Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis.

Cytosine methylation is important for transposon silencing and epigenetic regulation of endogenous genes, although the extent to which this DNA modification functions to regulate the genome is still unknown. Here we report the first comprehensive DNA methylation map of an entire genome, at 35 base pair resolution, using the flowering plant Arabidopsis thaliana as a model. We find that pericentromeric heterochromatin, repetitive sequences, and regions producing small interfering RNAs are heavily methylated. Unexpectedly, over one-third of expressed genes contain methylation within transcribed regions, whereas only approximately 5% of genes show methylation within promoter regions. Interestingly, genes methylated in transcribed regions are highly expressed and constitutively active, whereas promoter-methylated genes show a greater degree of tissue-specific expression. Whole-genome tiling-array transcriptional profiling of DNA methyltransferase null mutants identified hundreds of genes and intergenic noncoding RNAs with altered expression levels, many of which may be epigenetically controlled by DNA methylation.

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.

The mechanical integrity of fuel pin cladding in a pulsed-beam accelerator driven subcritical reactor

The Accelerator Driven Subcritical Reactor (ADSR) is one of the reactor designs proposed for future nuclear energy production. Interest in the ADSR arises from its enhanced and intrinsic safety characteristics, as well as its potential ability to utilize the large global reserves of thorium and to burn legacy actinide waste from other reactors and decommissioned nuclear weapons. The ADSR concept is based on the coupling of a particle accelerator and a subcritical core by means of a neutron spallation target interface. One of the candidate accelerator technologies receiving increasing attention, the Fixed Field Alternating Gradient (FFAG) accelerator, generates a pulsed proton beam. This paper investigates the impact of pulsed proton beam operation on the mechanical integrity of the fuel pin cladding. A pulsed beam induces repetitive temperature changes in the reactor core which lead to cyclic thermal stresses in the cladding. To perform the thermal analysis aspects of this study a code that couples the neutron kinetics of a subcritical core to a cylindrical geometry heat transfer model was developed. This code, named PTS-ADS, enables temperature variations in the cladding to be calculated. These results are then used to perform thermal fatigue analysis and to predict the stress-life behaviour of the cladding. © 2011 Elsevier Ltd. All rights reserved.

Field emission properties of single-walled carbon nanotubes with a variety of emitter morphologies

Field emission properties of single-walled carbon nanotubes (SWCNTs), which were prepared through alcohol catalytic chemical vapor deposition for 10-60s, were characterized in a diode configuration. Protrusive bundles at the top surface of samples act selectively as emission sites. The number of emission sites was controlled by emitter morphologies combined with texturing of Si substrates. SWCNTs grown on a textured Si substrate exhibited a turn-on field as low as 2.4 V/μm at a field emission current density of 1 μA/cm 2. Uniform spatial luminescence (0.5 cm2) from the rear surface of the anode was revealed for SWCNTs prepared on the textured Si substrate. Deterioration of field emission properties through repetitive measurements was reduced for the textured samples in comparison with vertically aligned SWCNTs and a random network of SWCNTs prepared on flat Si substrates. Emitter morphology resulting in improved field emission properties is a crucial factor for the fabrication of SWCNT-electron sources. Morphologically controlled SWCNTs with promising emitter performance are expected to be practical electron sources. © 2008 The Japan Society of Applied Physics.

The effect of beam interruptions on the integrity of ADSR fuel pin cladding: A thermo-mechanical analysis

During its lifetime in the core, the cladding of an Accelerator Driven Subcritical Reactor (ADSR) fuel pin is expected to experience variable stresses due to frequent interruptions in the accelerator proton beam. This paper investigates the thermal fatigue damage in the cladding due to repetitive and unplanned beam interruptions under certain operational conditions. Beam trip data was obtained for four operating high power proton accelerators, among which the Spallation Neutron Source (SNS) superconducting accelerator was selected for further analysis. 9Cr-1Mo-Nb-V (T91) steel was selected as the cladding material because of its proven compatibility with proposed ADSR design concepts. The neutronic, thermal and stress analyses were performed using the PTS-ADS, a code that has been specifically developed for studying the dynamic response to beam-induced transients in accelerator driven subcritical systems. The lifetime of the fuel cladding in the core was estimated for three levels of allowed pin power and specific operating conditions. © 2012 Elsevier Ltd. All rights reserved.

Epigenetic remodeling of meiotic crossover frequency in Arabidopsis thaliana DNA methyltransferase mutants.

Meiosis is a specialized eukaryotic cell division that generates haploid gametes required for sexual reproduction. During meiosis, homologous chromosomes pair and undergo reciprocal genetic exchange, termed crossover (CO). Meiotic CO frequency varies along the physical length of chromosomes and is determined by hierarchical mechanisms, including epigenetic organization, for example methylation of the DNA and histones. Here we investigate the role of DNA methylation in determining patterns of CO frequency along Arabidopsis thaliana chromosomes. In A. thaliana the pericentromeric regions are repetitive, densely DNA methylated, and suppressed for both RNA polymerase-II transcription and CO frequency. DNA hypomethylated methyltransferase1 (met1) mutants show transcriptional reactivation of repetitive sequences in the pericentromeres, which we demonstrate is coupled to extensive remodeling of CO frequency. We observe elevated centromere-proximal COs in met1, coincident with pericentromeric decreases and distal increases. Importantly, total numbers of CO events are similar between wild type and met1, suggesting a role for interference and homeostasis in CO remodeling. To understand recombination distributions at a finer scale we generated CO frequency maps close to the telomere of chromosome 3 in wild type and demonstrate an elevated recombination topology in met1. Using a pollen-typing strategy we have identified an intergenic nucleosome-free CO hotspot 3a, and we demonstrate that it undergoes increased recombination activity in met1. We hypothesize that modulation of 3a activity is caused by CO remodeling driven by elevated centromeric COs. These data demonstrate how regional epigenetic organization can pattern recombination frequency along eukaryotic chromosomes.

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.

Accelerator-induced transients in Accelerator Driven Subcritical Reactors

Achieving higher particles energies and beam powers have long been the main focus of research in accelerator technology. Since Accelerator Driven Subcritical Reactors (ADSRs) have become the subject of increasing interest, accelerator reliability and modes of operation have become important matters that require further research and development in order to accommodate the engineering and economic needs of ADSRs. This paper focuses on neutronic and thermo-mechanical analyses of accelerator-induced transients in an ADSR. Such transients fall into three main categories: beam interruptions (trips), pulsed-beam operation, and beam overpower. The concept of a multiple-target ADSR is shown to increase system reliability and to mitigate the negative effects of beam interruptions, such as thermal cyclic fatigue in the fuel cladding and the huge financial cost of total power loss. This work also demonstrates the effectiveness of the temperature-to-reactivity feedback mechanisms in ADSRs. A comparison of shutdown mechanisms using control rods and beam cut-off highlights the intrinsic safety features of ADSRs. It is evident that the presence of control rods is crucial in an industrial-scale ADSR. This paper also proposes a method to monitor core reactivity online using the repetitive pattern of beam current fluctuations in a pulsed-beam operation mode. Results were produced using PTS-ADS, a computer code developed specifically to study the dynamic neutronic and thermal responses to beam transients in subcritical reactor systems. © 2012 Elsevier B.V.