RIND-EDSBs and chromatin regulators.

<p>(A) The levels of RIND-EDSBs were measured in G0 cells of yeast strains lacking histone deacetylase genes, <i>SIR2, RPD3</i>, and <i>HDA1</i>. The level was decreased in the <i>sir2</i>Δ strain, while it was increased in <i>rpd3</i>Δ strain. (B) No significant change in the level of RIND-EDSBs was observed in yeast strains lacking the silent information regulator genes, <i>SIR1</i>, <i>SIR3</i>, or <i>SIR4</i>. (C) In contrast, deletions of <i>HTZ1</i> and <i>SWR1</i>, genes required for the prevention of heterochromatin spreading, led to significantly increased levels of RIND EDSBs. The values from 9 independent experiments are shown as box plots, with the boxes representing the interquartile ranges (25^th to 75^th percentile) and the median lines representing the 50^th percentile. The whiskers represent the minimum and the maximum values. <i>**P</i><0.001 (Mann-Whitney test).</p

EDSBs in various phases of the cell cycle.

<p>(A) EDSBs were measured in asynchronous culture and in yeast cells arrested in G0, G1, S, and M phases. The levels of EDSBs from 9 independent experiments are shown as box plots, with the boxes representing the interquartile ranges (25^th to 75^th percentile) and the median lines representing the 50^th percentile. The whiskers represent the minimum and the maximum values. There was a significant decrease in EDSBs in G0 cells compared to asynchronous culture, such that <i>**P</i><0.001 (Mann-Whitney test). (B) HMW DNA was isolated from apoptotic yeast cells, mixed with control DNA at varying percentages, and analyzed by Ty1-EDSB-LMPCR. The graph represents the mean levels of EDSBs with error bars representing standard deviations. The Ty1-EDSB-LMPCR assay could not detect DNA fragments from apoptotic cells (at 100% apoptotic DNA). Furthermore, apoptotic DNA fragments did not interfere with quantitative measurement of EDSBs.</p

Levels of RIND-EDSBs in yeast strains with mutations in DSB repair pathways.

<p>The levels of RIND-EDSBs were significantly increased in G0 cells of <i>mec1</i>Δ, <i>tel1</i>Δ, <i>mre11</i>Δ, <i>yku70</i>Δ, <i>yku80</i>Δ, and <i>rad51</i>Δ but not in <i>nej1</i>Δ strains. The levels of EDSBs from 9 independent experiments are shown as box plots, with the boxes representing the interquartile ranges (25^th to 75^th percentile) and the median lines representing the 50^th percentile. The whiskers represent the minimum and the maximum values. <i>**P</i><0.001 (Mann-Whitney test).</p

EDSBs were detected in different DNA preparations including HMW DNA (cell→gel), liquid DNA (cell→liquid), and liquid DNA extracted from in-gel HMW DNA (cell→gel→liquid).

<p>(A) The levels of EDSBs from different DNA preparation methods. (B) Subtracted DSBs levels between liquid DNA and other methods. When comparing cell→gel→liquid with cell→liquid, adding in gel preparation step did not increase the number of DSBs significantly. The average levels of EDSBs from 9 independent experiments are shown as histograms with error bars representing SEM.</p

Streaming Spectral Processing with Consumer-level Graphics Processing Units

This paper describes the implementation of a streaming spectral processing system for realtime audio in a consumer-level onboard GPU (Graphics Processing Unit) attached to an off-the-shelf laptop computer. It explores the implementation of four processes: standard phase vocoder analysis and synthesis, additive synthesis and the sliding phase vocoder. These were developed under the CUDA development environment as plugins for the Csound 6 audio programming language. Following a detailed exposition of the GPU code, results of performance tests are discussed for each algorithm. They demonstrate that such a system is capable of realtime audio, even under the restrictions imposed by a limited GPU capability

RIND-EDSBs in strains with mutations in genes encoding topoisomerases, their partners, and endonucleases.

<p>Deletions of genes encoding topoisomerases, their partners, and endonucleases did not reduce the levels of RIND-EDSBs in G0 cells. On the contrary, the levels of RIND-EDSBs were increased in G0 cells of <i>top3</i>Δ, <i>rad27</i>Δ, and <i>sae2</i>Δ strains. The values from 9 independent experiments are shown as box plots, with the boxes representing the interquartile ranges (25^th to 75^th percentile) and the median lines representing the 50^th percentile. The whiskers represent the minimum and the maximum values. <i>*P</i><0.05, <i>**P</i><0.001(Mann-Whitney test).</p

RIND-EDSBs levels using HMW DNA preparation and intranuclear ligation protocols.

<p>(A, B) The levels of RIND-EDSBs were measured in G0 cells of WT, <i>mec1</i>Δ, <i>yku70</i>Δ, <i>nhp6a</i>Δ strains using HMW DNA (A) and intranuclear ligation (B) protocols. (C, D) The levels of RIND-EDSBs in controls and TSA-treated WT and <i>mec1</i>Δ strains using HMW DNA (C) and intranuclear ligation (D) protocols. Bar graphs represent average values and error bars represent standard deviation of triplicate experiments.</p

Yeast strains used in this study.

<p>Yeast strains used in this study.</p

Levels of RIND-EDSBs in yeast strains with deletions of genes encoding proteins with the High-Mobility Group B (HMGB) domain.

<p>The levels of EDSBs were significantly decreased in G0 cells of yeast strains lacking <i>NHP6A</i>, <i>IXR1</i>, <i>ROX1</i>, and <i>HMO1</i>, suggesting that they play an important role in the production or retention of RIND-EDSBs. Nevertheless, the levels of RIND-EDSBs in <i>nhp6b</i>Δ, <i>nhp10</i>Δ, and <i>abf2</i>Δ strains were unchanged. The levels of EDSBs from 9 independent experiments are shown as box plots, with the boxes representing the interquartile ranges (25^th to 75^th percentile) and the median lines representing the 50^th percentile. The whiskers represent the minimum and the maximum values. <i>**P</i><0.001 (Mann-Whitney test).</p

Levels of RIND-EDSBs in HeLa cells transfected with HMGB1 siRNA.

<p>(A) The level of expression of HMGB1 mRNA was significantly downregulated in HMGB1 siRNA HeLa cells compared to control siRNA. <i>**P</i><0.001 (Paired t-test). (B) Downregulation of HMGB1 by HMGB1 siRNA in HeLa cells resulted in a decreased level of RIND-EDSBs when compared to the control. (C) Levels of L1 methylation as measured by COBRA-L1 assay were not changed in HMGB1 siRNA transfected cells. (D) L1–EDSB methylation levels were significantly lower in HMGB1 siRNA cells than in the control. The mean values from 9 independent experiments are shown as histograms with error bars representing SEM. <i>*P</i><0.05, <i>**P</i><0.001 (t-test).</p