Resource profile and user guide of the Polygenic Index Repository

Polygenic indexes (PGIs) are DNA-based predictors. Their value for research in many scientific disciplines is growing rapidly. As a resource for researchers, we used a consistent methodology to construct PGIs for 47 phenotypes in 11 datasets. To maximize the PGIs’ prediction accuracies, we constructed them using genome-wide association studies — some not previously published — from multiple data sources, including 23andMe and UK Biobank. We present a theoretical framework to help interpret analyses involving PGIs. A key insight is that a PGI can be understood as an unbiased but noisy measure of a latent variable we call the ‘additive SNP factor’. Regressions in which the true regressor is this factor but the PGI is used as its proxy therefore suffer from errors-in-variables bias. We derive an estimator that corrects for the bias, illustrate the correction, and make a Python tool for implementing it publicly available

Fire Emissions and Carbon Uptake in Severely Burned Lenga Beech (Nothofagus pumilio) Forests of Patagonia, Argentina

Los incendios forestales son reconocidos como fuentes de emisión de CO2 y otros gases de efecto invernadero (GHG) que, alterando la dinámica del intercambio entre el carbono (C) terrestre y el atmosférico, influencian el clima global. En la región central de la Patagonia Andina Argentina, incendios de características severas han afectado los bosques de lenga (Nothofagus pumilio Poepp. & Endl. Krasser), incrementando de esa manera las emisiones de CO2 a la atmósfera y alterando asimismo sus patrones sucesionales. En este estudio, determinamos las emisiones y el secuestro de C en tres rodales, quemados en 1976 (Lago Guacho), 1983 (La Torta), y 2008 (la Colisión). La estructura forestal, y los compartimientos de biomasa aérea y broza fueron cuantificados en cada rodal quemado y en sus adyacentes sin quemar. El stock de C y de otros GHG (CO2 , CO, CH4 , NO2 , NOx y Ce) emitidos por cada incendio, el CO2 capturado y el C anual incorporado a la biomasa fueron determinados en base a las guías propuestas por el Panel Internacional para el Cambio Climático. El carbono total (biomasa aérea más radical) antes de los incendios fue de 301,8 Mg C ha-1 para La Colisión, 258,13 Mg C ha-1 para La Torta, y 270,7 Mg C ha-1 para Lago Guacho, mientras que las pérdidas de C debido a los incendios fueron de 104,6 Mg C ha-1, 90,7 Mg C ha-1, and 94,7 Mg C ha-1 para cada uno de los sitios, respectivamente. Diferencias en la estructura forestal y en la biomasa de cada sitio previo a los incendios explican los valores de emisión de CO2 y otros GHG observados después de éstos. Al presente, el balance de C es negativo en los tres sitios. Sin ninguna acción de restauración activa y usando las tasas actuales de crecimiento para cada sitio, el tiempo estimado de recuperación del C perdido es de 105,5 años para La Colisión, 94,2 años para La Torta, y 150,2 años para Lago Guacho. Mediante el uso de tasas de captura de C variables (que decrecen a medida que la sucesión avanza), el tiempo de recuperación sería de 182 años para La Colisión, 154 años para La Torta, y 162 para Lago Guacho. El ambiente post-incendio y las condiciones de cada sitio parecen tener una mayor influencia en la recuperación de la vegetación que los efectos primarios del fuego. Tareas de restauración activas aparecen como necesarias para incrementar la tasa de recuperación del C post-fuego y ayudar a re-establecer el paisaje original en bosques de lenga.Forest wildfires are recognized as sources of CO2 and other greenhouse gases (GHG) that, altering the dynamics between terrestrial and atmospheric carbon (C) exchange, influence global climate. In central Andean Patagonia, Argentina, severe wildfires affect temperate lenga beech (Nothofagus pumilio Poepp. & Endl. Krasser) forests, thereby increasing atmospheric CO2 emissions and changing natural succession paths. In this study, we determined fire emissions and C uptake in three lenga beech forests stands burned in 1976 (Lago Guacho site), 1983 (La Torta site), and 2008 (La Colisión site). Forest structure and aboveground biomass and litter compartments in burned and adjacent unburned stands were quantified for each fire. Carbon stocks and GHG (CO2 , CO, CH4 , NO2 , NOx and Ce) released by the fires, CO2 removals, and mean annual C uptake were determined by following the International Panel of Climate Change guidelines. Total (aboveground plus root) C stock before fires was 301.8 Mg C ha-1 for La Colisión, 258.13 Mg C ha-1 for La Torta, and 270.7 Mg C ha-1 for Lago Guacho, while C losses due to the fires were 104.6 Mg C ha-1, 90.7 Mg C ha-1, and 94.7 Mg C ha-1 for the three sites, respectively. Differences in pre-fire forest structures and biomass explained the values observed in CO2 and other GHG emissions after the fires. Currently, the C balance is negative for the three sites. Without any active restoration and using actual growth rates for each site, the estimated C recovery time is 105.5 yr for La Colisión, 94.2 yr for La Torta, and 150.2 yr for Lago Guacho. By using variable rates of C uptake (which decrease as early succession proceeds), this recovery time will take 182 yr for La Colisión, 154 for La Torta, and 162 yr for Lago Guacho. Post-fire environmental and site conditions appeared to have a greater influence in forest recovery than primary fire effects. Active restoration activities may be necessary to increase C recovery rates and help to re-establish former lenga beech forest landscapes.Fil: Bertolin, María Lila. Centro de Investigación y Extensión Forestal Andino Patagónico; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Urretavizcaya, María Florencia. Centro de Investigación y Extensión Forestal Andino Patagónico; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Defossé, Guillermo Emilio. Centro de Investigación y Extensión Forestal Andino Patagónico; Argentina. Universidad Nacional de la Patagonia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Transcription reinitiation by recycling RNA polymerase that diffuses on DNA after releasing terminated RNA

Despite extensive studies on transcription mechanisms, it is unknown how termination complexes are disassembled, especially in what order the essential components dissociate. Our single-molecule fluorescence study unveils that RNA transcript release precedes RNA polymerase (RNAP) dissociation from the DNA template much more often than their concurrent dissociations in intrinsic termination of bacterial transcription. As termination is defined by the release of product RNA from the transcription complex, the subsequent retention of RNAP on DNA constitutes a previously unidentified stage, termed here as recycling. During the recycling stage, post-terminational RNAPs one-dimensionally diffuse on DNA in downward and upward directions, and can initiate transcription again at the original and nearby promoters in the case of retaining a sigma factor. The efficiency of this event, termed here as reinitiation, increases with supplement of a sigma factor. In summary, after releasing RNA product at intrinsic termination, recycling RNAP diffuses on the DNA template for reinitiation most of the time. Bacterial transcription is terminated when RNA polymerases encounter terminator sequences. Using a single-molecule fluorescence assay, here the authors show that the release of transcript RNA precedes RNA polymerase dissociation and that the remaining RNA polymerase can reinitiate at nearby promoters