Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters.

BACKGROUND: In mammals, ChIP-seq studies of RNA polymerase II (PolII) occupancy have been performed to reveal how recruitment, initiation and pausing of PolII may control transcription rates, but the focus is rarely on obtaining finely resolved profiles that can portray the progression of PolII through sequential promoter states. RESULTS: Here, we analyze PolII binding profiles from high-coverage ChIP-seq on promoters of actively transcribed genes in mouse and humans. We show that the enrichment of PolII near transcription start sites exhibits a stereotypical bimodal structure, with one peak near active transcription start sites and a second peak 110 base pairs downstream from the first. Using an empirical model that reliably quantifies the spatial PolII signal, gene by gene, we show that the first PolII peak allows for refined positioning of transcription start sites, which is corroborated by mRNA sequencing. This bimodal signature is found both in mouse and humans. Analysis of the pausing-related factors NELF and DSIF suggests that the downstream peak reflects widespread pausing at the +1 nucleosome barrier. Several features of the bimodal pattern are correlated with sequence features such as CpG content and TATA boxes, as well as the histone mark H3K4me3. CONCLUSIONS: We thus show how high coverage DNA sequencing experiments can reveal as-yet unnoticed bimodal spatial features of PolII accumulation that are frequent at individual mammalian genes and reminiscent of transcription initiation and pausing. The initiation-pausing hypothesis is corroborated by evidence from run-on sequencing and immunoprecipitation in other cell types and species

Kiyang-yang, a West-African Postwar Idiom of Distress

In 1984, a healing cult for young barren women in southern Guinea Bissau developed into a movement, Kiyang-yang, that shook society to its foundations and had national repercussions. “Idiom of distress” is used here as a heuristic tool to understand how Kiyang-yang was able to link war and post-war-related traumatic stress and suffering on both individual and group levels. An individual experience born from a traumatic origin may be generalized into an idiom that diverse sectors of society could embrace for a range of related reasons. We argue that, for an idiom to be understood and appropriated by others, there has to be resonance at the level of symbolic language and shared experiences as well as at the level of the culturally mediated contingent emotions it communicates. We also argue that through its symbolic references to structural causes of suffering, an idiom of distress entails a danger for those in power. It can continue to exist only if its etiology is not exposed or the social suffering it articulates is not eliminated. We finally argue that idioms of distress are not to be understood as discrete diagnostic categories or as monodimensional expressions of “trauma” that can be addressed

Pinyon and juniper encroachment into sagebrush ecosystems impacts distribution and survival of greater sage-grouse

In sagebrush (Artemisia spp.) ecosystems, encroachment of pinyon (Pinus spp.) and juniper (Juniperus spp.; hereafter, "pinyon-junipeR&Rdquo;) trees has increased dramatically since European settlement. Understanding the impacts of this encroachment on behavioral decisions, distributions, and population dynamics of greater sage-grouse (Centrocercus urophasianus) and other sagebrush obligate species could help benefit sagebrush ecosystem management actions. We employed a novel two-stage Bayesian model that linked avoidance across different levels of pinyon-juniper cover to sage-grouse survival. Our analysis relied on extensive telemetry data collected across 6 yr and seven subpopulations within the Bi-State Distinct Population Segment (DPS), on the border of Nevada and California. The first model stage indicated avoidance behavior for all canopy cover classes on average, but individual grouse exhibited a high degree of heterogeneity in avoidance behavior of the lowest cover class (e.g., scattered isolated trees). The second stage modeled survival as a function of estimated avoidance parameters and indicated increased survival rates for individuals that exhibited avoidance of the lowest cover class. A post hoc frailty analysis revealed the greatest increase in hazard (i.e., mortality risk) occurred in areas with scattered isolated trees consisting of relatively high primary plant productivity. Collectively, these results provide clear evidence that local sage-grouse distributions and demographic rates are influenced by pinyon-juniper, especially in habitats with higher primary productivity but relatively low and seemingly benign tree cover. Such areas may function as ecological traps that convey attractive resources but adversely affect population vital rates. To increase sage-grouse survival, our model predictions support reducing actual pinyon-juniper cover as low as 1.5%, which is lower than the published target of 4.0%. These results may represent effects of pinyon-juniper cover in areas with similar ecological conditions to those of the Bi-State DPS, where populations occur at relatively high elevations and pinyon-juniper is abundant and widespread.The Rangeland Ecology & Management archives are made available by the Society for Range Management and the University of Arizona Libraries. Contact [email protected] for further information

Encounters with pinyon-juniper influence riskier movements in greater sage-grouse across the great basin

