VUV Photoionization Cross Sections of HO_2, H_2O_2, and H_2CO

The absolute vacuum ultraviolet (VUV) photoionization spectra of the hydroperoxyl radical (HO_2), hydrogen peroxide (H_2O_2), and formaldehyde (H_2CO) have been measured from their first ionization thresholds to 12.008 eV. HO_2, H_2O_2, and H_2CO were generated from the oxidation of methanol initiated by pulsed-laser-photolysis of Cl_2 in a low-pressure slow flow reactor. Reactants, intermediates, and products were detected by time-resolved multiplexed synchrotron photoionization mass spectrometry. Absolute concentrations were obtained from the time-dependent photoion signals by modeling the kinetics of the methanol oxidation chemistry. Photoionization cross sections were determined at several photon energies relative to the cross section of methanol, which was in turn determined relative to that of propene. These measurements were used to place relative photoionization spectra of HO_2, H_2O_2, and H_2CO on an absolute scale, resulting in absolute photoionization spectra

Imaging aspects of cardiovascular disease at the cell and molecular level

Cell and molecular imaging has a long and distinguished history. Erythrocytes were visualized microscopically by van Leeuwenhoek in 1674, and microscope technology has evolved mightily since the first single-lens instruments, and now incorporates many types that do not use photons of light for image formation. The combination of these instruments with preparations stained with histochemical and immunohistochemical markers has revolutionized imaging by allowing the biochemical identification of components at subcellular resolution. The field of cardiovascular disease has benefited greatly from these advances for the characterization of disease etiologies. In this review, we will highlight and summarize the use of microscopy imaging systems, including light microscopy, electron microscopy, confocal scanning laser microscopy, laser scanning cytometry, laser microdissection, and atomic force microscopy in conjunction with a variety of histochemical techniques in studies aimed at understanding mechanisms underlying cardiovascular diseases at the cell and molecular level

The impact of the third O-2 addition reaction network on ignition delay times of neo-pentane

We studied the oxidation of neo-pentane by combining experiments, theoretical calculations, and mechanistic developments to elucidate the impact of the 3rd O 2 addition reaction network on ignition delay time predictions. The experiments are based on photoionization mass spectrometry in jet-stirred and time-resolved flow reactors allowing for sensitive detection of the keto-hydroperoxide (KHP) and keto-dihydroperoxide (KDHP) intermediates. With neo-pentane exhibiting a unique symmetric molecular structure, which consequently results only in single KHP and KDHP isomers, theoretical calculations of ionization and fragment appearance energies and of absolute photoionization cross sections enabled the unambiguous identification and quantification of the KHP intermediate. Its temperature and time-resolved profiles together with calculated and experimentally observed KHP-to-KDHP signal ratios were compared to simulation results based on a newly developed mechanism that describes the 3rd O-2 addition reaction network. A satisfactory agreement has been observed between the experimental data points and the simulation results, thus adding confidence to the model's overall performance. Finally, this mechanism was used to predict ignition delay times reported previously in shock tube and rapid compression machine experiments (J. Bugler et al., Combust. Flame 163 (2016) 138-156). While the model accurately reproduces the experimental data, simulations with and without the 3rd O-2 addition reaction network included reveal only a negligible effect on the predicted ignition delay times at 10 and 20 atm. According to model calculations, low temperatures and high pressures promote the importance of the 3rd O-2 addition reactions. (c) 2020 The Combustion Institute. Published by Elsevier Inc. All rights reserved.Peer reviewe

Molecular Architecture of the Human Mediator–RNA Polymerase II–TFIIF Assembly

The authors perform a cryo-EM study of the 1.9 MDa human Mediator-RNA polymerase II-TFIIF assembly, which reveals the structural organization of the human transcription initiation apparatus

Mediator and cohesin connect gene expression and chromatin architecture

Transcription factors control cell-specific gene expression programs through interactions with diverse coactivators and the transcription apparatus. Gene activation may involve DNA loop formation between enhancer-bound transcription factors and the transcription apparatus at the core promoter, but this process is not well understood. Here we report that mediator and cohesin physically and functionally connect the enhancers and core promoters of active genes in murine embryonic stem cells. Mediator, a transcriptional coactivator, forms a complex with cohesin, which can form rings that connect two DNA segments. The cohesin-loading factor Nipbl is associated with mediator–cohesin complexes, providing a means to load cohesin at promoters. DNA looping is observed between the enhancers and promoters occupied by mediator and cohesin. Mediator and cohesin co-occupy different promoters in different cells, thus generating cell-type-specific DNA loops linked to the gene expression program of each cell.National Institutes of Health (U.S.) (Fellowship)Canadian Institutes of Health Research (Research Fellowship)National Institutes of Health (U.S.) (Grant R01 HG002668

Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes

The gene expression programs that define the identity of each cell are controlled by master transcription factors (TFs) that bind cell-type-specific enhancers, as well as signaling factors, which bring extracellular stimuli to these enhancers. Recent studies have revealed that master TFs form phase-separated condensates with the Mediator coactivator at super-enhancers. Here, we present evidence that signaling factors for the WNT, TGF-β, and JAK/STAT pathways use their intrinsically disordered regions (IDRs) to enter and concentrate in Mediator condensates at super-enhancers. We show that the WNT coactivator β-catenin interacts both with components of condensates and DNA-binding factors to selectively occupy super-enhancer-associated genes. We propose that the cell-type specificity of the response to signaling is mediated in part by the IDRs of the signaling factors, which cause these factors to partition into condensates established by the master TFs and Mediator at genes with prominent roles in cell identity

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

The synthesis of pre-mRNA by RNA polymerase II (Pol II) involves the formation of a transcription initiation complex, and a transition to an elongation complex. The large subunit of Pol II contains an intrinsically disordered C-terminal domain that is phosphorylated by cyclin-dependent kinases during the transition from initiation to elongation, thus influencing the interaction of the C-terminal domain with different components of the initiation or the RNA-splicing apparatus. Recent observations suggest that this model provides only a partial picture of the effects of phosphorylation of the C-terminal domain. Both the transcription-initiation machinery and the splicing machinery can form phase-separated condensates that contain large numbers of component molecules: hundreds of molecules of Pol II and mediator are concentrated in condensates at super-enhancers, and large numbers of splicing factors are concentrated in nuclear speckles, some of which occur at highly active transcription sites. Here we investigate whether the phosphorylation of the Pol II C-terminal domain regulates the incorporation of Pol II into phase-separated condensates that are associated with transcription initiation and splicing. We find that the hypophosphorylated C-terminal domain of Pol II is incorporated into mediator condensates and that phosphorylation by regulatory cyclin-dependent kinases reduces this incorporation. We also find that the hyperphosphorylated C-terminal domain is preferentially incorporated into condensates that are formed by splicing factors. These results suggest that phosphorylation of the Pol II C-terminal domain drives an exchange from condensates that are involved in transcription initiation to those that are involved in RNA processing, and implicates phosphorylation as a mechanism that regulates condensate preference