Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes.

Mutations in whole organisms are powerful ways of interrogating gene function in a realistic context. We describe a program, the Sanger Institute Mouse Genetics Project, that provides a step toward the aim of knocking out all genes and screening each line for a broad range of traits. We found that hitherto unpublished genes were as likely to reveal phenotypes as known genes, suggesting that novel genes represent a rich resource for investigating the molecular basis of disease. We found many unexpected phenotypes detected only because we screened for them, emphasizing the value of screening all mutants for a wide range of traits. Haploinsufficiency and pleiotropy were both surprisingly common. Forty-two percent of genes were essential for viability, and these were less likely to have a paralog and more likely to contribute to a protein complex than other genes. Phenotypic data and more than 900 mutants are openly available for further analysis. PAPERCLIP:

New land-use-change emissions indicate a declining CO2 airborne fraction.

About half of the anthropogenic CO2 emissions remain in the atmosphere and half are taken up by the land and ocean1. If the carbon uptake by land and ocean sinks becomes less efficient, for example, owing to warming oceans2 or thawing permafrost3, a larger fraction of anthropogenic emissions will remain in the atmosphere, accelerating climate change. Changes in the efficiency of the carbon sinks can be estimated indirectly by analysing trends in the airborne fraction, that is, the ratio between the atmospheric growth rate and anthropogenic emissions of CO2 (refs. 4-10). However, current studies yield conflicting results about trends in the airborne fraction, with emissions related to land use and land cover change (LULCC) contributing the largest source of uncertainty7,11,12. Here we construct a LULCC emissions dataset using visibility data in key deforestation zones. These visibility observations are a proxy for fire emissions13,14, which are - in turn - related to LULCC15,16. Although indirect, this provides a long-term consistent dataset of LULCC emissions, showing that tropical deforestation emissions increased substantially (0.16 Pg C decade-1) since the start of CO2 concentration measurements in 1958. So far, these emissions were thought to be relatively stable, leading to an increasing airborne fraction4,5. Our results, however, indicate that the CO2 airborne fraction has decreased by 0.014 ± 0.010 decade-1 since 1959. This suggests that the combined land-ocean sink has been able to grow at least as fast as anthropogenic emissions.

Mapping carbon accumulation potential from global natural forest regrowth.

To constrain global warming, we must strongly curtail greenhouse gas emissions and capture excess atmospheric carbon dioxide1,2. Regrowing natural forests is a prominent strategy for capturing additional carbon3, but accurate assessments of its potential are limited by uncertainty and variability in carbon accumulation rates2,3. To assess why and where rates differ, here we compile 13,112 georeferenced measurements of carbon accumulation. Climatic factors explain variation in rates better than land-use history, so we combine the field measurements with 66 environmental covariate layers to create a global, one-kilometre-resolution map of potential aboveground carbon accumulation rates for the first 30 years of natural forest regrowth. This map shows over 100-fold variation in rates across the globe, and indicates that default rates from the Intergovernmental Panel on Climate Change (IPCC)4,5 may underestimate aboveground carbon accumulation rates by 32 per cent on average and do not capture eight-fold variation within ecozones. Conversely, we conclude that maximum climate mitigation potential from natural forest regrowth is 11 per cent lower than previously reported3 owing to the use of overly high rates for the location of potential new forest. Although our data compilation includes more studies and sites than previous efforts, our results depend on data availability, which is concentrated in ten countries, and data quality, which varies across studies. However, the plots cover most of the environmental conditions across the areas for which we predicted carbon accumulation rates (except for northern Africa and northeast Asia). We therefore provide a robust and globally consistent tool for assessing natural forest regrowth as a climate mitigation strategy.

The global potential for increased storage of carbon on land.

