DNS of EGR-type turbulent flame in MILD condition

Three-dimensional direct numerical simulation (DNS) of exhaust gas recirculation (EGR)-type turbulent combustion operated in moderate and intense low-oxygen dilution (MILD) condition has been carried out to study the flame structure and flame interaction. In order to achieve adequate EGR-type initial/inlet mixture fields, partially premixed mixture fields which are correlated with the turbulence are carefully preprocessed. The chemical kinetics is modelled using a skeletal mechanism for methane-air combustion. The results suggest that the flame fronts have thin flame structure and the direct link between the mean reaction rate and scalar dissipation rate remains valid in the EGR-type combustion with MILD condition. However, the commonly used canonical flamelet is not fully representative for MILD combustion. During the flame-flame interactions, the heat release rate increases higher than the maximum laminar flame value, while the gradient of progress variable becomes smaller than laminar value. It is also proposed that the reaction rate and the scalar gradient can be used as a marker for the flame interaction. © 2012 The Combustion Institute. Published by Elsevier Inc. All rights reserved.

Complex chemistry DNS of n-heptane spray autoignition at high pressure and intermediate temperature conditions

Direct Numerical Simulations (DNS) of turbulent n-heptane sprays autoigniting at high pressure (P=24bar) and intermediate air temperature (Tair=1000K) have been performed to investigate the physical mechanisms present under conditions where low-temperature chemistry is expected to be important. The initial turbulence in the carrier gas, the global equivalence ratio in the spray region, and the initial droplet size distribution of the spray were varied. Results show that spray ignition exhibits a spotty nature, with several kernels developing independently in those regions where the mixture fraction is close to its most reactive value ξMR (as determined from homogeneous reactor calculations) and the scalar dissipation rate is low. Turbulence reduces the ignition delay time as it promotes mixing between air and the fuel vapor, eventually resulting in lower values of scalar dissipation. High values of the global equivalence ratio are responsible for a larger number of ignition kernels, due to the higher probability of finding regions where ξ=ξMR. Spray polydispersity results in the occurrence of ignition over a wider range of mixture fraction values. This is a consequence of the inhomogeneities in the mixing field that characterize these sprays, where poorly mixed rich spots are seen to alternate with leaner ones which are well-mixed. The DNS simulations presented in this work have also been used to assess the applicability of the Conditional Moment Closure (CMC) method to the simulation of spray combustion. CMC is found to be a valid method for capturing spray autoignition, although care should be taken in the modelling of the unclosed terms appearing in the CMC equations. © 2013 The Combustion Institute.

Statistics of reaction progress variable and mixture fraction gradients from DNS of turbulent partially premixed flames

Statistically planar turbulent partially premixed flames for different initial intensities of decaying turbulence have been simulated for global equivalence ratios = 0.7 and 1.0 using three-dimensional, simplified chemistry-based direct numerical simulations (DNS). The simulation parameters are chosen such that the flames represent the thin reaction zones regime combustion. A random bimodal distribution of equivalence ratio is introduced in the unburned gas ahead of the flame to account for the mixture inhomogeneity. The results suggest that the probability density functions (PDFs) of the mixture fraction gradient magnitude |Δξ| (i.e., P(|Δξ|)) can be reasonably approximated using a log-normal distribution. However, this presumed PDF distribution captures only the qualitative nature of the PDF of the reaction progress variable gradient magnitude |Δc| (i.e., P(|Δc|)). It has been found that a bivariate log-normal distribution does not sufficiently capture the quantitative behavior of the joint PDF of |Δξ| and |Δc| (i.e., P(|Δξ|, |Δc|)), and the agreement with the DNS data has been found to be poor in certain regions of the flame brush, particularly toward the burned gas side of the flame brush. Moreover, the variables |Δξ| and |Δc| show appreciable correlation toward the burned gas side of the flame brush. These findings are corroborated further using a DNS data of a lifted jet flame to study the flame geometry dependence of these statistics. © 2013 Copyright Taylor and Francis Group, LLC.

Cytological and Molecular Identification of Alien Chromatin in Giant Spike Wheat Germplasm

Alien chromosomes of twelve giant spike wheat germplasm lines were identified by C-banding, genomic in situ hybridization (GISH), sequence characterized amplified region (SCAR), and random amplified polymorphic DNA (RAPD). All lines showed a chromosome number of 2n = 42, five of them carried both a pair of wheat-rye (Triticum aestivum-Secale cereal) 1BL/1RS translocation chromosomes and a pair of Agropyron intermedium (Ai) chromosomes, three carried a pair of Ai chromosomes only, three others carried a pair of 1BL/1RS chromosomes only, and one carried neither 1BL/1BS nor Ai chromosome. Further identification revealed that the identical Ai chromosome in these germplasm lines substituted the chromosome 2D of common wheat (Triticum aestivum L.), designated as 2Ai. The genetic implication and further utilization of 2Ai in wheat improvement were also discussed.

Protocolo para determinação de açúcares totais em hortaliças pelo método de DNS.

2013

DNS-based Internet Client Clustering and Characterization

This paper proposes a novel protocol which uses the Internet Domain Name System (DNS) to partition Web clients into disjoint sets, each of which is associated with a single DNS server. We define an L-DNS cluster to be a grouping of Web Clients that use the same Local DNS server to resolve Internet host names. We identify such clusters in real-time using data obtained from a Web Server in conjunction with that server's Authoritative DNS―both instrumented with an implementation of our clustering algorithm. Using these clusters, we perform measurements from four distinct Internet locations. Our results show that L-DNS clustering enables a better estimation of proximity of a Web Client to a Web Server than previously proposed techniques. Thus, in a Content Distribution Network, a DNS-based scheme that redirects a request from a web client to one of many servers based on the client's name server coordinates (e.g., hops/latency/loss-rates between the client and servers) would perform better with our algorithm.

