An explicit GIS-based river basin framework for aquatic ecosystem conservation in the Amazon

Despite large-scale infrastructure development, deforestation, mining and petroleum exploration in the Amazon Basin, relatively little attention has been paid to the management scale required for the protection of wetlands, fisheries and other aspects of aquatic ecosystems. This is due, in part, to the enormous size, multinational composition and interconnected nature of the Amazon River system, as well as to the absence of an adequate spatial model for integrating data across the entire Amazon Basin. In this data article we present a spatially uniform multi-scale GIS framework that was developed especially for the analysis, management and monitoring of various aspects of aquatic systems in the Amazon Basin. The Amazon GIS-Based River Basin Framework is accessible as an ESRI geodatabase at doi:10.5063/F1BG2KX8. © Author(s) 2016

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Water temperature differences in interfluvial palm swamp habitats of Paracheirodon axelrodi and P. simulans (Osteichthyes: Characidae) in the middle Rio Negro, Brazil

The cardinal (Paracheirodon axelrodi) and green neon tetras (P. simulans) are ornamental fish species which occur separately in two different types of palm swamp habitat in the middle Rio Negro, Amazonas State, Brazil. These palm swamp habitats are part of extensive interfluvial regions which flood as a function of seasonal precipitation and remain flooded in some regions even during dry periods, due to a high water table and waterlogged, hydromorphic soils. Hydrostatic sensors installed in P. axelrodi and P. simulans habitats recorded daily changes in water level and water temperature every 15 minutes during a 5-month period between September 2009 and January 2010. Significant differences in water temperature were encountered between the two habitats, especially in regards to maximum daily water temperatures. In P. simulans habitats water temperatures ranged from a low of 24.6 to a high of 35.2 °C, while in P. axelrodi habitats temperatures varied between 25.1 and 29.9 °C. The high values recorded at P. simulans sites may indicate a possible thermal tolerance to extreme temperatures, which could partially explain the segregation of the two species in distinctive interfluvial habitats. © 2011 by Verlag Dr. Friedrich Pfeil

The importance of forest cover for fish richness and abundance on the Amazon floodplain

Flooded forest is one of the most important fish habitats in Neotropical rivers, and one that is increasingly subjected to negative impacts from logging, agriculture, and other human activities. The purpose of our study was to test quantitatively whether fish richness and abundance in Amazonian floodplain lakes are associated with the area of flooded forest. We sampled fish and several other variables in 35 Amazonian floodplain lakes during the high-water season. Our results highlighted that fish richness and abundance were directly related to flooded forest, inversely related to distance from the river, and influenced by dissolved oxygen concentration &lt;1 mg l−1. The same result applied to fish richness and abundance landed by fisheries. Other variables such as depth and area of open water habitat were also related but the results were less consistent and apparently reliant on sampling methodology. Our results suggest that conservation of the flooded forest is critical for the maintenance of fish assemblages in the Amazon, and that removal of flooded forest will reduce fish richness, fish abundance, and fisheries yield. © 2014, Springer International Publishing Switzerland

Regionalization of methane emissions in the Amazon Basin with microwave remote sensing

Wetlands of the Amazon River basin are globally significant sources of atmospheric methane. Satellite remote sensing (passive and active microwave) of the temporally varying extent of inundation and vegetation was combined with field measurements to calculate regional rates of methane emission for Amazonian wetlands. Monthly inundation areas for the fringing floodplains of the mainstem Solimões/Amazon River were derived from analysis of the 37 GHz polarization difference observed by the Scanning Multichannel Microwave Radiometer from 1979 to 1987. L-band synthetic aperture radar data (Japanese Earth Resources Satellite-1) were used to determine inundation and wetland vegetation for the Amazon basin (&lt;500 m elevation) at high (May-June 1996) and low water (October 1995). An extensive set of measurements of methane emission is available from the literature for the fringing floodplains of the central Amazon, segregated into open water, flooded forest and floating macrophyte habitats. Uncertainties in the regional emission rates were determined by Monte Carlo error analyses that combined error estimates for the measurements of emission and for calculations of inundation and habitat areas. The mainstem Solimões/Amazon floodplain (54-70°W) emitted methane at a mean annual rate of 1.3 Tg C yr-1, with a standard deviation (SD) of the mean of 0.3 Tg C yr-1; 67% of this range in uncertainty is owed to the range in rates of methane emission and 33% is owed to uncertainty in the areal estimates of inundation and vegetative cover. Methane emission from a 1.77 million square kilometers area in the central basin had a mean of 6.8 Tg C yr-1 with a SD of 1.3 Tg C yr-1. If extrapolated to the whole basin below the 500 m contour, approximately 22 Tg C yr-1 is emitted; this mean flux has a greenhouse warming potential of about 0.5 Pg C as CO2. Improvement of these regional estimates will require many more field measurements of methane emission, further examination of remotely sensed data for types of wetlands not represented in the central basin, and process-based models of methane production and emission. © 2004 Blackwell Publishing Ltd

Identificação de buritizais através do sensor orbital ALOS PALSAR e estimativa de estoque do recurso

This study used the ALOS PALSAR sensor (bands L-HH and L-HV) to estimate the area of Mauritia palm stands within the savanna environment of the Araça Indigenous Area, in Roraima. A fuzzy classifier was trained with four land-cover classes observed in a high spatial resolution QuickBird image that covered parts of the PALSAR scene outside the Indigenous Area. For each pixel in the entire PALSAR scene, the classifier provided a probability for each cover type, expressed as four grey-scale images. Based on independent validation sites in the QuickBird image, all pixels with >80% probability for the class Mauritia were taken to be stands of pure Mauritia palm, giving a total area of 144 hectares within the Indigenous Area. Based on previous studies of Mauritia fruit production, we estimated 189 trees ha-1 and 7,4 ton ha-1 y-1, giving a total potential production from pure Mauritia stands in the Araçá indigenous lands of 1066 ton y-1. Utilizing merchant study analyses in the states of Roraima and Pará, we estimated that revenue of wine (juice) and Mauritia oil production for the entire Araçá indigenous lands could be 266.400 liters of wine per year, which could be worth an estimated R$302.400. This same production could produce 47.520 liters of oil. This income potential could help preserve the Mauritia palm swamps in the indigenous communities of the savanna region.Pages: 8336-834

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that -80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAFPeer reviewe

Sex differences in oncogenic mutational processes

Funder: Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology); doi: https://doi.org/10.13039/501100002790Funder: Genome Canada (Génome Canada); doi: https://doi.org/10.13039/100008762Funder: Canada Foundation for Innovation (Fondation canadienne pour l'innovation); doi: https://doi.org/10.13039/501100000196Funder: Terry Fox Research Institute (Institut de Recherche Terry Fox); doi: https://doi.org/10.13039/501100004376Abstract: Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research

Sex differences in oncogenic mutational processes

Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Peer reviewe

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts