Stage-specific histone modification profiles reveal global transitions in the Xenopus embryonic epigenome.

Vertebrate embryos are derived from a transitory pool of pluripotent cells. By the process of embryonic induction, these precursor cells are assigned to specific fates and differentiation programs. Histone post-translational modifications are thought to play a key role in the establishment and maintenance of stable gene expression patterns underlying these processes. While on gene level histone modifications are known to change during differentiation, very little is known about the quantitative fluctuations in bulk histone modifications during development. To investigate this issue we analysed histones isolated from four different developmental stages of Xenopus laevis by mass spectrometry. In toto, we quantified 59 modification states on core histones H3 and H4 from blastula to tadpole stages. During this developmental period, we observed in general an increase in the unmodified states, and a shift from histone modifications associated with transcriptional activity to transcriptionally repressive histone marks. We also compared these naturally occurring patterns with the histone modifications of murine ES cells, detecting large differences in the methylation patterns of histone H3 lysines 27 and 36 between pluripotent ES cells and pluripotent cells from Xenopus blastulae. By combining all detected modification transitions we could cluster their patterns according to their embryonic origin, defining specific histone modification profiles (HMPs) for each developmental stage. To our knowledge, this data set represents the first compendium of covalent histone modifications and their quantitative flux during normogenesis in a vertebrate model organism. The HMPs indicate a stepwise maturation of the embryonic epigenome, which may be causal to the progressing restriction of cellular potency during development

Impact of meteorological conditions on airborne fine particle composition and secondary pollutant characteristics in urban area during winter-time

The assessment of airborne fine particle composition and secondary pollutant characteristics in the case of Augsburg, Germany, during winter (31 January–12 March 2010) is studied on the basis of aerosol mass spectrometry (3 non-refractory components and organic matter, 3 positive matrix factorizations (PMF) factors), particle size distributions (PSD, 5 size modes, 5 PMF factors), further air pollutant mass concentrations (7 gases and VOC, black carbon, PM10, PM2.5) and meteorological measurements, including mixing layer height (MLH), with one-hourly temporal resolution. Data were subjectively assigned to 10 temporal phases which are characterised by different meteorological influences and air pollutant concentrations. In each phase hierarchical clustering analysis with the Ward method was applied to the correlations of air pollutants, PM components, PM source contributions and PSD modes and correlations of these data with all meteorological parameters. This analysis resulted in different degrees of sensitivities of these air pollutant data to single meteorological parameters. It is generally found that wind speed (negatively), MLH (negatively), relative humidity (positively) and wind direction influence primary pollutant and accumulation mode particle (size range 100–500 nm) concentrations. Temperature (negatively), absolute humidity (negatively) and also relative humidity (positively) are relevant for secondary compounds of PM and particle (PM2.5, PM10) mass concentrations. NO, nucleation and Aitken mode particle and the fresh traffic aerosol concentrations are only weakly dependent on meteorological parameters and thus are driven by emissions. These daily variation data analyses provide new, detailed meteorological influences on air pollutant data with the focus on fine particle composition and secondary pollutant characteristics and can explain major parts of certain PM component and gaseous pollutant exposure

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research

Catalog of functional groups of ZREs.

*<p>n.o.s. not otherwise specified.</p

Catalog of functional groups of ZREs.

*<p>n.o.s. not otherwise specified.</p

The DNA methylation profile of Raji EBV DNA does not change upon induction of EBV's lytic phase.

<p>DNA of Raji cells or Raji-BZLF1 cells, which had been induced with doxycycline for 15 hours and sorted for expression of GFP, were treated with bisulfite and amplified with primers specific for (<b>A</b>) the early lytic <i>BBLF4</i> promoter, (<b>B</b>) the immediate early <i>BZLF1</i> promoter, (<b>C</b>) the latent <i>Qp/Fp</i> promoter, and (<b>D</b>) the late lytic <i>BDLF4</i>/<i>BDRF1</i> promoter. PCR fragments were directly sequenced by the Sanger method as in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002902#ppat-1002902-g001" target="_blank">Fig. 1E</a>. The percentage of CpG methylation in Raji cells (latent) is depicted in red; the percentage of methylation in lytically induced Raji-BZLF1 cells (lytic) is indicated as black bars.</p

Kinetics of promoter activation after induction of EBV's lytic phase.

<p>(<b>A</b>) Evaluation of lytic transcript levels by quantitative RT-PCR. Raji-BZLF1 cells were induced with 100 ng/ml doxycycline for 46 h. A fraction of the cells was harvested every four hours. The temporal induction of different EBV genes suggests four different functional groups of viral genes. Group 1 (red) responds within four hours to the addition of doxycycline and encompasses <i>BZLF1 (Z)</i>, <i>BMRF1</i>, and <i>BMLF1</i>. Group 2 (orange) consists of <i>BBLF4</i>, <i>BBLF2</i>, and <i>BALF5</i>. They reached the expression peak eight hours post induction. <i>EBNA1</i> and <i>BSLF1</i> levels increased slowly over time (group 3, green) peaking at 28 hours after induction, while the late lytic genes (group 4, grey) showed no or only a very low expression upon lytic induction with kinetics comparable to group 3. (<b>B–E</b>) Chromatin immunoprecipitation experiments of Raji-BZLF1 cells upon lytic stimulation determined the occupancy of histones and their posttranslational modifications and the proteins EZH2 and RNA polymerase II in time course experiments. The experiments were conducted as described in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002902#ppat-1002902-g005" target="_blank">Fig. 5</a>. The loss of the repressive chromatin mark H3K27me3 and of the H3K27me3 methyltransferase EZH2 could already be detected after three hours post induction with doxycycline (B, D). The increase of the activation mark H3K4me3 was only visible 15 hours post induction (<b>C</b>) Binding of RNA polymerase II to early lytic promoters could be detected after 15 hours, but the very early responder BMRF1 was occupied by the protein already 7 hours post induction in line with the RT-PCR analysis, which identified this gene to be quickly induced upon lytic stimulation (<b>E</b>).</p

Chromatin state of Raji cells in the latent and the lytic phase.

<p>Three independent sets of chromatin immunoprecipitations (ChIPs) followed by quantitative PCR analysis of latent, early lytic, late lytic viral promoters, and cellular control loci are shown. Black bars represent uninduced, latent Raji-BZLF1 cells; grey bars represent lytically induced cells after treatment with doxycycline for 15 h. Data are represented as mean +/− SD. Asterisks indicate the p-value of each data point (*** p-value<0.001, ** p-value<0.01, * p-value<0.05). (<b>A</b>) histone H3; (<b>B</b>) repressive H3K27me3 histone modification; (<b>C</b>) activating H3K4me3 histone modification; (<b>D</b>) repressive H3K9me3 histone modification; (<b>E</b>) histone methyltransferase EZH2; (<b>F</b>) PolII ; (<b>G</b>) Western blot immunodetection of EZH2.</p

Epigenetic regulation of EBV: Close-up of the <i>BBLF4</i> promoter.

<p>On the lower half of the y-axis the binding profile of BZLF1 <i>in vivo</i> is shown as a green line, it's binding to methylated DNA <i>in vitro</i> as a red line. Red bars indicate the extent of CpG methylation (<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002902#ppat-1002902-g001" target="_blank">Fig. 1D</a>). The dark grey area indicates relative nucleosomal occupancy. On the upper half of the y-axis, the black area indicates EZH2, the light grey area H3K27me3, the red area H3K4me3, and the orange area PolII. <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002902#s2" target="_blank">Results</a> are provided as relative, dimensionless numbers; their scaling is identical in both graphs. (<b>A</b>) Repressive modifications characterize the <i>BBLF4</i> promoter during latency. (<b>B</b>) A hypersensitive site becomes established at meZREs immediately upstream of the coding sequence of <i>BBLF4</i> (grey area). H3K27me3 and EZH2 are lost and H3K4me3 and PolII indicate active transcription.</p