Constraining the climate crisis requires urgent action to reduce anthropogenic emissions while simultaneously removing carbon dioxide from the atmosphere. Improved information about the maximum magnitude and spatial distribution of opportunities for additional land-based removals of CO2 is needed to guide on-the-ground decision-making about where to implement climate change mitigation strategies. Here, we present a globally consistent spatial dataset (approximately 500-m resolution) of current, potential, and unrealized potential carbon storage in woody plant biomass and soil organic matter. We also provide a framework for prioritizing actions related to the restoration, management, and maintenance of woody carbon stocks and associated soils. By comparing current to potential carbon storage, while excluding areas critical to food production and human habitation, we find 287 petagrams (PgC) of unrealized potential storage opportunity, of which 78% (224 PgC) is in biomass and 22% (63 PgC) is in soil. Improved management of existing forests may offer nearly three-fourths (206 PgC) of the total unrealized potential, with the majority (71%) concentrated in tropical ecosystems. However, climate change is a source of considerable uncertainty. While additional research is needed to understand the impact of natural disturbances and biophysical feedbacks, we project that the potential for additional carbon storage in woody biomass will increase (+17%) by 2050 despite projected decreases (−12%) in the tropics. Our results establish an absolute reference point and conceptual framework for national and jurisdictional prioritization of locations and actions to increase land-based carbon storage.

Modeling Manifest Huntington's Disease Prevalence Using Diagnosed Incidence and Survival Time.

INTRODUCTION: Understanding the epidemiology of Huntington's disease (HD) is key to assessing disease burden and the healthcare resources required to meet patients' needs. We aimed to develop and validate a model to estimate the diagnosed prevalence of manifest HD by the Shoulson-Fahn stage. METHODS: A literature review identified epidemiological data from Brazil, Canada, France, Germany, Italy, Spain, the UK, and the USA. Data on staging distribution at diagnosis, progression, and mortality were derived from Enroll-HD. Newly diagnosed patients with manifest HD were simulated by applying annual diagnosed incidence rates to the total population in each country, each year from 1950 onwards. The number of diagnosed prevalent patients from the previous year who remained in each stage was estimated in line with the probability of death or progression. Diagnosed prevalence in 2020 was estimated as the sum of simulated patients, from all the incident cohorts, still alive. RESULTS: The model estimates that in 2020, there were 66,787 individuals diagnosed with HD in the 8 included countries, of whom 62-63% were in Shoulson-Fahn stages 1 and 2 (with less severely limited functional capacity than those in stages 3-5). Diagnosed prevalence is estimated to be 8.2-9.0 per 100,000 in the USA, Canada, and the 5 included European countries and 3.5 per 100,000 in Brazil. CONCLUSION: The modeled estimates generally accord with the previously published data. This analysis contributes to better understanding of the epidemiology of HD and highlights areas of uncertainty.

A naturally occurring variant of the human prion protein completely prevents prion disease.

Mammalian prions, transmissible agents causing lethal neurodegenerative diseases, are composed of assemblies of misfolded cellular prion protein (PrP). A novel PrP variant, G127V, was under positive evolutionary selection during the epidemic of kuru--an acquired prion disease epidemic of the Fore population in Papua New Guinea--and appeared to provide strong protection against disease in the heterozygous state. Here we have investigated the protective role of this variant and its interaction with the common, worldwide M129V PrP polymorphism. V127 was seen exclusively on a M129 PRNP allele. We demonstrate that transgenic mice expressing both variant and wild-type human PrP are completely resistant to both kuru and classical Creutzfeldt-Jakob disease (CJD) prions (which are closely similar) but can be infected with variant CJD prions, a human prion strain resulting from exposure to bovine spongiform encephalopathy prions to which the Fore were not exposed. Notably, mice expressing only PrP V127 were completely resistant to all prion strains, demonstrating a different molecular mechanism to M129V, which provides its relative protection against classical CJD and kuru in the heterozygous state. Indeed, this single amino acid substitution (G→V) at a residue invariant in vertebrate evolution is as protective as deletion of the protein. Further study in transgenic mice expressing different ratios of variant and wild-type PrP indicates that not only is PrP V127 completely refractory to prion conversion but acts as a potent dose-dependent inhibitor of wild-type prion propagation.

Effect of remote ischaemic conditioning on clinical outcomes in patients with acute myocardial infarction (CONDI-2/ERIC-PPCI): a single-blind randomised controlled trial.

BACKGROUND: Remote ischaemic conditioning with transient ischaemia and reperfusion applied to the arm has been shown to reduce myocardial infarct size in patients with ST-elevation myocardial infarction (STEMI) undergoing primary percutaneous coronary intervention (PPCI). We investigated whether remote ischaemic conditioning could reduce the incidence of cardiac death and hospitalisation for heart failure at 12 months. METHODS: We did an international investigator-initiated, prospective, single-blind, randomised controlled trial (CONDI-2/ERIC-PPCI) at 33 centres across the UK, Denmark, Spain, and Serbia. Patients (age >18 years) with suspected STEMI and who were eligible for PPCI were randomly allocated (1:1, stratified by centre with a permuted block method) to receive standard treatment (including a sham simulated remote ischaemic conditioning intervention at UK sites only) or remote ischaemic conditioning treatment (intermittent ischaemia and reperfusion applied to the arm through four cycles of 5-min inflation and 5-min deflation of an automated cuff device) before PPCI. Investigators responsible for data collection and outcome assessment were masked to treatment allocation. The primary combined endpoint was cardiac death or hospitalisation for heart failure at 12 months in the intention-to-treat population. This trial is registered with ClinicalTrials.gov (NCT02342522) and is completed. FINDINGS: Between Nov 6, 2013, and March 31, 2018, 5401 patients were randomly allocated to either the control group (n=2701) or the remote ischaemic conditioning group (n=2700). After exclusion of patients upon hospital arrival or loss to follow-up, 2569 patients in the control group and 2546 in the intervention group were included in the intention-to-treat analysis. At 12 months post-PPCI, the Kaplan-Meier-estimated frequencies of cardiac death or hospitalisation for heart failure (the primary endpoint) were 220 (8·6%) patients in the control group and 239 (9·4%) in the remote ischaemic conditioning group (hazard ratio 1·10 [95% CI 0·91-1·32], p=0·32 for intervention versus control). No important unexpected adverse events or side effects of remote ischaemic conditioning were observed. INTERPRETATION: Remote ischaemic conditioning does not improve clinical outcomes (cardiac death or hospitalisation for heart failure) at 12 months in patients with STEMI undergoing PPCI. FUNDING: British Heart Foundation, University College London Hospitals/University College London Biomedical Research Centre, Danish Innovation Foundation, Novo Nordisk Foundation, TrygFonden.

Terrestrial fluxes of carbon in GCP carbon budgets.

The Global Carbon Project (GCP) has published global carbon budgets annually since 2007 (Canadell et al. [2007], Proc Natl Acad Sci USA, 104, 18866-18870; Raupach et al. [2007], Proc Natl Acad Sci USA, 104, 10288-10293). There are many scientists involved, but the terrestrial fluxes that appear in the budgets are not well understood by ecologists and biogeochemists outside of that community. The purpose of this paper is to make the terrestrial fluxes of carbon in those budgets more accessible to a broader community. The GCP budget is composed of annual perturbations from pre-industrial conditions, driven by addition of carbon to the system from combustion of fossil fuels and by transfers of carbon from land to the atmosphere as a result of land use. The budget includes a term for each of the major fluxes of carbon (fossil fuels, oceans, land) as well as the rate of carbon accumulation in the atmosphere. Land is represented by two terms: one resulting from direct anthropogenic effects (Land Use, Land-Use Change, and Forestry or land management) and one resulting from indirect anthropogenic (e.g., CO2 , climate change) and natural effects. Each of these two net terrestrial fluxes of carbon, in turn, is composed of opposing gross emissions and removals (e.g., deforestation and forest regrowth). Although the GCP budgets have focused on the two net terrestrial fluxes, they have paid little attention to the gross components, which are important for a number of reasons, including understanding the potential for land management to remove CO2 from the atmosphere and understanding the processes responsible for the sink for carbon on land. In contrast to the net fluxes of carbon, which are constrained by the global carbon budget, the gross fluxes are largely unconstrained, suggesting that there is more uncertainty than commonly believed about how terrestrial carbon emissions will respond to future fossil fuel emissions and a changing climate.

