Concordance of freshwater and terrestrial biodiversity

Efforts to set global conservation priorities have largely ignored freshwater diversity, thereby excluding some of the world\u27s most speciose, threatened, and valuable taxa. Using a new global map of freshwater ecoregions and distribution data for about 13,300 fish species, we identify regions of exceptional freshwater biodiversity and assess their overlap with regions of equivalent terrestrial importance. Overlap is greatest in the tropics and is higher than expected by chance. These high-congruence areas offer opportunities for integrated conservation efforts, which could be of particular value when economic conditions force conservation organizations to narrow their focus. Areas of low overlap-missed by current terrestrially based priority schemes-merit independent freshwater conservation efforts. These results provide new information to conservation investors setting priorities at global or regional scales and argue for a potential reallocation of future resources to achieve representation of overlooked biomes. © 2010 Wiley Periodicals, Inc

The role of multiple marks in epigenetic silencing and the emergence of a stable bivalent chromatin state

We introduce and analyze a minimal model of epigenetic silencing in budding yeast, built upon known biomolecular interactions in the system. Doing so, we identify the epigenetic marks essential for the bistability of epigenetic states. The model explicitly incorporates two key chromatin marks, namely H4K16 acetylation and H3K79 methylation, and explores whether the presence of multiple marks lead to a qualitatively different systems behavior. We find that having both modifications is important for the robustness of epigenetic silencing. Besides the silenced and transcriptionally active fate of chromatin, our model leads to a novel state with bivalent (i.e., both active and silencing) marks under certain perturbations (knock-out mutations, inhibition or enhancement of enzymatic activity). The bivalent state appears under several perturbations and is shown to result in patchy silencing. We also show that the titration effect, owing to a limited supply of silencing proteins, can result in counter-intuitive responses. The design principles of the silencing system is systematically investigated and disparate experimental observations are assessed within a single theoretical framework. Specifically, we discuss the behavior of Sir protein recruitment, spreading and stability of silenced regions in commonly-studied mutants (e.g., sas2, dot1) illuminating the controversial role of Dot1 in the systems biology of yeast silencing.Comment: Supplementary Material, 14 page

Partial joint processing with efficient backhauling using particle swarm optimization

In cellular communication systems with frequency reuse factor of one, user terminals (UT) at the cell-edge are prone to intercell interference. Joint processing is one of the coordinated multipoint transmission techniques proposed to mitigate this interference. In the case of centralized joint processing, the channel state information fed back by the users need to be available at the central coordination node for precoding. The precoding weights (with the user data) need to be available at the corresponding base stations to serve the UTs. These increase the backhaul traffic. In this article, partial joint processing (PJP) is considered as a general framework that allows reducing the amount of required feedback. However, it is difficult to achieve a corresponding reduction on the backhaul related to the precoding weights, when a linear zero forcing beamforming technique is used. In this work, particle swarm optimization is proposed as a tool to design the precoding weights under feedback and backhaul constraints related to PJP. The precoder obtained with the objective of weighted interference minimization allows some multiuser interference in the system, and it is shown to improve the sum rate by 66% compared to a conventional zero forcing approach, for those users experiencing low signal to interference plus noise ratio

Transcriptional Repressive H3K9 and H3K27 Methylations Contribute to DNMT1-Mediated DNA Methylation Recovery

DNA methylation and histone modifications are two major epigenetic events regulating gene expression and chromatin structure, and their alterations are linked to human carcinogenesis. DNA methylation plays an important role in tumor suppressor gene inactivation, and can be revised by DNA methylation inhibitors. The reversible nature of DNA methylation forms the basis of epigenetic cancer therapy. However, it has been reported that DNA re-methylation and gene re-silencing could occur after removal of demethylation treatment and this may significantly hamper the therapeutic value of DNA methylation inhibitors. In this study we have provided detailed evidence demonstrating that mammalian cells possess a bona fide DNA methylation recovery system. We have also shown that DNA methylation recovery was mediated by the major human DNA methyltransferase, DNMT1. In addition, we found that H3K9-tri-methylation and H3K27-tri-methylation were closely associated with this DNA methylation recovery. These persistent transcriptional repressive histone modifications may have a crucial role in regulating DNMT1-mediated DNA methylation recovery. Our findings may have important implications towards a better understanding of epigenetic regulation and future development of epigenetic therapeutic intervention

Freshwater ecoregions of the world: A new map of biogeographic units for freshwater biodiversity conservation

We present a new map depicting the first global biogeographic regionalization of Earth's freshwater systems. This map of freshwater ecoregions is based on the distributions and compositions of freshwater fish species and incorporates major ecological and evolutionary patterns. Covering virtually all freshwater habitats on Earth, this ecoregion map, together with associated species data, is a useful tool for underpinning global and regional conservation planning efforts (particularly to identify outstanding and imperiled freshwater systems); for serving as a logical framework for large-scale conservation strategies; and for providing a global-scale knowledge base for increasing freshwater biogeographic literacy. Preliminary data for fish species compiled by ecoregion reveal some previously unrecognized areas of high biodiversity, highlighting the benefit of looking at the world's freshwaters through a new framework.La lista completa de autores que integran el documento puede consultarse en el archivo.Facultad de Ciencias Naturales y Muse

Freshwater ecoregions of the world: A new map of biogeographic units for freshwater biodiversity conservation

We present a new map depicting the first global biogeographic regionalization of Earth's freshwater systems. This map of freshwater ecoregions is based on the distributions and compositions of freshwater fish species and incorporates major ecological and evolutionary patterns. Covering virtually all freshwater habitats on Earth, this ecoregion map, together with associated species data, is a useful tool for underpinning global and regional conservation planning efforts (particularly to identify outstanding and imperiled freshwater systems); for serving as a logical framework for large-scale conservation strategies; and for providing a global-scale knowledge base for increasing freshwater biogeographic literacy. Preliminary data for fish species compiled by ecoregion reveal some previously unrecognized areas of high biodiversity, highlighting the benefit of looking at the world's freshwaters through a new framework.La lista completa de autores que integran el documento puede consultarse en el archivo.Facultad de Ciencias Naturales y Muse

Global, regional, and national comparative risk assessment of 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks, 1990-2015: a systematic analysis for the Global Burden of Disease Study 2015

SummaryBackground The Global Burden of Diseases, Injuries, and Risk Factors Study 2015 provides an up-to-date synthesis of the evidence for risk factor exposure and the attributable burden of disease. By providing national and subnational assessments spanning the past 25 years, this study can inform debates on the importance of addressing risks in context. Methods We used the comparative risk assessment framework developed for previous iterations of the Global Burden of Disease Study to estimate attributable deaths, disability-adjusted life-years (DALYs), and trends in exposure by age group, sex, year, and geography for 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks from 1990 to 2015. This study included 388 risk-outcome pairs that met World Cancer Research Fund-defined criteria for convincing or probable evidence. We extracted relative risk and exposure estimates from randomised controlled trials, cohorts, pooled cohorts, household surveys, census data, satellite data, and other sources. We used statistical models to pool data, adjust for bias, and incorporate covariates. We developed a metric that allows comparisons of exposure across risk factors—the summary exposure value. Using the counterfactual scenario of theoretical minimum risk level, we estimated the portion of deaths and DALYs that could be attributed to a given risk. We decomposed trends in attributable burden into contributions from population growth, population age structure, risk exposure, and risk-deleted cause-specific DALY rates. We characterised risk exposure in relation to a Socio-demographic Index (SDI). Findings Between 1990 and 2015, global exposure to unsafe sanitation, household air pollution, childhood underweight, childhood stunting, and smoking each decreased by more than 25%. Global exposure for several occupational risks, high body-mass index (BMI), and drug use increased by more than 25% over the same period. All risks jointly evaluated in 2015 accounted for 57·8% (95% CI 56·6–58·8) of global deaths and 41·2% (39·8–42·8) of DALYs. In 2015, the ten largest contributors to global DALYs among Level 3 risks were high systolic blood pressure (211·8 million [192·7 million to 231·1 million] global DALYs), smoking (148·6 million [134·2 million to 163·1 million]), high fasting plasma glucose (143·1 million [125·1 million to 163·5 million]), high BMI (120·1 million [83·8 million to 158·4 million]), childhood undernutrition (113·3 million [103·9 million to 123·4 million]), ambient particulate matter (103·1 million [90·8 million to 115·1 million]), high total cholesterol (88·7 million [74·6 million to 105·7 million]), household air pollution (85·6 million [66·7 million to 106·1 million]), alcohol use (85·0 million [77·2 million to 93·0 million]), and diets high in sodium (83·0 million [49·3 million to 127·5 million]). From 1990 to 2015, attributable DALYs declined for micronutrient deficiencies, childhood undernutrition, unsafe sanitation and water, and household air pollution; reductions in risk-deleted DALY rates rather than reductions in exposure drove these declines. Rising exposure contributed to notable increases in attributable DALYs from high BMI, high fasting plasma glucose, occupational carcinogens, and drug use. Environmental risks and childhood undernutrition declined steadily with SDI; low physical activity, high BMI, and high fasting plasma glucose increased with SDI. In 119 countries, metabolic risks, such as high BMI and fasting plasma glucose, contributed the most attributable DALYs in 2015. Regionally, smoking still ranked among the leading five risk factors for attributable DALYs in 109 countries; childhood underweight and unsafe sex remained primary drivers of early death and disability in much of sub-Saharan Africa. Interpretation Declines in some key environmental risks have contributed to declines in critical infectious diseases. Some risks appear to be invariant to SDI. Increasing risks, including high BMI, high fasting plasma glucose, drug use, and some occupational exposures, contribute to rising burden from some conditions, but also provide opportunities for intervention. Some highly preventable risks, such as smoking, remain major causes of attributable DALYs, even as exposure is declining. Public policy makers need to pay attention to the risks that are increasingly major contributors to global burden. Funding Bill & Melinda Gates Foundation

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin