capture the qualitative and quantitative behaviour obtained from DNS data for both the corrugated flamelets and thin reaction zones regimes without the need to adjust any of the model constants. © 2010 Springer Science+Business Media B.V.

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.

On the stabilisation of turbulent lifted flames

This study explores the stabilisation mechanisms of turbulent lifted flames by examining the scalar dissipation rate (SDR) of both passive and reactive scalars and their cross dissipation (CDR) in the stabilisation region. DNS results of a laboratory scale hydrogen turbulent lifted flame has been used for this analysis. Various definitions of the flame leading edge (FLE) has been compared and differences are illustrated. Time and spatial averaged statistic of SDR and CDR were examined. It was found that the averaged SDR for the mixture fraction at FLE was well below the reference quenching value for stoichiometric mixture. The averaged SDR for the progress variable is in the same order of the unstrained premixed laminar flame value. It was observed that the averaged CDR changed from negative to weakly positive at FLE. The change in sign was explained by a change in the relative alignment of the gradients of mixture fraction and progress variable. It was thus evident that the CDR was a good marker for stabilisation region and an important quantity in stabilisation mechanism.

Effects of flow-geometry and Damkohler number on turbulence-flame interaction

DNS of turbulent hydrogen-air premixed flame is conducted for freely propagating and V-flames, using complex chemical kinetics. The results are analysed to study the influence of flame configuration on the turbulence-scalar interaction, which is critical for the scalar gradient generation process. The result suggests that this interaction process is not influenced by the flame configuration and the flame normal is found to predominantly align with the most extensive strain in the region of intense heat release.

Scalar dissipation rate transport in the corrugated flamelets and thin reaction zones regime for turbulent premixed flames

The characteristics of the scalar dissipation rate transport in the corrugated flamelets and the thin reaction zones regimes are studied based on two three-dimensional Direct Numerical Simulation (DNS) databases for freely propagating statistically planar turbulent premixed flames. The turbulent flame parameters are so chosen that the database which represents the corrugated flamelets regime has a global Damköhler number Da>1 whereas the database representing the thin reaction zones regime has Da <1. It is demonstrated that the terms originating from the correlation between fluctuating velocity and scalar gradient T1 shows strong Da dependence. The terms originating from dilatation T2, the scalar inner product of gradients of velocity and scalar fields T3 and the correlation between reaction rate and scalar gradients T4 and the dissipation term D2 remain important for both the flames. However, T3 dissipates scalar dissipation rate in the Da > 1 flame while it produces scalar dissipation rate in the Da < 1 flame. This difference is because of the change in the alignment between scalar and velocity gradients

Piezo-assisted nuclear transfer affects cloning efficiency and may cause apoptosis

Even though it generates healthy adults, nuclear transfer in mammals remains an inefficient process. Mainly attributed to abnormal reprograming of the donor chromatin, this inefficiency may also be caused at least partly by a specific effect of the clonin

The survey of sexual maturity in Mugil cephalus so measuring sex hormones and histologic studies

In this study the process of female gray mullet brooders was carried out by using histological study and masurment of sex steroids. Results of histological studies showed that oocyte of gray mullet brooders in Gomishan Rearing Center conditions of develop to the end of yolk globule stage. The results were observed with oocyte in chromatin nucleolar stage (first stage) with means of diameter of 20 p m, in August, perinucleolar stage (second stage) in September with mean diameter of 87 p m, yolk vesicle stage (third stage) in October with mean diameter 200 p m and yolk granules stage (forth stage) from October to November with average diameter of 180 — 650 p m. For the reason of stopping oocyte develop at the end of fourth stage, hormonal induction to final oocyte maturation and ovulation was used. For this purpose, carp pituitary , HCG and LRH-A2 with different combinations were used in two stages, second injection was used 24 hours after first injection. 15 females brooders were divided in 5 groups, different hormonal combinations were injected to four groups and to fifth group as control, only saline, was injected. The process of female brooder rippening in hormonal induction was studied via masurment of sex steroids including 17 a - hydroxy progestrone, estradio1-17)6 and testosterone. Blood samples were collected from caudal vein during first injection, 24, 30 and 48 hours after the first injection. At the same time, for distinguishing histological changes the sample has been attained from the gonads Sex stroid fluctuation patterns in different brooder groups that injected hormon were similar, however hormonal composition had similar effects. All brooder that their oocyte in the beginning of hormonal injection were At the end of fourth stage with oocyte diameter average of 600 p m received to final maturation and ovulation. The brooder that its oocytes were At the begining or mid-fourth stage did not show ovulation but hormonal induction caused oocyte develop at the beginning of fifth stage. Study of 17-hydroxy progestrone fluctuation showed that the maximum level of this steroid (0.347 ng/ml) measured 30 hours after the first injection and was significantly higher (p< 0.05) than those of control group. So, 17-hydroxy progestrone is probably precursor of maturation inducing steroid (MIS). However the maximum level of that observed was coincident with germinal vesicle breakdown, oil droplets coalescence and dissolution of yolk granuls The maximum levels of esteradiol— 17/0 and testosterone (3.778 and 16.801ng/ml,respectively) in spawned brooders,were observed 24 hours after the first injection. levels of those steroids were significantly higher (p<0.05) than control group. Maximum level of sex steroids in the brooders that did not spawn to the end of treatment was observed with more delay than those in spawned brooders. Therefor maximum level of 17a-hydroxy progestrone (0.264 ng/ml) in those brooders observed in fourth sampling time and the maximum levels of estradio1-17a and testosterone (2.944 and 18.993 ng/ml, respectivly)observed in third sampling time that was significantly higher (p<0.05) than those of control group. For the study of stress effect on brooders during the hormonal induction, level of cortisol was measured in every sampling time. level of cortisol had high fluctuation that showed handling level and stress effect on brooders. However maximum level of cortisol in majority of brooders was dominant in third sampling time that was coincident with final maturation.

