Snaps and mends: DNA breaks and chromosomal translocations

Integrity in entirety is the preferred state of any organism. The temporal and spatial integrity of the genome ensures continued survival of a cell. DNA breakage is the first step towards creation of chromosomal translocations. In this review, we highlight the factors contributing towards the breakage of chromosomal DNA. It has been well-established that the structure and sequence of DNA play a critical role in selective fragility of the genome. Several non-B-DNA structures such as Z-DNA, cruciform DNA, G-quadruplexes, R loops and triplexes have been implicated in generation of genomic fragility leading to translocations. Similarly, specific sequences targeted by proteins such as Recombination Activating Genes and Activation Induced Cytidine Deaminase are involved in translocations. Processes that ensure the integrity of the genome through repair may lead to persistence of breakage and eventually translocations if their actions are anomalous. An insufficient supply of nucleotides and chromatin architecture may also play a critical role. This review focuses on a range of events with the potential to threaten the genomic integrity of a cell, leading to cancer.

TURBULENCE-TRANSPORT-CHEMISTRY INTERACTION IN STATISTICALLY PLANAR PREMIXED FLAMES AND IGNITION KERNELS IN NEAR ISOTROPIC TURBULENCE

Turbulence-transport-chemistry interaction plays a crucial role on the flame surface geometry, local and global reactionrates, and therefore, on the propagation and extinction characteristics of intensely turbulent, premixed flames encountered in LPP gas-turbine combustors. The aim of the present work is to understand these interaction effects on the flame surface annihilation and extinction of lean premixed flames, interacting with near isotropic turbulence. As an example case, lean premixed H-2-air mixture is considered so as to enable inclusion of detailed chemistry effects in Direct Numerical Simulations (DNS). The work is carried out in two phases namely, statistically planar flames and ignition kernel, both interacting with near isotropic turbulence, using the recently proposed Flame Particle Tracking (FPT) technique. Flame particles are surface points residing and commoving with an iso-scalar surface within a premixed flame. Tracking flame particles allows us to study the evolution of propagating surface locations uniquely identified with time. In this work, using DNS and FPT we study the flame speed, reaction rate and transport histories of such flame particles residing on iso-scalar surfaces. An analytical expression for the local displacement flame speed (SO is derived, and the contribution of transport and chemistry on the displacement flame speed is identified. An examination of the results of the planar case leads to a conclusion that the cause of variation in S-d may be attributed to the effects of turbulent transport and heat release rate. In the second phase of this work, the sustenance of an ignition kernel is examined in light of the S-curve. A newly proposed Damkohler number accounting for local turbulent transport and reaction rates is found to explain either the sustenance or otherwise propagation of flame kernels in near isotropic turbulence.

Hypothetical protein Rv3423.1 of Mycobacterium tuberculosis is a histone acetyltransferase

We isolated an 8 kDa mycobacterial hypothetical protein, Rv3423.1, from the chromatin of human macrophages infected with Mycobacterium tuberculosis H37Rv. Bioinformatics predictions followed by in vitro biochemical assays with purified recombinant protein showed that Rv3423.1 is a novel histone acetyltransferase that acetylates histone H3 at the K9/K14 positions. Transient transfection of macrophages containing GFP-tagged histone H1 with RFP-tagged Rv3423.1 revealed that the protein co-localizes with the chromatin in the nucleus. Co-immunoprecipitation assays confirmed that the Rv3423.1-histone interaction is specific. Rv3423.1 protein was detected in the culture filtrate of virulent but not avirulent M. tuberculosis. Infection of macrophages with recombinant Mycobacterium smegmatis constitutively expressing Rv3423.1 resulted in a significant increase in the number of intracellular bacteria. However, the protein did not seem to offer any growth advantage to free-living recombinant M. smegmatis. It is highly likely that, by binding to the host chromatin, this histone acetyltransferase from M. tuberculosis may manipulate the expression of host genes involved in anti-inflammatory responses to evade clearance and to survive in the intracellular environment.

