Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations

DNA-associated proteins (DAPs) classically regulate gene expression by binding to regulatory loci such as enhancers or promoters. As expanding catalogs of genome-wide DAP binding maps reveal thousands of loci that, unlike the majority of conventional enhancers and promoters, associate with dozens of different DAPs with apparently little regard for motif preference, an understanding of DAP association and coordination at such regulatory loci is essential to deciphering how these regions contribute to normal development and disease. In this study, we aggregated publicly available ChIP-seq data from 469 human DAPs assayed in three cell lines and integrated these data with an orthogonal data set of 352 nonredundant, in vitro–derived motifs mapped to the genome within DNase I hypersensitivity footprints to characterize regions with high numbers of DAP associations. We establish a generalizable definition for high occupancy target (HOT) loci and identify putative driver DAP motifs in HepG2 cells, including HNF4A, SP1, SP5, and ETV4, that are highly prevalent and show sequence conservation at HOT loci. The number of different DAPs associated with an element is positively associated with evidence of regulatory activity, and by systematically mutating 245 HOT loci with a massively parallel mutagenesis assay, we localized regulatory activity to a central core region that depends on the motif sequences of our previously nominated driver DAPs. In sum, this work leverages the increasingly large number of DAP motif and ChIP-seq data publicly available to explore how DAP associations contribute to genome-wide transcriptional regulation

Electron-correlation effects in appearance-potential spectra of Ni

Spin-resolved and temperature-dependent appearance-potential spectra of ferromagnetic Nickel are measured and analyzed theoretically. The Lander self-convolution model which relates the line shape to the unoccupied part of the local density of states turns out to be insufficient. Electron correlations and orbitally resolved transition-matrix elements are shown to be essential for a quantitative agreement between experiment and theory.Comment: LaTeX, 6 pages, 2 eps figures included, Phys. Rev. B (in press

Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations

DNA-associated proteins (DAPs) classically regulate gene expression by binding to regulatory loci such as enhancers or promoters. As expanding catalogs of genome-wide DAP binding maps reveal thousands of loci that, unlike the majority of conventional enhancers and promoters, associate with dozens of different DAPs with apparently little regard for motif preference, an understanding of DAP association and coordination at such regulatory loci is essential to deciphering how these regions contribute to normal development and disease. In this study, we aggregated publicly available ChIP-seq data from 469 human DAPs assayed in three cell lines and integrated these data with an orthogonal data set of 352 nonredundant, in vitro–derived motifs mapped to the genome within DNase I hypersensitivity footprints to characterize regions with high numbers of DAP associations. We establish a generalizable definition for high occupancy target (HOT) loci and identify putative driver DAP motifs in HepG2 cells, including HNF4A, SP1, SP5, and ETV4, that are highly prevalent and show sequence conservation at HOT loci. The number of different DAPs associated with an element is positively associated with evidence of regulatory activity, and by systematically mutating 245 HOT loci with a massively parallel mutagenesis assay, we localized regulatory activity to a central core region that depends on the motif sequences of our previously nominated driver DAPs. In sum, this work leverages the increasingly large number of DAP motif and ChIP-seq data publicly available to explore how DAP associations contribute to genome-wide transcriptional regulation

Modelling CO formation in the turbulent interstellar medium

We present results from high-resolution three-dimensional simulations of turbulent interstellar gas that self-consistently follow its coupled thermal, chemical and dynamical evolution, with a particular focus on the formation and destruction of H2 and CO. We quantify the formation timescales for H2 and CO in physical conditions corresponding to those found in nearby giant molecular clouds, and show that both species form rapidly, with chemical timescales that are comparable to the dynamical timescale of the gas. We also investigate the spatial distributions of H2 and CO, and how they relate to the underlying gas distribution. We show that H2 is a good tracer of the gas distribution, but that the relationship between CO abundance and gas density is more complex. The CO abundance is not well-correlated with either the gas number density n or the visual extinction A_V: both have a large influence on the CO abundance, but the inhomogeneous nature of the density field produced by the turbulence means that n and A_V are only poorly correlated. There is a large scatter in A_V, and hence CO abundance, for gas with any particular density, and similarly a large scatter in density and CO abundance for gas with any particular visual extinction. This will have important consequences for the interpretation of the CO emission observed from real molecular clouds. Finally, we also examine the temperature structure of the simulated gas. We show that the molecular gas is not isothermal. Most of it has a temperature in the range of 10--20 K, but there is also a significant fraction of warmer gas, located in low-extinction regions where photoelectric heating remains effective.Comment: 37 pages, 15 figures; minor revisions, matches version accepted by MNRA

