Effect of impurities on microstructural evolution under irradiation in beryllium

Impurities are known to affect mechanical properties of beryllium, but their effect on development of irradiation induced microstructure is still unknown. In this contribution we are making further attempt to reveal behavior of impurities in neutron irradiated beryllium pebbles by using both analytical transmission electron microscope (TEM) and first principles computer simulations. TEM studies have revealed Al-Fe-Be precipitates, complex multiple phase precipitates, homogeneous segregations of elements to grain boundaries as well as abundant precipitation along dislocations. All precipitates are richly decorated with helium bubbles which are smaller in size than typical bubbles inside grains. Precipitate-free and helium-bubble-free zones were observed along grain boundaries. Using density functional theory approach, we have calculated interaction of typical solutes found in beryllium, namely, Al, Fe, Cr, Mg and Si with vacancies, interstitials and free surfaces which can simulate a surface of helium bubbles. Interesting correlation has been revealed: an impurity which has attractive binding with a vacancy has also positive affinity to free surface. In particular, Al, Mg and Si are strongly bound with vacancies and also attracted by the free surfaces. This result is supported by the EDX measurements, (see Fig. above) which reveal decoration of He bubbles with Al, Si and Mg, while Fe is homogeneously distributed. Those impurities which repulse vacancies are attracted by self-interstitials, however, no correlation with the formation volume of respective substitutional atoms was found in this case

New insights into microstructure of irradiated beryllium based on experiments and computer simulations

The microstructural response of beryllium after neutron irradiation at various temperatures (643–923 K) was systematically studied using analytical transmission electron microscope that together with outcomes from advanced atomistic modelling provides new insights in the mechanisms of microstructural changes in this material. The most prominent feature of microstructural modification is the formation of gas bubbles, which is revealed at all studied irradiation temperatures. Except for the lowest irradiation temperature, gas bubbles have the shape of thin hexagonal prisms with average height and diameter increasing with temperature. A high number density of small bubbles is observed within grains, while significantly larger bubbles are formed along high-angle grain boundaries (GB). Denuded zones (DZ) nearly free from bubbles are found along both high- and low-angle grain boundaries. Precipitations of secondary phases (mainly intermetallic Al-Fe-Be) were observed inside grains, along dislocation lines and at GBs. EDX analysis has revealed homogeneous segregation of chromium and iron along GBs. The observed features are discussed with respect to the available atomistic modelling results. In particular, we present a plausible reasoning for the abundant formation of gas bubbles on intermetallic precipitates, observation of various thickness of zones denuded in gas bubbles and precipitates, and their relation to the atomic scale diffusion mechanisms of solute-vacancy clusters

RNA polymerase II stalling promotes nucleosome occlusion and pTEFb recruitment to drive immortalization by Epstein-Barr virus

Epstein-Barr virus (EBV) immortalizes resting B-cells and is a key etiologic agent in the development of numerous cancers. The essential EBV-encoded protein EBNA 2 activates the viral C promoter (Cp) producing a message of ~120 kb that is differentially spliced to encode all EBNAs required for immortalization. We have previously shown that EBNA 2-activated transcription is dependent on the activity of the RNA polymerase II (pol II) C-terminal domain (CTD) kinase pTEFb (CDK9/cyclin T1). We now demonstrate that Cp, in contrast to two shorter EBNA 2-activated viral genes (LMP 1 and 2A), displays high levels of promoter-proximally stalled pol II despite being constitutively active. Consistent with pol II stalling, we detect considerable pausing complex (NELF/DSIF) association with Cp. Significantly, we observe substantial Cp-specific pTEFb recruitment that stimulates high-level pol II CTD serine 2 phosphorylation at distal regions (up to +75 kb), promoting elongation. We reveal that Cp-specific pol II accumulation is directed by DNA sequences unfavourable for nucleosome assembly that increase TBP access and pol II recruitment. Stalled pol II then maintains Cp nucleosome depletion. Our data indicate that pTEFb is recruited to Cp by the bromodomain protein Brd4, with polymerase stalling facilitating stable association of pTEFb. The Brd4 inhibitor JQ1 and the pTEFb inhibitors DRB and Flavopiridol significantly reduce Cp, but not LMP1 transcript production indicating that Brd4 and pTEFb are required for Cp transcription. Taken together our data indicate that pol II stalling at Cp promotes transcription of essential immortalizing genes during EBV infection by (i) preventing promoter-proximal nucleosome assembly and ii) necessitating the recruitment of pTEFb thereby maintaining serine 2 CTD phosphorylation at distal regions

Modulation of enhancer looping and differential gene targeting by Epstein-Barr virus transcription factors directs cellular reprogramming

Epstein-Barr virus (EBV) epigenetically reprogrammes B-lymphocytes to drive immortalization and facilitate viral persistence. Host-cell transcription is perturbed principally through the actions of EBV EBNA 2, 3A, 3B and 3C, with cellular genes deregulated by specific combinations of these EBNAs through unknown mechanisms. Comparing human genome binding by these viral transcription factors, we discovered that 25% of binding sites were shared by EBNA 2 and the EBNA 3s and were located predominantly in enhancers. Moreover, 80% of potential EBNA 3A, 3B or 3C target genes were also targeted by EBNA 2, implicating extensive interplay between EBNA 2 and 3 proteins in cellular reprogramming. Investigating shared enhancer sites neighbouring two new targets (WEE1 and CTBP2) we discovered that EBNA 3 proteins repress transcription by modulating enhancer-promoter loop formation to establish repressive chromatin hubs or prevent assembly of active hubs. Re-ChIP analysis revealed that EBNA 2 and 3 proteins do not bind simultaneously at shared sites but compete for binding thereby modulating enhancer-promoter interactions. At an EBNA 3-only intergenic enhancer site between ADAM28 and ADAMDEC1 EBNA 3C was also able to independently direct epigenetic repression of both genes through enhancer-promoter looping. Significantly, studying shared or unique EBNA 3 binding sites at WEE1, CTBP2, ITGAL (LFA-1 alpha chain), BCL2L11 (Bim) and the ADAMs, we also discovered that different sets of EBNA 3 proteins bind regulatory elements in a gene and cell-type specific manner. Binding profiles correlated with the effects of individual EBNA 3 proteins on the expression of these genes, providing a molecular basis for the targeting of different sets of cellular genes by the EBNA 3s. Our results therefore highlight the influence of the genomic and cellular context in determining the specificity of gene deregulation by EBV and provide a paradigm for host-cell reprogramming through modulation of enhancer-promoter interactions by viral transcription factors