Natural climate solutions.

Better stewardship of land is needed to achieve the Paris Climate Agreement goal of holding warming to below 2 °C; however, confusion persists about the specific set of land stewardship options available and their mitigation potential. To address this, we identify and quantify "natural climate solutions" (NCS): 20 conservation, restoration, and improved land management actions that increase carbon storage and/or avoid greenhouse gas emissions across global forests, wetlands, grasslands, and agricultural lands. We find that the maximum potential of NCS-when constrained by food security, fiber security, and biodiversity conservation-is 23.8 petagrams of CO2 equivalent (PgCO2e) y-1 (95% CI 20.3-37.4). This is ≥30% higher than prior estimates, which did not include the full range of options and safeguards considered here. About half of this maximum (11.3 PgCO2e y-1) represents cost-effective climate mitigation, assuming the social cost of CO2 pollution is ≥100 USD MgCO2e-1 by 2030. Natural climate solutions can provide 37% of cost-effective CO2 mitigation needed through 2030 for a >66% chance of holding warming to below 2 °C. One-third of this cost-effective NCS mitigation can be delivered at or below 10 USD MgCO2-1 Most NCS actions-if effectively implemented-also offer water filtration, flood buffering, soil health, biodiversity habitat, and enhanced climate resilience. Work remains to better constrain uncertainty of NCS mitigation estimates. Nevertheless, existing knowledge reported here provides a robust basis for immediate global action to improve ecosystem stewardship as a major solution to climate change.

Negative emissions from stopping deforestation and forest degradation, globally.

Forest growth provides negative emissions of carbon that could help keep the earth's surface temperature from exceeding 2°C, but the global potential is uncertain. Here we use land-use information from the FAO and a bookkeeping model to calculate the potential negative emissions that would result from allowing secondary forests to recover. We find the current gross carbon sink in forests recovering from harvests and abandoned agriculture to be -4.4 PgC/year, globally. The sink represents the potential for negative emissions if positive emissions from deforestation and wood harvest were eliminated. However, the sink is largely offset by emissions from wood products built up over the last century. Accounting for these committed emissions, we estimate that stopping deforestation and allowing secondary forests to grow would yield cumulative negative emissions between 2016 and 2100 of about 120 PgC, globally. Extending the lifetimes of wood products could potentially remove another 10 PgC from the atmosphere, for a total of approximately 130 PgC, or about 13 years of fossil fuel use at today's rate. As an upper limit, the estimate is conservative. It is based largely on past and current practices. But if greater negative emissions are to be realized, they will require an expansion of forest area, greater efficiencies in converting harvested wood to long-lasting products and sources of energy, and novel approaches for sequestering carbon in soils. That is, they will require current management practices to change.

Tropical nighttime warming as a dominant driver of variability in the terrestrial carbon sink.

The terrestrial biosphere is currently a strong carbon (C) sink but may switch to a source in the 21st century as climate-driven losses exceed CO2-driven C gains, thereby accelerating global warming. Although it has long been recognized that tropical climate plays a critical role in regulating interannual climate variability, the causal link between changes in temperature and precipitation and terrestrial processes remains uncertain. Here, we combine atmospheric mass balance, remote sensing-modeled datasets of vegetation C uptake, and climate datasets to characterize the temporal variability of the terrestrial C sink and determine the dominant climate drivers of this variability. We show that the interannual variability of global land C sink has grown by 50-100% over the past 50 y. We further find that interannual land C sink variability is most strongly linked to tropical nighttime warming, likely through respiration. This apparent sensitivity of respiration to nighttime temperatures, which are projected to increase faster than global average temperatures, suggests that C stored in tropical forests may be vulnerable to future warming.