Nuclear matrix of the most primitive eukaryote Archezoa

Accumulating evidence suggests that unicellular Archezoa are the most primitive eukaryotes and their nuclei are of significance to the study of evolution of the eukaryotic nucleus. Nuclear matrix is an ubiquitous important structure of eukaryotic nucleus; its evolution is certainly one of the most important parts of the evolution of nucleus. To study the evolution of nuclear matrix, nuclear matrices of Archezoa are investigated. Giardia lamblia cells are extracted sequentially. Both embedment-free section EM and whole mount cell EM of the extracted cells show that, like higher eukaryotes, this species has a residual nuclear matrix in its nucleus and rich intermediate filaments in its cytoplasm, and the two networks connect with each other to form a united network. But its nuclear matrix does not have nucleolar matrix and its lamina is not as typical as that of higher eukaryotes; Western blotting shows that lamina of Giardia and two other Archezoa Entamoeba invadens and Trichomonas vaginali all contain only one polypeptide each which reacts with a mammalia anti-lamin polyclonal serum and is similar to lamin B (67 ku) of mammlia in molecular weight. According to the results and references, it is suggested that nuclear matrix is an early acquisition of the eukaryotic nucleus, and it and the "eukaryotic chromatin" as a whole must have originated very early in the process of evolution of eukaryotic cell, and their origin should be an important prerequisite of the origin of eukaryotic nucleus; in the iamin (gene) family, B-type lamins (gene) should be the ancestral type and that A-type lamins (gene) might derive therefrom.

The nuclear matrix of Euglena gracilis (Euglenophyta): A stage of nuclear matrix evolution?

Euglena gracilis cell was extracted sequentially with CSK-Triton buffer, RSB-Magik solution and DNase-As solution. DGD embedment-free electron microscopy showed that in the extracted nucleus there was a residual non-chromatin fibrous network. That it could not be removed by hot trichloroacetic acid further supported the idea that it was a non-histone, non-chromatin fibrous protein network, and should be the internal network of the nuclear matrix. After the sequential extraction, the nuclear membrane was removed, leaving behind a layer of lamina; the chromatin was digested and eluted from the dense chromosomes and residual chromosomal structures that should be chromosomal scaffold were revealed. Western blot analysis with antiserum against rat lamins showed that nuclear lamina of the cell possessed two positive polypeptides, a major one and a minor one, which had molecular masses similar to lamin B and lamin A, respectively. Comparing these data with those of the most primitive eukaryote Archezoa and of higher eukaryotes, it was suggested that the lower unicellular eukaryote E. gracillis already had the nuclear matrix structure, and its nuclear matrix (especially the lamina) might represent a stage of evolutionary history of the nuclear matrix. (C) 2000 Editions scientifiques et medicales Elsevier SAS.

Scalar and its dissipation in the near field of turbulent lifted jet flame

In this study various scalar dissipation rates and their modelling in the context of partially premixed flame are investigated. A DNS dataset of the near field of a turbulent hydrogen lifted jet flame is processed to analyse the mixture fraction and progress variable dissipation rates and their cross dissipation rate at several axial positions. It is found that the classical model for the passive scalar dissipation rate ε{lunate}̃ZZ gives good agreement with the DNS, while models developed based on premixed flames for the reactive scalar dissipation rate ε{lunate}̃cc only qualitatively capture the correct trend. The cross dissipation rate ε{lunate}̃cZ is mostly negative and can be reasonably approximated at downstream positions once ε{lunate}̃ZZ and ε{lunate}̃cc are known, although the sign cannot be determined. This approach gives better results than one employing a constant ratio of turbulent timescale and the scalar covariance c'Z'̃. The statistics of scalar gradients are further examined and lognormal distributions are shown to be very good approximations for the passive scalar and acceptable for the reactive scalar. The correlation between the two gradients increases downstream as the partially premixed flame in the near field evolves ultimately to a diffusion flame in the far field. A bivariate lognormal distribution is tested and found to be a reasonable approximation for the joint PDF of the two scalar gradients. © 2011 The Combustion Institute.

Effects of flow geometry and Damkohler number on turbulent premixed flame

DNS of planar turbulent flame and turbulent V-flame has been conducted to investigate turbulence-scalar interaction in relatively practical turbulent combustion. Several turbulence quantities are examined for the understandings of fundamental characteristics of flow field in V-flame. Due to the additional turbulence production by the hot-rod, turbulence does not simply decay in V-flame. Turbulence-scalar interaction, scalar alignments with the principal strain rate in other words, is then clarified. The competition of turbulence and dilatation can be found in the conditional PDF of flame normal alignment. The results suggests that the alignment characteristics in high Da flames are applicable to low Da flames in the region of intense heat release.