Regulation of the ESC transcriptome by nuclear long non-coding RNAs

Long noncoding (lnc)RNAs have recently emerged as key regulators of gene expression. Here, we performed high-depth poly(A)+ RNA sequencing across multiple clonal populations of mouse embryonic stem cells (ESCs) and neural progenitor cells (NPCs) to comprehensively identify differentially regulated lncRNAs. We establish a biologically robust profile of lncRNA expression in these two cell types and further confirm that the majority of these lncRNAs are enriched in the nucleus. Applying weighted gene co-expression network analysis, we define a group of lncRNAs that are tightly associated with the pluripotent state of ESCs. Among these, we show that acute depletion of PAT-14 using antisense oligonucleotides impacts the differentiation- and development-associated gene expression program of ESCs. Furthermore, we demonstrate that Firre, a lncRNA highly enriched in the nucleoplasm and previously reported to mediate chromosomal contacts in ESCs, controls a network of genes related to RNA processing. Together, we provide a comprehensive, up-to-date and high resolution compilation of lncRNA expression in ESCs and NPCs and show that nuclear lncRNAs are tightly integrated into the regulation of ESC gene expression

East African lake evidence for Pliocene millennial-scale climate variability

Late Cenozoic climate history in Africa was punctuated by episodes of variability, characterized by the appearance and disappearance of large freshwater lakes within the East African Rift Valley. In the Baringo-Bogoria basin, a well-dated sequence of diatomites and fluviolacustrine sediments documents the precessionally forced cycling of an extensive lake system between 2.70 Ma and 2.55 Ma. One diatomite unit was studied, using the oxygen isotope composition of diatom silica combined with X-ray fluorescence spectrometry and taxonomic assemblage changes, to explore the nature of climate variability during this interval. Data reveal a rapid onset and gradual decline of deepwater lake conditions, which exhibit millennial-scale cyclicity of ∼1400–1700 yr, similar to late Quaternary Dansgaard-Oeschger events. These cycles are thought to reflect enhanced precipitation coincident with increased monsoonal strength, suggesting the existence of a teleconnection between the high latitudes and East Africa during this period. Such climatic variability could have affected faunal and floral evolution at the time

Phase Angle and Bio-Impedance Values during the First Year after Delivery in Women with Previous Excessive Gestational Weight Gain: Innovative Data from the Belgian INTER-ACT Study

Phase angle (PhA) is a body composition parameter that measures changes in the amount and quality of soft tissue. Few studies have explored PhA in pregnancy or postpartum. The aim of this study was to explore the PhA during the first year postpartum in a Belgian cohort using data from the control group of the INTER-ACT study, an intervention trial targeting those with excess gestational weight gain. A secondary aim was to examine associations between PhA and potential explanatory variables. Women aged ≥18 with excessive weight gain in a singleton pregnancy and without a chronic disease were eligible. Data collection included anthropometry as well as demographic and lifestyle questionnaires at 6 weeks, 6 months and 12 months postpartum. Body composition, including PhA, was measured with the Tanita MC780SMA device. Data was analysed using correlation and mixed model analyses. A total of 509 participants (median age 31.2) were included. The median PhA at 6 weeks postpartum was 5.8°. Higher PhA values were seen in multiparous women (p = 0.02) but there was no association with any other lifestyle or demographic factors. PhA values were positively associated with muscle mass and BMI (r = 0.13, p = 0.004 and r = 0.18, p &lt; 0.001) at 6 weeks postpartum. PhA increased slightly in the 12 months postpartum, which was related to a decrease in fat percentage (p = 0.004). Further research in the pregnant/postpartum population is needed to elucidate any links with perinatal or future health outcomes.</jats:p

Adaptation responses to climate change differ between global megacities

Urban areas are increasingly at risk from climate change, with negative impacts predicted for human health, the economy and ecosystems1, 2. These risks require responses from cities to improve their resilience. Policymakers need to understand current adaptation spend to plan comprehensively and effectively. Through the measurement of spend in the newly defined ‘adaptation economy’, we analyse current climate change adaptation efforts in ten megacities. In all cases, the adaptation economy remains a small part of the overall economy, representing a maximum of 0.33% of a city’s gross domestic product (here referred to as GDPc). Differences in total spend are significant between cities in developed, emerging and developing countries, ranging from £15 million to £1,600 million. Comparing key subsectors, we demonstrate the differences in adaptation profiles. Developing cities have higher proportional spend on health and agriculture, whereas developed cities have higher spend on energy and water. Spend per capita and percentage of GDPc comparisons more clearly show disparities between cities. Developing country cities spend half the proportion of GDPc and significantly less per capita, suggesting that adaptation spend is driven by wealth rather than the number of vulnerable people. This indicates that current adaptation activities are insufficient in major population centres in developing and emerging economies