Chromatin: bind at your own RSC.

Recent work has identified a novel RSC-nucleosome complex that both strongly phases flanking nucleosomes and presents regulatory sites for ready access. These results challenge several widely held views.

Interactions of chromatin context, binding site sequence content, and sequence evolution in stress-induced p53 occupancy and transactivation.

Cellular stresses activate the tumor suppressor p53 protein leading to selective binding to DNA response elements (REs) and gene transactivation from a large pool of potential p53 REs (p53REs). To elucidate how p53RE sequences and local chromatin context interact to affect p53 binding and gene transactivation, we mapped genome-wide binding localizations of p53 and H3K4me3 in untreated and doxorubicin (DXR)-treated human lymphoblastoid cells. We examined the relationships among p53 occupancy, gene expression, H3K4me3, chromatin accessibility (DNase 1 hypersensitivity, DHS), ENCODE chromatin states, p53RE sequence, and evolutionary conservation. We observed that the inducible expression of p53-regulated genes was associated with the steady-state chromatin status of the cell. Most highly inducible p53-regulated genes were suppressed at baseline and marked by repressive histone modifications or displayed CTCF binding. Comparison of p53RE sequences residing in different chromatin contexts demonstrated that weaker p53REs resided in open promoters, while stronger p53REs were located within enhancers and repressed chromatin. p53 occupancy was strongly correlated with similarity of the target DNA sequences to the p53RE consensus, but surprisingly, inversely correlated with pre-existing nucleosome accessibility (DHS) and evolutionary conservation at the p53RE. Occupancy by p53 of REs that overlapped transposable element (TE) repeats was significantly higher (p<10-7) and correlated with stronger p53RE sequences (p<10-110) relative to nonTE-associated p53REs, particularly for MLT1H, LTR10B, and Mer61 TEs. However, binding at these elements was generally not associated with transactivation of adjacent genes. Occupied p53REs located in L2-like TEs were unique in displaying highly negative PhyloP scores (predicted fast-evolving) and being associated with altered H3K4me3 and DHS levels. These results underscore the systematic interaction between chromatin status and p53RE context in the induced transactivation response. This p53 regulated response appears to have been tuned via evolutionary processes that may have led to repression and/or utilization of p53REs originating from primate-specific transposon elements.

Chromatin accessibility mapping identifies mediators of basal transcription and retinoid-induced repression of OTX2 in medulloblastoma.

Despite an emerging understanding of the genetic alterations giving rise to various tumors, the mechanisms whereby most oncogenes are overexpressed remain unclear. Here we have utilized an integrated approach of genomewide regulatory element mapping via DNase-seq followed by conventional reporter assays and transcription factor binding site discovery to characterize the transcriptional regulation of the medulloblastoma oncogene Orthodenticle Homeobox 2 (OTX2). Through these studies we have revealed that OTX2 is differentially regulated in medulloblastoma at the level of chromatin accessibility, which is in part mediated by DNA methylation. In cell lines exhibiting chromatin accessibility of OTX2 regulatory regions, we found that autoregulation maintains OTX2 expression. Comparison of medulloblastoma regulatory elements with those of the developing brain reveals that these tumors engage a developmental regulatory program to drive OTX2 transcription. Finally, we have identified a transcriptional regulatory element mediating retinoid-induced OTX2 repression in these tumors. This work characterizes for the first time the mechanisms of OTX2 overexpression in medulloblastoma. Furthermore, this study establishes proof of principle for applying ENCODE datasets towards the characterization of upstream trans-acting factors mediating expression of individual genes.

HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells

BACKGROUND: Small molecule inhibitors of histone deacetylases (HDACi) hold promise as anticancer agents for particular malignancies. However, clinical use is often confounded by toxicity, perhaps due to indiscriminate hyperacetylation of cellular proteins. Therefore, elucidating the mechanisms by which HDACi trigger differentiation, cell cycle arrest, or apoptosis of cancer cells could inform development of more targeted therapies. We used the myelogenous leukemia line K562 as a model of HDACi-induced differentiation to investigate chromatin accessibility (DNase-seq) and expression (RNA-seq) changes associated with this process. RESULTS: We identified several thousand specific regulatory elements [~10 % of total DNase I-hypersensitive (DHS) sites] that become significantly more or less accessible with sodium butyrate or suberanilohydroxamic acid treatment. Most of the differential DHS sites display hallmarks of enhancers, including being enriched for non-promoter regions, associating with nearby gene expression changes, and increasing luciferase reporter expression in K562 cells. Differential DHS sites were enriched for key hematopoietic lineage transcription factor motifs, including SPI1 (PU.1), a known pioneer factor. We found PU.1 increases binding at opened DHS sites with HDACi treatment by ChIP-seq, but PU.1 knockdown by shRNA fails to block the chromatin accessibility and expression changes. A machine-learning approach indicates H3K27me3 initially marks PU.1-bound sites that open with HDACi treatment, suggesting these sites are epigenetically poised. CONCLUSIONS: We find HDACi treatment of K562 cells results in site-specific chromatin remodeling at epigenetically poised regulatory elements. PU.1 shows evidence of a pioneer role in this process by marking poised enhancers but is not required for transcriptional activation.