Fine-scale spatiotemporal studies can better identify relationships between individual survival and habitat fragmentation so thatmechanistic interpretations can be made at the population level. Recent advances in Global Positioning System(GPS) technology and statistical models capable of deconstructing high-frequency location data have facilitated interpretation of animal movement within a behaviorally mechanistic framework. Habitat fragmentation due to singleleaf pinyon (Pinus monophylla; hereafter pinyon) and Utah juniper (Juniperus osteosperma; hereafter juniper) encroachment into sagebrush (Artemisia spp.) communities is a commonly implicated perturbation that can adversely influence greater sage-grouse (Centrocercus urophasianus; hereafter sage-grouse) demographic rates. Using an extensive GPS data set (233 birds and 282,954 locations) across 12 study sites within the Great Basin, we conducted a behavioral change point analysis and constructed Brownian bridgemovementmodels fromeach behaviorally homogenous section.Wefound the probability of encountering pinyon-juniper among adults was two and three times greater than that of yearlings and juveniles, respectively. However, the movement rate in response to the probability of encountering pinyon-juniper trees was 1.5 times greater for juveniles. Parameter estimates indicated a 6.1% increase in the probability of encountering pinyonjuniper coupled with a 6.2 km/hour increase in movement speed resulted in a 56%, 42% and 16% increase in risk of daily mortality, for juveniles, yearlings, and adults, respectively. The effect of pinyon-juniper encounters on survival was dependent on movement rate and differed among age class. Under fast speed movements (i.e., flight), mortality risk increased as encountering pinyon-juniper increased across all age classes. In contrast, slower speeds (i.e., average) yielded similar adverse effects for juveniles and yearlings but not for adults. This analytical framework supports a behavioral mechanism that explains reduced survival related to pinyon-juniper within sagebrush environments,whereby encountering pinyon-juniper stimulates riskier movements that likely increase vulnerability to visually acute predators.The Rangeland Ecology & Management archives are made available by the Society for Range Management and the University of Arizona Libraries. Contact [email protected] for further information

Encounters with pinyon-juniper influence riskier movements in greater sage-grouse across the great basin

Fine-scale spatiotemporal studies can better identify relationships between individual survival and habitat fragmentation so thatmechanistic interpretations can be made at the population level. Recent advances in Global Positioning System(GPS) technology and statistical models capable of deconstructing high-frequency location data have facilitated interpretation of animal movement within a behaviorally mechanistic framework. Habitat fragmentation due to singleleaf pinyon (Pinus monophylla; hereafter pinyon) and Utah juniper (Juniperus osteosperma; hereafter juniper) encroachment into sagebrush (Artemisia spp.) communities is a commonly implicated perturbation that can adversely influence greater sage-grouse (Centrocercus urophasianus; hereafter sage-grouse) demographic rates. Using an extensive GPS data set (233 birds and 282,954 locations) across 12 study sites within the Great Basin, we conducted a behavioral change point analysis and constructed Brownian bridgemovementmodels fromeach behaviorally homogenous section.Wefound the probability of encountering pinyon-juniper among adults was two and three times greater than that of yearlings and juveniles, respectively. However, the movement rate in response to the probability of encountering pinyon-juniper trees was 1.5 times greater for juveniles. Parameter estimates indicated a 6.1% increase in the probability of encountering pinyonjuniper coupled with a 6.2 km/hour increase in movement speed resulted in a 56%, 42% and 16% increase in risk of daily mortality, for juveniles, yearlings, and adults, respectively. The effect of pinyon-juniper encounters on survival was dependent on movement rate and differed among age class. Under fast speed movements (i.e., flight), mortality risk increased as encountering pinyon-juniper increased across all age classes. In contrast, slower speeds (i.e., average) yielded similar adverse effects for juveniles and yearlings but not for adults. This analytical framework supports a behavioral mechanism that explains reduced survival related to pinyon-juniper within sagebrush environments,whereby encountering pinyon-juniper stimulates riskier movements that likely increase vulnerability to visually acute predators.The Rangeland Ecology & Management archives are made available by the Society for Range Management and the University of Arizona Libraries. Contact [email protected] for further information

New measurement of ξ- → Λπ- decay parameters

A study on the measurement of φ≡ using a sample of 144×106 ≡- →λπ- decays having an average polarization of 3.7% was presented. The polarized ≡-'s were produced by directing an 800 geV÷c proton beam onto a 2 mm ×2 mm× 60 mm cu target at angles of +3 and -3 mrad. The results were shown to be a 2.9× improvement over the best previous mesurements. It was shown that CP violation in charged ≡→λπ decays are not suppressed by a vanishing final phase shift difference