A practical solution: the Anthropocene is a geological event, not a formal epoch

The Anthropocene has yet to be defined in a way that is functional both to the international geological community and to the broader fields of environmental and social sciences. Formally defining the Anthropocene as a chronostratigraphical series and geochronological epoch with a precise global start date would drastically reduce the Anthropocene’s utility across disciplines. Instead, we propose the Anthropocene be defined as a geological event, thereby facilitating a robust geological definition linked with a scholarly framework more useful to and congruent with the many disciplines engaging with human-environment interactions. Unlike formal epochal definitions, geological events can recognize the spatial and temporal heterogeneity and diverse social and environmental processes that interact to produce anthropogenic global environmental changes. Consequently, an Anthropocene Event would incorporate a far broader range of transformative human cultural practices and would be more readily applicable across academic fields than an Anthropocene Epoch, while still enabling a robust stratigraphic characterization

Triggering mechanism and tsunamogenic potential of the Cape Fear Slide complex, U.S. Atlantic margin

Author Posting. © American Geophysical Union, 2007. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 8 (2007): Q12008, doi:10.1029/2007GC001722.Analysis of new multibeam bathymetry data and seismic Chirp data acquired over the Cape Fear Slide complex on the U.S. Atlantic margin suggests that at least 5 major submarine slides have likely occurred there within the past 30,000 years, indicating that repetitive, large-scale mass wasting and associated tsunamis may be more common in this area than previously believed. Gas hydrate deposits and associated free gas as well as salt tectonics have been implicated in previous studies as triggers for the major Cape Fear slide events. Analysis of the interaction of the gas hydrate phase boundary and the various generations of slides indicates that only the most landward slide likely intersected the phase boundary and inferred high gas pressures below it. For much of the region, we believe that displacement along a newly recognized normal fault led to upward migration of salt, oversteepening of slopes, and repeated slope failures. Using new constraints on slide morphology, we develop the first tsunami model for the Cape Fear Slide complex. Our results indicate that if the most seaward Cape Fear slide event occurred today, it could produce waves in excess of 2 m at the present-day 100 m bathymetric contour.Acquisition of new data was funded by NOAA Ocean Exploration grant NA03OAR4600100 to C.R., and we thank the National Science Foundation for contributing to transit costs for the ship

The Anthropocene is best understood as an ongoing, intensifying, diachronous event

Current debate on the status and character of the Anthropocene is focussed on whether this interval of geological time should be designated as a formal unit of epoch/series rank in the International Chronostratigraphic Chart/Geological Time Scale, or whether it is more appropriate for it to be considered as an informal ‘event’ comparable in significance with other major transformative events in deeper geological time. The case for formalizing the Anthropocene as a chronostratigraphical unit with a base at approximately 1950 CE is being developed by the Anthropocene Working Group of the Subcommission on Quaternary Stratigraphy. Here we outline the alternative position and explain why the time‐transgressive nature of human impact on global environmental systems that is reflected in the recent stratigraphical record means that the Anthropocene is better seen not as a series/epoch with a fixed lower boundary, but rather as an unfolding, transforming and intensifying geological event

Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

BACKGROUND: Circular chromosome conformation capture (4C) has provided important insights into three dimensional (3D) genome organization and its critical impact on the regulation of gene expression. We developed a new quantitative framework based on polymer physics for the analysis of paired-end sequencing 4C (PE-4Cseq) data. We applied this strategy to the study of chromatin interaction changes upon a 4.3 Mb DNA deletion in mouse region 4E2. RESULTS: A significant number of differentially interacting regions (DIRs) and chromatin compaction changes were detected in the deletion chromosome compared to a wild-type (WT) control. Selected DIRs were validated by 3D DNA FISH experiments, demonstrating the robustness of our pipeline. Interestingly, significant overlaps of DIRs with CTCF/Smc1 binding sites and differentially expressed genes were observed. CONCLUSIONS: Altogether, our PE-4Cseq analysis pipeline provides a comprehensive characterization of DNA deletion effects on chromatin structure and function

A Systematic Literature Review of Emotion Regulation Measurement in Individuals With Autism Spectrum Disorder

DOI: 10.1002/aur.1426Emotion regulation (ER) difficulties are a potential common factor underlying the presentation of multiple emotional and behavioral problems in individuals with Autism Spectrum Disorder (ASD). To provide an overview of how ER has been studied in individuals with ASD, we conducted a systematic review of the past 20 years of ER research in the ASD population, using established keywords from the most comprehensive ER literature review of the typically developing population to date. Out of an initial sampling of 305 studies, 32 were eligible for review. We examined the types of methods (self-report, informant report, naturalistic observation/ behavior coding, physiological, and open-ended) and the ER constructs based on Gross and Thompson’s modal model (situation selection, situation modification, attention deployment, cognitive change, and response modulation). Studies most often assessed ER using one type of method and from a unidimensional perspective. Across the 32 studies, we documented the types of measures used and found that 38% of studies used self-report, 44% included an informant report measure, 31% included at least one naturalistic observation/behavior coding measure, 13% included at least one physiological measure, and 13% included at least one open-ended measure. Only 25% of studies used more than one method of measurement. The findings of the current review provide the field with an in-depth analysis of various ER measures and how each measure taps into an ER framework. Future research can use this model to examine ER in a multicomponent way and through multiple methods.Spectrum of Hope Autism Foundation, Canadian Institutes of Health Research, NeuroDevNet, Sinneave Family Foundation, CASDA, Autism Speaks Canada, Health Canad