Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Multi-decadal improvements in the ecological quality of European rivers are not consistently reflected in biodiversity metrics

Humans impact terrestrial, marine and freshwater ecosystems, yet many broad-scale studies have found no systematic, negative biodiversity changes (for example, decreasing abundance or taxon richness). Here we show that mixed biodiversity responses may arise because community metrics show variable responses to anthropogenic impacts across broad spatial scales. We first quantified temporal trends in anthropogenic impacts for 1,365 riverine invertebrate communities from 23 European countries, based on similarity to least-impacted reference communities. Reference comparisons provide necessary, but often missing, baselines for evaluating whether communities are negatively impacted or have improved (less or more similar, respectively). We then determined whether changing impacts were consistently reflected in metrics of community abundance, taxon richness, evenness and composition. Invertebrate communities improved, that is, became more similar to reference conditions, from 1992 until the 2010s, after which improvements plateaued. Improvements were generally reflected by higher taxon richness, providing evidence that certain community metrics can broadly indicate anthropogenic impacts. However, richness responses were highly variable among sites, and we found no consistent responses in community abundance, evenness or composition. These findings suggest that, without sufficient data and careful metric selection, many common community metrics cannot reliably reflect anthropogenic impacts, helping explain the prevalence of mixed biodiversity trends.We thank J. England for assistance with calculating ecological quality and the biomonitoring indices in the UK. Funding for authors, data collection and processing was provided by the European Union Horizon 2020 project eLTER PLUS (grant number 871128). F.A. was supported by the Swiss National Science Foundation (grant numbers 310030_197410 and 31003A_173074) and the University of Zurich Research Priority Program Global Change and Biodiversity. J.B. and M.A.-C. were funded by the European Commission, under the L‘Instrument Financier pour l’Environnement (LIFE) Nature and Biodiversity program, as part of the project LIFE-DIVAQUA (LIFE18 NAT/ES/000121) and also by the project ‘WATERLANDS’ (PID2019-107085RB-I00) funded by the Ministerio de Ciencia, Innovación y Universidades (MCIN) and Agencia Estatal de Investigación (AEI; MCIN/AEI/10.13039/501100011033/ and by the European Regional Development Fund (ERDF) ‘A way of making Europe’. N.J.B. and V.P. were supported by the Lithuanian Environmental Protection Agency (https://aaa.lrv.lt/) who collected the data and were funded by the Lithuanian Research Council (project number S-PD-22-72). J.H. was supported by the Academy of Finland (grant number 331957). S.C.J. acknowledges funding by the Leibniz Competition project Freshwater Megafauna Futures and the German Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung or BMBF; 033W034A). A.L. acknowledges funding by the Spanish Ministry of Science and Innovation (PID2020-115830GB-100). P.P., M.P. and M.S. were supported by the Czech Science Foundation (GA23-05268S and P505-20-17305S) and thank the Czech Hydrometeorological Institute and the state enterprises Povodí for the data used to calculate ecological quality metrics from the Czech surface water monitoring program. H.T. was supported by the Estonian Research Council (number PRG1266) and by the Estonian national program ‘Humanitarian and natural science collections’. M.J.F. acknowledges the support of Fundação para a Ciência e Tecnologia, Portugal, through the projects UIDB/04292/2020 and UIDP/04292/2020 granted to the Marine and Environmental Sciences Centre, LA/P/0069/2020 granted to the Associate Laboratory Aquatic Research Network (ARNET), and a Call Estímulo ao Emprego Científico (CEEC) contract.Peer reviewe

The recovery of European freshwater biodiversity has come to a halt

Owing to a long history of anthropogenic pressures, freshwater ecosystems are among the most vulnerable to biodiversity loss1. Mitigation measures, including wastewater treatment and hydromorphological restoration, have aimed to improve environmental quality and foster the recovery of freshwater biodiversity2. Here, using 1,816 time series of freshwater invertebrate communities collected across 22 European countries between 1968 and 2020, we quantified temporal trends in taxonomic and functional diversity and their responses to environmental pressures and gradients. We observed overall increases in taxon richness (0.73% per year), functional richness (2.4% per year) and abundance (1.17% per year). However, these increases primarily occurred before the 2010s, and have since plateaued. Freshwater communities downstream of dams, urban areas and cropland were less likely to experience recovery. Communities at sites with faster rates of warming had fewer gains in taxon richness, functional richness and abundance. Although biodiversity gains in the 1990s and 2000s probably reflect the effectiveness of water-quality improvements and restoration projects, the decelerating trajectory in the 2010s suggests that the current measures offer diminishing returns. Given new and persistent pressures on freshwater ecosystems, including emerging pollutants, climate change and the spread of invasive species, we call for additional mitigation to revive the recovery of freshwater biodiversity.N. Kaffenberger helped with initial data compilation. Funding for authors and data collection and processing was provided by the EU Horizon 2020 project eLTER PLUS (grant agreement no. 871128); the German Federal Ministry of Education and Research (BMBF; 033W034A); the German Research Foundation (DFG FZT 118, 202548816); Czech Republic project no. P505-20-17305S; the Leibniz Competition (J45/2018, P74/2018); the Spanish Ministerio de Economía, Industria y Competitividad—Agencia Estatal de Investigación and the European Regional Development Fund (MECODISPER project CTM 2017-89295-P); Ramón y Cajal contracts and the project funded by the Spanish Ministry of Science and Innovation (RYC2019-027446-I, RYC2020-029829-I, PID2020-115830GB-100); the Danish Environment Agency; the Norwegian Environment Agency; SOMINCOR—Lundin mining & FCT—Fundação para a Ciência e Tecnologia, Portugal; the Swedish University of Agricultural Sciences; the Swiss National Science Foundation (grant PP00P3_179089); the EU LIFE programme (DIVAQUA project, LIFE18 NAT/ES/000121); the UK Natural Environment Research Council (GLiTRS project NE/V006886/1 and NE/R016429/1 as part of the UK-SCAPE programme); the Autonomous Province of Bolzano (Italy); and the Estonian Research Council (grant no. PRG1266), Estonian National Program ‘Humanitarian and natural science collections’. The Environment Agency of England, the Scottish Environmental Protection Agency and Natural Resources Wales provided publicly available data. We acknowledge the members of the Flanders Environment Agency for providing data. This article is a contribution of the Alliance for Freshwater Life (www.allianceforfreshwaterlife.org).Peer reviewe

Effect of Corneal Transplantation on Patient-Reported Outcomes and Potential Predictors:A Systematic Review

Purpose: To investigate the effect and potential predictors of corneal transplantation on patient-reported outcomes such as quality of life, visual functioning, and mental health by systematically reviewing the literature. Methods: Studies with 1 preoperative and at least 1 postoperative measurement were searched for in relevant literature databases. Methodological quality was assessed using the Quality Assessment Tool for Quantitative Studies, and effect sizes were calculated. Results: Of 1445 unique publications, 14 studies, including 15 study designs, were described in 16 publications. Four randomized controlled trials, 1 controlled clinical trial, 1 cohort study, and 1 before-after study (BA) were of good quality; 6 BAs were of moderate quality; and 2 BAs were of weak quality. Patients generally improved 12 months after transplantation on health-related quality of life (effect size between 0.08 and -3.06), vision-related quality of life (-0.67 and -6.65), visual functioning (-0.55 and -0.63), and subjective visual symptoms (-0.31 and -0.86). Patient satisfaction was high (-0.95). Patients improved on depression (-0.31) but remained stable on anxiety (-0.05) 4 months after transplantation. Predictors of positive outcomes were lower preoperative visual acuity and visual functioning, better postoperative visual factors, younger age, and male sex. Conclusions: Corneal transplantation showed overall beneficial effects on patient-reported outcomes. Knowledge of these effects and predictors might result in better treatment, more patient-centered care, and more realistic expectations on the part of patients and ophthalmologists. Future studies should focus on not only health- and vision-related quality of life but also mental health and labor participation using longitudinal study designs

Sex on demand: geosocial networking phone apps and risk of sexually transmitted infections among a cross-sectional sample of men who have sex with men in Los Angeles county

BACKGROUND: Geosocial networking applications (GSN apps) used to meet sexual partners have become increasingly popular with men who have sex with men (MSM) since 2009. The current study aimed to determine if self-identified HIV negative, MSM clinic attendees who used GSN apps have an increased incidence of sexually transmitted infections (STIs) compared to self-identified HIV negative, MSM attendees who met sexual partners via in-person venues such as bars or clubs or through MSM-specific hook-up websites. METHODS: Data were collected between August 2011 and January 2013 on all self-identified HIV-negative, MSM clients visiting the L.A. Gay & Lesbian Center for STI screening. A total of 7,184 individuals tested for STIs and self-reported behaviours on drug use and social networking methods to meet sexual partners. Multivariate logistic regression models were used to analyze the results. RESULTS: Individuals who used GSN apps to meet sexual partners had greater odds of testing positive for gonorrhoea (OR: 1.25; 95% CI: 1.06–1.48) and for chlamydia (OR: 1.37; 95% CI: 1.13–1.65) compared to individuals who met partners through in-person methods only. There were no significant differences in syphilis and HIV incidence between those who met partners via in-person venues only, on the internet or through GSN apps. CONCLUSIONS: The present study concludes that sexual health clinic MSM attendees who are meeting on GSN apps are at greater risk for gonorrhoea and chlamydia than MSM attendees who meet in-person or on the internet. Future interventions should explore the use of these novel technologies for testing promotion, prevention and education