Fire and deforestation dynamics in Amazonia (1973-2014).

Consistent long-term estimates of fire emissions are important to understand the changing role of fire in the global carbon cycle and to assess the relative importance of humans and climate in shaping fire regimes. However, there is limited information on fire emissions from before the satellite era. We show that in the Amazon region, including the Arc of Deforestation and Bolivia, visibility observations derived from weather stations could explain 61% of the variability in satellite-based estimates of bottom-up fire emissions since 1997 and 42% of the variability in satellite-based estimates of total column carbon monoxide concentrations since 2001. This enabled us to reconstruct the fire history of this region since 1973 when visibility information became available. Our estimates indicate that until 1987 relatively few fires occurred in this region and that fire emissions increased rapidly over the 1990s. We found that this pattern agreed reasonably well with forest loss data sets, indicating that although natural fires may occur here, deforestation and degradation were the main cause of fires. Compared to fire emissions estimates based on Food and Agricultural Organization's Global Forest and Resources Assessment data, our estimates were substantially lower up to the 1990s, after which they were more in line. These visibility-based fire emissions data set can help constrain dynamic global vegetation models and atmospheric models with a better representation of the complex fire regime in this region.

Evidence for environmentally enhanced forest growth.

Forests in the middle and high latitudes of the northern hemisphere function as a significant sink for atmospheric carbon dioxide (CO2). This carbon (C) sink has been attributed to two processes: age-related growth after land use change and growth enhancement due to environmental changes, such as elevated CO2, nitrogen deposition, and climate change. However, attribution between these two processes is largely controversial. Here, using a unique time series of an age-class dataset from six national forest inventories in Japan and a new approach developed in this study (i.e., examining changes in biomass density at each age class over the inventory periods), we quantify the growth enhancement due to environmental changes and its contribution to biomass C sink in Japan's forests. We show that the growth enhancement for four major plantations was 4.0∼7.7 Mg C⋅ha(-1) from 1980 to 2005, being 8.4-21.6% of biomass C sequestration per hectare and 4.1-35.5% of the country's total net biomass increase of each forest type. The growth enhancement differs among forest types, age classes, and regions. Our results provide, to our knowledge, the first ground-based evidence that global environmental changes can increase C sequestration in forests on a broad geographic scale and imply that both the traits and age of trees regulate the responses of forest growth to environmental changes. These findings should be incorporated into the prediction of forest C cycling under a changing climate.

Joint CO2 and CH4 accountability for global warming.

We propose a transparent climate debt index incorporating both methane (CH4) and carbon dioxide (CO2) emissions. We develop national historic emissions databases for both greenhouse gases to 2005, justifying 1950 as the starting point for global perspectives. We include CO2 emissions from fossil sources [CO2(f)], as well as, in a separate analysis, land use change and forestry. We calculate the CO2(f) and CH4 remaining in the atmosphere in 2005 from 205 countries using the Intergovernmental Panel on Climate Change's Fourth Assessment Report impulse response functions. We use these calculations to estimate the fraction of remaining global emissions due to each country, which is applied to total radiative forcing in 2005 to determine the combined climate debt from both greenhouse gases in units of milliwatts per square meter per country or microwatts per square meter per person, a metric we term international natural debt (IND). Australia becomes the most indebted large country per capita because of high CH4 emissions, overtaking the United States, which is highest for CO2(f). The differences between the INDs of developing and developed countries decline but remain large. We use IND to assess the relative reduction in IND from choosing between CO2(f) and CH4`control measures and to contrast the imposed versus experienced health impacts from climate change. Based on 2005 emissions, the same hypothetical impact on world 2050 IND could be achieved by decreasing CH4 emissions by 46% as stopping CO2 emissions entirely, but with substantial differences among countries, implying differential optimal strategies. Adding CH4 shifts the basic narrative about differential international accountability for climate change.