Elucidating the cancer-specific genetic alteration spectrum of glioblastoma derived cell lines from whole exome and RNA sequencing

Cell lines derived from tumor tissues have been used as a valuable system to study gene regulation and cancer development. Comprehensive characterization of the genetic background of cell lines could provide clues on novel genes responsible for carcinogenesis and help in choosing cell lines for particular studies. Here, we have carried out whole exome and RNA sequencing of commonly used glioblastoma (GBM) cell lines (U87, T98G, LN229, U343, U373 and LN18) to unearth single nucleotide variations (SNVs), indels, differential gene expression, gene fusions and RNA editing events. We obtained an average of 41,071 SNVs out of which 1,594 (3.88%) were potentially cancer-specific. The cell lines showed frequent SNVs and indels in some of the genes that are known to be altered in GBM-EGFR, TP53, PTEN, SPTA1 and NF1. Chromatin modifying genes-ATRX, MLL3, MLL4, SETD2 and SRCAP also showed alterations. While no cell line carried IDH1 mutations, five cell lines showed hTERT promoter activating mutations with a concomitant increase in hTERT transcript levels. Five significant gene fusions were found of which NUP93-CYB5B was validated. An average of 18,949 RNA editing events was also obtained. Thus we have generated a comprehensive catalogue of genetic alterations for six GBM cell lines.

Elucidating the cancer-specific genetic alteration spectrum of glioblastoma derived cell lines from whole exome and RNA sequencing

Cell lines derived from tumor tissues have been used as a valuable system to study gene regulation and cancer development. Comprehensive characterization of the genetic background of cell lines could provide clues on novel genes responsible for carcinogenesis and help in choosing cell lines for particular studies. Here, we have carried out whole exome and RNA sequencing of commonly used glioblastoma (GBM) cell lines (U87, T98G, LN229, U343, U373 and LN18) to unearth single nucleotide variations (SNVs), indels, differential gene expression, gene fusions and RNA editing events. We obtained an average of 41,071 SNVs out of which 1,594 (3.88%) were potentially cancer-specific. The cell lines showed frequent SNVs and indels in some of the genes that are known to be altered in GBM-EGFR, TP53, PTEN, SPTA1 and NF1. Chromatin modifying genes-ATRX, MLL3, MLL4, SETD2 and SRCAP also showed alterations. While no cell line carried IDH1 mutations, five cell lines showed hTERT promoter activating mutations with a concomitant increase in hTERT transcript levels. Five significant gene fusions were found of which NUP93-CYB5B was validated. An average of 18,949 RNA editing events was also obtained. Thus we have generated a comprehensive catalogue of genetic alterations for six GBM cell lines.

Inhibition of p300 lysine acetyltransferase activity by luteolin reduces tumor growth in head and neck squamous cell carcinoma (HNSCC) xenograft mouse model

Chromatin acetylation is attributed with distinct functional relevance with respect to gene expression in normal and diseased conditions thereby leading to a topical interest in the concept of epigenetic modulators and therapy. We report here the identification and characterization of the acetylation inhibitory potential of an important dietary flavonoid, luteolin. Luteolin was found to inhibit p300 acetyltransferase with competitive binding to the acetyl CoA binding site. Luteolin treatment in a xenografted tumor model of head and neck squamous cell carcinoma (HNSCC), led to a dramatic reduction in tumor growth within 4 weeks corresponding to a decrease in histone acetylation. Cells treated with luteolin exhibit cell cycle arrest and decreased cell migration. Luteolin treatment led to an alteration in gene expression and miRNA profile including up-regulation of p53 induced miR-195/215, let7C; potentially translating into a tumor suppressor function. It also led to down regulation of oncomiRNAs such as miR-135a, thereby reflecting global changes in the microRNA network. Furthermore, a direct correlation between the inhibition of histone acetylation and gene expression was established using chromatin immunoprecipitation on promoters of differentially expressed genes. A network of dysregulated genes and miRNAs was mapped along with the gene ontology categories, and the effects of luteolin were observed to be potentially at multiple levels: at the level of gene expression, miRNA expression and miRNA processing.

Repeat-Associated Fission Yeast-Like Regional Centromeres in the Ascomycetous Budding Yeast Candida tropicalis

The centromere, on which kinetochore proteins assemble, ensures precise chromosome segregation. Centromeres are largely specified by the histone H3 variant CENP-A (also known as Cse4 in yeasts). Structurally, centromere DNA sequences are highly diverse in nature. However, the evolutionary consequence of these structural diversities on de novo CENP-A chromatin formation remains elusive. Here, we report the identification of centromeres, as the binding sites of four evolutionarily conserved kinetochore proteins, in the human pathogenic budding yeast Candida tropicalis. Each of the seven centromeres comprises a 2 to 5 kb non-repetitive mid core flanked by 2 to 5 kb inverted repeats. The repeat-associated centromeres of C. tropicalis all share a high degree of sequence conservation with each other and are strikingly diverged from the unique and mostly non-repetitive centromeres of related Candida species-Candida albicans, Candida dubliniensis, and Candida lusitaniae. Using a plasmid-based assay, we further demonstrate that pericentric inverted repeats and the underlying DNA sequence provide a structural determinant in CENP-A recruitment in C. tropicalis, as opposed to epigenetically regulated CENP-A loading at centromeres in C. albicans. Thus, the centromere structure and its influence on de novo CENP-A recruitment has been significantly rewired in closely related Candida species. Strikingly, the centromere structural properties along with role of pericentric repeats in de novo CENP-A loading in C. tropicalis are more reminiscent to those of the distantly related fission yeast Schizosaccharomyces pombe. Taken together, we demonstrate, for the first time, fission yeast-like repeat-associated centromeres in an ascomycetous budding yeast.

Burst Detection in Turbulent Channel Flows Based on Large Eddy Simulation Databases

Reliable turbulent channel flow databases at several Reynolds numbers have been established by large eddy simulation (LES), with two of them validated by comparing with typical direct numerical simulation (DNS) results. Furthermore, the statistics, such as velocity profile, turbulent intensities and shear stress, were obtained as well as the temporal and spatial structure of turbulent bursts. Based on the LES databases available, the conditional sampling methods are used to detect the structures of burst events. A method to deterimine the grouping parameter from the probability distribution function (pdf) curve of the time separation between ejection events is proposed to avoid the errors in detected results. And thus, the dependence of average burst period on thresholds is considerably weakened. Meanwhile, the average burst-to-bed area ratios are detected. It is found that the Reynolds number exhibits little effect on the burst period and burst-to-bed area ratio.

Effects of Subgrid-Scale Modeling on Time Correlations in Large Eddy Simulation

The effects of the unresolved subgrid-scale (SGS) motions on the energy balance of the resolved scales in large eddy simulation (LES) have been investigated actively because modeling the energy transfer between the resolved and unresolved scales is crucial to constructing accurate SGS models. But the subgrid scales not only modify the energy balance, they also contribute to temporal decorrelation of the resolved scales. The importance of this effect in applications including the predictability problem and the evaluation of sound radiation by turbulent flows motivates the present study of the effect of SGS modeling on turbulent time correlations. This paper compares the two-point, two-time Eulerian velocity correlation in isotropic homogeneous turbulence evaluated by direct numerical simulation (DNS) with the correlations evaluated by LES using a standard spectral eddy viscosity. It proves convenient to express the two-point correlations in terms of spatial Fourier decomposition of the velocity field. The LES fields are more coherent than the DNS fields: their time correlations decay more slowly at all resolved scales of motion and both their integral scales and microscales are larger than those of the DNS field. Filtering alone is not responsible for this effect: in the Fourier representation, the time correlations of the filtered DNS field are identical to those of the DNS field itself. The possibility of modeling the decorrelating effects of the unresolved scales of motion by including a random force in the model is briefly discussed. The results could have applications to the problem of computing sound sources in isotropic homogeneous turbulence by LES

Mapping Closure Approximation for Reactive Scalars in Random Flows

The Mapping Closure Approximation (MCA) approach is developed to describe the statistics of both conserved and reactive scalars in random flows. The statistics include Probability Density Function (PDF), Conditional Dissipation Rate (CDR) and Conditional Laplacian (CL). The statistical quantities are calculated using the MCA and compared with the results of the Direct Numerical Simulation (DNS). The results obtained from the MCA are in agreement with those from the DNS. It is shown that the MCA approach can predict the statistics of reactive scalars in random flows.

Coherent Structures in Transition of a Flat-Plate Boundary Layer at Ma=0.7

Direct numerical simulation (DNS) of a spatially evolving flat-plate boundary layer transition process at free stream Mach number 0.7 is performed. Tollmien-Schlichting (T-S) waves are added on the inlet boundary as the disturbances before transition. Typical coherent structures in the transition process are investigated based on the second invariant of velocity gradient tensor. The instantaneous shear stress and the mean velocity profile in the transition region are studied. In our view, the fact that the peak value of shear stress in the stress concentration area increases and exceeds a threshold value during the later stage of the transition process plays an important role in the laminar breakdown process.

圆柱绕流三维不稳定性的低维Galerkin法分析

利用低维Galerkin方法及Floquet稳定性分析理论,计算分析了圆柱绕流的三维线性不稳定性.分析中构造了能较好描述尾迹区流动的周向基函数,建立了完备的合理的基函数组,改进了计算机算法.结果证实圆柱二维周期流对展向小扰动为不稳定的,正确地预计了出现三维长波不稳定性的临界雷诺数Re_c=190,扰动展向波长为λ_c=3.6d.对雷诺数Re为180,190两种工况下的圆柱三维绕流流场的计算进一步证实了这种流动的整体不稳定性.该文所预计的临界值比Noack等人的结果更为精确,与Barkley等人的DNS解一致,与Williamson的实验相符.

Numerical Study Of Heat Transfer Mechanism In Turbulent Supercritical Co2 Channel Flow

Direct numerical simulation (DNS) of supercritical CO2 turbulent channel flow has been performed to investigate the heat transfer mechanism of supercritical fluid. In the present DNS, full compressible Navier-Stokes equations and Peng-Robison state equation are solved. Due to effects of the mean density variation in the wall normal direction, mean velocity in the cooling region becomes high compared with that in the heating region. The mean width between high-and low-speed streaks near the wall decreases in the cooling region, which means that turbulence in the cooling region is enhanced and lots of fine scale eddies are created due to the local high Reynolds number effects. From the turbulent kinetic energy budget, it is found that compressibility effects related with pressure fluctuation and dilatation of velocity fluctuation can be ignored even for supercritical condition. However, the effect of density fluctuation on turbulent kinetic energy cannot be ignored. In the cooling region, low kinematic viscosity and high thermal conductivity in the low speed streaks modify fine scale structure and turbulent transport of temperature, which results in high Nusselt number in the cooling condition of the supercritical CO2.

Receptivity To Free-Stream Disturbance Waves For Hypersonic Flow Over A Blunt Cone

A high-order shock-fitting finite difference scheme is studied and used to do direction numerical simulation (DNS) of hypersonic unsteady flow over a blunt cone with fast acoustic waves in the free stream, and the receptivity problem in the blunt cone hypersonic boundary layers is studied. The results show that the acoustic waves are the strongest disturbance in the blunt cone hypersonic boundary layers. The wave modes of disturbance in the blunt cone boundary layers are first, second, and third modes which are generated and propagated downstream along the wall. The results also show that as the frequency decreases, the amplitudes of wave modes of disturbance increase, but there is a critical value. When frequency is over the critial value, the amplitudes decrease. Because of the discontinuity of curvature along the blunt cone body, the maximum amplitudes as a function of frequencies are not monotone.

Effects Of Subgrid-Scale Modeling On Lagrangian Statistics In Large-Eddy Simulation

The application of large-eddy simulation (LES) to turbulent transport processes requires accurate prediction of the Lagrangian statistics of flow fields. However, in most existing SGS models, no explicit consideration is given to Lagrangian statistics. In this paper, we focus on the effects of SGS modeling on Lagrangian statistics in LES ranging from statistics determining single-particle dispersion to those of pair dispersion and multiparticle dispersion. Lagrangian statistics in homogeneous isotropic turbulence are extracted from direct numerical simulation (DNS) and the LES with a spectral eddy-viscosity model. For the case of longtime single-particle dispersion, it is shown that, compared to DNS, LES overpredicts the time scale of the Lagrangian velocity correlation but underpredicts the Lagrangian velocity fluctuation. These two effects tend to cancel one another leading to an accurate prediction of the longtime turbulent dispersion coefficient. Unlike the single-particle dispersion, LES tends to underestimate significantly the rate of relative dispersion of particle pairs and multiple-particles, when initial separation distances are less than the minimum resolved scale due to the lack of subgrid fluctuations. The overprediction of LES on the time scale of the Lagrangian velocity correlation is further confirmed by a theoretical analysis using a turbulence closure theory.