Long-term psychosocial functioning after Ilizarov limb lengthening during childhood: 37 patients followed for 2–14 years

Background and purpose Few studies have been concerned with the patient's perception of the outcome of limb lengthening. We describe the psychological and social functioning after at least 2 years of follow-up in patients who had had a leg length discrepancy and who had undergone an Ilizarov limb lengthening procedure

Absence of Metallization in Solid Molecular Hydrogen

Being the simplest element with just one electron and proton the electronic structure of the Hydrogen atom is known exactly. However, this does not hold for the complex interplay between them in a solid and in particular not at high pressure that is known to alter the crystal as well as the electronic structure. Back in 1935 Wigner and Huntington predicted that at very high pressure solid molecular hydrogen would dissociate and form an atomic solid that is metallic. In spite of intense research efforts the experimental realization, as well as the theoretical determination of the crystal structure has remained elusive. Here we present a computational study showing that the distorted hexagonal P6$_3$/m structure is the most likely candidate for Phase III of solid hydrogen. We find that the pairing structure is very persistent and insulating over the whole pressure range, which suggests that metallization due to dissociation may precede eventual bandgap closure. Due to the fact that this not only resolve one of major disagreement between theory and experiment, but also excludes the conjectured existence of phonon-driven superconductivity in solid molecular hydrogen, our results involve a complete revision of the zero-temperature phase diagram of Phase III

Pharmacometabolomics reveals that serotonin is implicated in aspirin response variability.

While aspirin is generally effective for prevention of cardiovascular disease, considerable variation in drug response exists, resulting in some individuals displaying high on-treatment platelet reactivity. We used pharmacometabolomics to define pathways implicated in variation of response to treatment. We profiled serum samples from healthy subjects pre- and postaspirin (14 days, 81 mg/day) using mass spectrometry. We established a strong signature of aspirin exposure independent of response (15/34 metabolites changed). In our discovery (N = 80) and replication (N = 125) cohorts, higher serotonin levels pre- and postaspirin correlated with high, postaspirin, collagen-induced platelet aggregation. In a third cohort, platelets from subjects with the highest levels of serotonin preaspirin retained higher reactivity after incubation with aspirin than platelets from subjects with the lowest serotonin levels preaspirin (72 ± 8 vs. 61 ± 11%, P = 0.02, N = 20). Finally, ex vivo, serotonin strongly increased platelet reactivity after platelet incubation with aspirin (+20%, P = 4.9 × 10(-4), N = 12). These results suggest that serotonin is implicated in aspirin response variability.Analytical BioScience

Response to Therapeutic Sleep Deprivation: A Naturalistic Study of Clinical and Genetic Factors and Post-treatment Depressive Symptom Trajectory

Research has shown that therapeutic sleep deprivation (SD) has rapid antidepressant effects in the majority of depressed patients. Investigation of factors preceding and accompanying these effects may facilitate the identification of the underlying biological mechanisms. This exploratory study aimed to examine clinical and genetic factors predicting response to SD and determine the impact of SD on illness course. Mood during SD was also assessed via visual analogue scale. Depressed inpatients (n = 78) and healthy controls (n = 15) underwent ~36 h of SD. Response to SD was defined as a score of ≤ 2 on the Clinical Global Impression Scale for Global Improvement. Depressive symptom trajectories were evaluated for up to a month using self/expert ratings. Impact of genetic burden was calculated using polygenic risk scores for major depressive disorder. In total, 72% of patients responded to SD. Responders and non-responders did not differ in baseline self/expert depression symptom ratings, but mood differed. Response was associated with lower age (p = 0.007) and later age at life-time disease onset (p = 0.003). Higher genetic burden of depression was observed in non-responders than healthy controls. Up to a month post SD, depressive symptoms decreased in both patients groups, but more in responders, in whom effects were sustained. The present findings suggest that re-examining SD with a greater focus on biological mechanisms will lead to better understanding of mechanisms of depression