The Bangladesh Risk of Acute Vascular Events (BRAVE) Study: objectives and design.

During recent decades, Bangladesh has experienced a rapid epidemiological transition from communicable to non-communicable diseases. Coronary heart disease (CHD), with myocardial infarction (MI) as its main manifestation, is a major cause of death in the country. However, there is limited reliable evidence about its determinants in this population. The Bangladesh Risk of Acute Vascular Events (BRAVE) study is an epidemiological bioresource established to examine environmental, genetic, lifestyle and biochemical determinants of CHD among the Bangladeshi population. By early 2015, the ongoing BRAVE study had recruited over 5000 confirmed first-ever MI cases, and over 5000 controls "frequency-matched" by age and sex. For each participant, information has been recorded on demographic factors, lifestyle, socioeconomic, clinical, and anthropometric characteristics. A 12-lead electrocardiogram has been recorded. Biological samples have been collected and stored, including extracted DNA, plasma, serum and whole blood. Additionally, for the 3000 cases and 3000 controls initially recruited, genotyping has been done using the CardioMetabochip+ and the Exome+ arrays. The mean age (standard deviation) of MI cases is 53 (10) years, with 88 % of cases being male and 46 % aged 50 years or younger. The median interval between reported onset of symptoms and hospital admission is 5 h. Initial analyses indicate that Bangladeshis are genetically distinct from major non-South Asian ethnicities, as well as distinct from other South Asian ethnicities. The BRAVE study is well-placed to serve as a powerful resource to investigate current and future hypotheses relating to environmental, biochemical and genetic causes of CHD in an important but under-studied South Asian population.

Rapid conversion of EUCOMM/KOMP-CSD alleles in mouse embryos using a cell-permeable Cre recombinase.

We describe here use of a cell-permeable Cre to efficiently convert the EUCOMM/KOMP-CSD tm1a allele to the tm1b form in preimplantation mouse embryos in a high-throughput manner, consistent with the requirements of the International Mouse Phenotyping Consortium-affiliated NIH KOMP2 project. This method results in rapid allele conversion and minimizes the use of experimental animals when compared to conventional Cre transgenic mouse breeding, resulting in a significant reduction in costs and time with increased welfare benefits.

Genomic analysis of a novel spontaneous albino C57BL/6N mouse strain.

We report an albino C57BL/6N mouse strain carrying a spontaneous mutation in the tyrosinase gene (C57BL/6N-Tyr(cWTSI)). Deep whole genome sequencing of founder mice revealed very little divergence from C57BL/6NJ and C57BL/6N (Taconic). This coisogenic strain will be of great utility for the International Mouse Phenotyping Consortium (IMPC), which uses the EUCOMM/KOMP targeted C57BL/6N ES cell resource, and other investigators wishing to work on a defined C57BL/6N background.

Molecular characterization of mutant mouse strains generated from the EUCOMM/KOMP-CSD ES cell resource.

The Sanger Mouse Genetics Project generates knockout mice strains using the EUCOMM/KOMP-CSD embryonic stem (ES) cell collection and characterizes the consequences of the mutations using a high-throughput primary phenotyping screen. Upon achieving germline transmission, new strains are subject to a panel of quality control (QC) PCR- and qPCR-based assays to confirm the correct targeting, cassette structure, and the presence of the 3' LoxP site (required for the potential conditionality of the allele). We report that over 86 % of the 731 strains studied showed the correct targeting and cassette structure, of which 97 % retained the 3' LoxP site. We discuss the characteristics of the lines that failed QC and postulate that the majority of these may be due to mixed ES cell populations which were not detectable with the original screening techniques employed when creating the ES cell resource.