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Global net biome production (NBP), or net land carbon uptake, has been repeatedly shown to increase during recent decades. However, whether the temporal variability and autocorrelation of NBP has changed during this period remains elusive. Answering this question is particularly relevant given that an increase in both could indicate destabilising C sinks and potentially lead to abrupt changes. We investigated the trends and controls of net land C uptake and its temporal variability and autocorrelation, from 1981 to 2018, using two atmospheric inversion models, the amplitude of the seasonal cycle of atmospheric CO2 derived from nine monitoring stations distributed across the Pacific Ocean, and 12 dynamic global vegetation models. Spatially, we found that plant biodiversity presented a convex parabolic relationship with NBP and its temporal variability at the global scale while nitrogen deposition generally increased annual NBP. We also found that annual NBP and its interdecadal temporal variability globally increased, but temporal autocorrelation decreased. Regions characterized by increasingly variable NBP were usually with warmer and with increasingly variable temperatures, and lower and weaker trends in NBP compared to those where NBP variability did not increase, where NBP became stronger. Annual temperature increase and its increasing temporal variability were the most important drivers of declining NBP and increasingly its variability. Our results show that increasing regional NBP variability can be mostly attributed to climate change.

Carbon and water cycle dynamics of vegetation are controlled primarily by photosynthesis and stomatal conductance (gs). Our goal is to improve the representation of these key physiological processes within the JULES land surface model, with a particular focus on refining the temperature sensitivity of photosynthesis, impacting modelled carbon, energy and water fluxes. We test (1) an implementation of the Farquhar et al. (1980) photosynthesis scheme and associated plant functional type-dependent photosynthetic temperature response functions, (2) the optimality-based gs scheme from Medlyn et al. (2011) and (3) the Kattge and Knorr (2007) photosynthetic capacity thermal acclimation scheme. New parameters for each model configuration are adopted from recent large observational datasets that synthesise global experimental data. These developments to JULES incorporate current physiological understanding of vegetation behaviour into the model and enable users to derive direct links between model parameters and ongoing measurement campaigns that refine such parameter values. Replacement of the original Collatz et al. (1991) C3 photosynthesis model with the Farquhar scheme results in large changes in GPP for the current day, with ∼ 10 % reduction in seasonal (June–August, JJA, and December–February, DJF) mean GPP in tropical forests and ∼ 20 % increase in the northern high-latitude forests in JJA. The optimality-based gs model decreases the latent heat flux for the present day (∼ 10 %, with an associated increase in sensible heat flux) across regions dominated by needleleaf evergreen forest in the Northern Hemisphere summer. Thermal acclimation of photosynthesis coupled with the Medlyn gs scheme reduced tropical forest GPP by up to 5 % and increased GPP in the high-northern-latitude forests by between 2 % and 5 %. Evaluation of simulated carbon and water fluxes by each model configuration against global data products shows this latter configuration generates improvements in these key areas. Thermal acclimation of photosynthesis coupled with the Medlyn gs scheme improved modelled carbon fluxes in tropical and high-northern-latitude forests in JJA and improved the simulation of evapotranspiration across much of the Northern Hemisphere in JJA. Having established good model performance for the contemporary period, we force this new version of JULES offline with a future climate scenario corresponding to rising atmospheric greenhouse gases (Shared Socioeconomic Pathway (SSP5), Representative Concentration Pathway 8.5 (RCP8.5)). In particular, these calculations allow for understanding of the effects of long-term warming. We find that the impact of thermal acclimation coupled with the optimality-based gs model on simulated fluxes increases latent heat flux (+50 %) by the year 2050 compared to the JULES model configuration without acclimation. This new JULES configuration also projects increased GPP across tropical (+10 %) and northern-latitude regions (+30 %) by 2050. We conclude that thermal acclimation of photosynthesis with the Farquhar photosynthesis scheme and the new optimality-based gs scheme together improve the simulation of carbon and water fluxes for the current day and have a large impact on modelled future carbon cycle dynamics in a warming world.

Background: Inheritance of BRCA1 and BRCA2 mutations is associated with increased risk of breast and ovarian cancers. Previous studies with low-throughput flow cytometry-based assays suggested elevated number of luminal progenitor cells in the breast tissues of BRCA1 mutation carriers compared to breast tissues of non-carriers. However, breast epithelial cell-specific transcriptome differences between BRCA1, BRCA2 mutation carriers, and non-carriers and how these differences alter susceptibility to transformation are yet to be elucidated. Methods: We generated a single cell transcriptome atlas of breast tissues from BRCA1 (six samples, 17,220 cells), BRCA2 (four samples, 25,046 cells) mutation carriers and non-carriers (11 samples, >50,000 cells). Using previously described markers, epithelial cells were sub-clustered into basal, luminal progenitor, and mature luminal cells. Genes differentially expressed in epithelial cells of BRCA1 and BRCA2 mutation carriers compared to those in non-carrier donors were subjected to Ingenuity Pathway Analysis to determine signaling pathways uniquely active in BRCA1 and BRCA2 mutant epithelial cells. Breast epithelial cells derived from three donor types were immortalized using hTERT and then transformed with PIK3CAH1047R mutant or H-RasG12V ± SV40-T/t antigens, and tumorigenicity was determined in vivo. Results: BRCA1 but not BRCA2 mutations altered the ratio between basal, luminal progenitor and mature luminal cells in breast tissues compared to breast tissues in non-carriers. A unique cluster of cells within luminal progenitors was underrepresented in case of BRCA2 mutation carriers compared to non-carriers or BRCA1 mutation carriers. BRCA1 or BRCA2 mutations specifically altered transcriptomes which are an integral part of mTOR and MYCN signaling, and the translational machinery. Signaling pathway alterations in epithelial cells unique to BRCA1 mutations included YAP1, BRD4, SMARCA4, and TGFβ1 signaling. BRCA2 mutations were associated with upregulation of IL-6, FOXO3, and TNFSF11 signaling. Breast epithelial cells from BRCA2 mutation carriers but not BRCA1 mutation carriers or non-carriers modified to overexpress hTERT + PIK3CAH1047R generated tumors in NSG mice. These tumors displayed large cystic structures with basilar epithelial cells lining the rim of cysts with focal areas of cellular hyperplasia and neoplastic cells that extended into the lumen. However, BRCA1/2 mutation status did not influence tumorigenicity by hTERT+ H-RASG12V +SV40-T/t antigens. Conclusions: Our studies provide a high resolution transcriptome atlas of breast epithelial cells of BRCA1 and BRCA2 mutation carriers, which also reveal potentially targetable signaling networks uniquely deregulated in these cells. BRCA2 mutations are associated with distinct susceptibility to PIK3CA mutation-driven transformation. Since PIK3CA mutations are observed in clinically normal breast tissues, screening for such mutations in BRCA2 mutation carriers may help to detect pre-neoplastic or early stage breast cancer. Citation Format: Harikrishna Nakshatri, Poornima Bhat-Nakshatri, Duojiao Chen, Katie Chen, Henry Mang, Christopher A Herodotou, Aditi S Khatpe, Patrick C McGuire, Xiaoling Xuei, Yunlong Liu, George Sandusky, Anna Maria Storniolo. Single cell transcriptomic analysis reveals the effects of BRCA1 and BRCA2 mutations on distinct signaling networks and cancer susceptibility [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-07-09.

Global net land carbon uptake or net biome production (NBP) has increased during recent decades1. Whether its temporal variability and autocorrelation have changed during this period, however, remains elusive, even though an increase in both could indicate an increased potential for a destabilized carbon sink2,3. Here, we investigate the trends and controls of net terrestrial carbon uptake and its temporal variability and autocorrelation from 1981 to 2018 using two atmospheric-inversion models, the amplitude of the seasonal cycle of atmospheric CO2 concentration derived from nine monitoring stations distributed across the Pacific Ocean and dynamic global vegetation models. We find that annual NBP and its interdecadal variability increased globally whereas temporal autocorrelation decreased. We observe a separation of regions characterized by increasingly variable NBP, associated with warm regions and increasingly variable temperatures, lower and weaker positive trends in NBP and regions where NBP became stronger and less variable. Plant species richness presented a concave-down parabolic spatial relationship with NBP and its variability at the global scale whereas nitrogen deposition generally increased NBP. Increasing temperature and its increasing variability appear as the most important drivers of declining and increasingly variable NBP. Our results show increasing variability of NBP regionally that can be mostly attributed to climate change and that may point to destabilization of the coupled carbon–climate system.

Site-level observations have shown pervasive cold season CO2 release across Arctic and boreal ecosystems, impacting annual carbon budgets. Still, the seasonality of CO2 emissions are poorly quantified across much of the high latitudes due to the sparse coverage of site-level observations. Space-based observations provide the opportunity to fill some observational gaps for studying these high-latitude ecosystems, particularly across poorly sampled regions of Eurasia. Here, we show that data-driven net ecosystem exchange (NEE) from atmospheric CO2 observations implies strong summer uptake followed by strong autumn release of CO2 over the entire cold northeastern region of Eurasia during the 2015–2019 study period. Combining data-driven NEE with satellite-based estimates of gross primary production (GPP), we show that this seasonality implies less summer heterotrophic respiration (Rh) and greater autumn Rh than would be expected given an exponential relationship between respiration and surface temperature. Furthermore, we show that this seasonality of NEE and Rh over northeastern Eurasia is not captured by the TRENDY v8 ensemble of dynamic global vegetation models (DGVMs), which estimate that 47 %–57 % (interquartile range) of annual Rh occurs during August–April, while the data-driven estimates suggest 59 %–76 % of annual Rh occurs over this period. We explain this seasonal shift in Rh by respiration from soils at depth during the zero-curtain period, when sub-surface soils remain unfrozen up to several months after the surface has frozen. Additional impacts of physical processes related to freeze–thaw dynamics may contribute to the seasonality of Rh. This study confirms a significant and spatially extensive early cold season CO2 efflux in the permafrost-rich region of northeast Eurasia and suggests that autumn Rh from subsurface soils in the northern high latitudes is not well captured by current DGVMs.

Quantifying the net carbon flux from land use and land cover changes (fLULCC) is critical for understanding the global carbon cycle and, hence, to support climate change mitigation. However, large-scale fLULCC is not directly measurable and has to be inferred from models instead, such as semi-empirical bookkeeping models and process-based dynamic global vegetation models (DGVMs). By definition, fLULCC estimates are not directly comparable between these two different model types. As an important example, DGVM-based fLULCC in the annual global carbon budgets is estimated under transient environmental forcing and includes the so-called loss of additional sink capacity (LASC). The LASC results from the impact of environmental changes on land carbon storage potential of managed land compared to potential vegetation and accumulates over time, which is not captured in bookkeeping models. The fLULCC from transient DGVM simulations, thus, strongly depends on the timing of land use and land cover changes mainly because LASC accumulation is cut off at the end of the simulated period. To estimate the LASC, the fLULCC from pre-industrial DGVM simulations, which is independent of changing environmental conditions, can be used. Additionally, DGVMs using constant present-day environmental forcing enable an approximation of bookkeeping estimates. Here, we analyse these three DGVM-derived fLULCC estimations (under transient, pre-industrial, and present-day forcing) for 12 models within 18 regions and quantify their differences as well as climate- and CO2-induced components and compare them to bookkeeping estimates. Averaged across the models, we find a global fLULCC (under transient conditions) of 2.0±0.6 PgC yr−1 for 2009–2018, of which ∼40 % are attributable to the LASC (0.8±0.3 PgC yr−1). From 1850 onward, the fLULCC accumulated to 189±56 PgC with 40±15 PgC from the LASC. Around 1960, the accumulating nature of the LASC causes global transient fLULCC estimates to exceed estimates under present-day conditions, despite generally increased carbon stocks in the latter. Regional hotspots of high cumulative and annual LASC values are found in the USA, China, Brazil, equatorial Africa, and Southeast Asia, mainly due to deforestation for cropland. Distinct negative LASC estimates in Europe (early reforestation) and from 2000 onward in the Ukraine (recultivation of post-Soviet abandoned agricultural land), indicate that fLULCC estimates in these regions are lower in transient DGVM compared to bookkeeping approaches. Our study unravels the strong dependence of fLULCC estimates on the time a certain land use and land cover change event happened to occur and on the chosen time period for the forcing of environmental conditions in the underlying simulations. We argue for an approach that provides an accounting of the fLULCC that is more robust against these choices, for example by estimating a mean DGVM ensemble fLULCC and LASC for a defined reference period and homogeneous environmental changes (CO2 only).

Observations from the Orbiting Carbon Observatory 2 (OCO-2) satellite have been used to estimate CO2 fluxes in many regions of the globe and provide new insight into the global carbon cycle. The objective of this study is to infer the relationships between patterns in OCO-2 observations and environmental drivers (e.g., temperature, precipitation) and therefore inform a process understanding of carbon fluxes using OCO-2. We use a multiple regression and inverse model, and the regression coefficients quantify the relationships between observations from OCO-2 and environmental driver datasets within individual years for 2015–2018 and within seven global biomes. We subsequently compare these inferences to the relationships estimated from 15 terrestrial biosphere models (TBMs) that participated in the TRENDY model inter-comparison. Using OCO-2, we are able to quantify only a limited number of relationships between patterns in atmospheric CO2 observations and patterns in environmental driver datasets (i.e., 10 out of the 42 relationships examined). We further find that the ensemble of TBMs exhibits a large spread in the relationships with these key environmental driver datasets. The largest uncertainty in the models is in the relationship with precipitation, particularly in the tropics, with smaller uncertainties for temperature and photosynthetically active radiation (PAR). Using observations from OCO-2, we find that precipitation is associated with increased CO2 uptake in all tropical biomes, a result that agrees with half of the TBMs. By contrast, the relationships that we infer from OCO-2 for temperature and PAR are similar to the ensemble mean of the TBMs, though the results differ from many individual TBMs. These results point to the limitations of current space-based observations for inferring environmental relationships but also indicate the potential to help inform key relationships that are very uncertain in state-of-the-art TBMs.

Kidney intercalated cells are involved in acid-base homeostasis via vacuolar ATPase expression. Here we report six human intercalated cell subtypes, including hybrid principal-intercalated cells identified from single cell transcriptomics. Phagosome maturation is a biological process that increases in biological pathway analysis rank following exposure to uropathogenic Escherichia coli in two of the intercalated cell subtypes. Real time confocal microscopy visualization of murine renal tubules perfused with green fluorescent protein expressing Escherichia coli or pHrodo Green E. coli BioParticles demonstrates that intercalated cells actively phagocytose bacteria then acidify phagolysosomes. Additionally, intercalated cells have increased vacuolar ATPase expression following in vivo experimental UTI. Taken together, intercalated cells exhibit a transcriptional response conducive to the kidney’s defense, engulf bacteria and acidify the internalized bacteria. Intercalated cells represent an epithelial cell with characteristics of professional phagocytes like macrophages., Kidney intercalated cells are involved in acid-base homeostasis in the kidneys. Here, the authors use single cell transcriptomics and find that interalated cells exhibit a transcriptional response conducive to defense and can engulf and acidify internalized bacteria, similarly to professional phagocytes.

Ensemble runs of high-resolution (~10 km; N1280) global climate simulations (2005–2010) with the Met Office HadGEM3 model are analysed over large urban areas in the south-east UK (London) and south-east China (Shanghai, Hangzhou, Nanjing region). With a focus on urban areas, we compare meteorological observations to study the response of modelled surface heat fluxes and screen-level temperatures to urbanisation. HadGEM3 has a simple urban slab scheme with prescribed, globally fixed bulk parameters. Misrepresenting the magnitude or the extent of urban land cover can result in land-surface model bias. As urban land-cover fractions are severely under-estimated in China, this impacts surface heat-flux partitioning and quintessential features such as the urban heat island. Combined with the neglect of anthropogenic heat emissions, this can result in misrepresentation of heat-wave intensities (or cold spells) in cities. The model performance in urban areas could be improved if bulk parameters are modelled instead of prescribed, but this necessitates the availability of local morphology data on a global level. Improving land-cover information and providing more flexible ways to account for differences between cities (e.g. anthropogenic emission; morphology) is essential for realistic future projections of city climates, especially if model output is intended for urban climate services.

Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere in a changing climate is critical to better understand the global carbon cycle, support the development of climate policies, and project future climate change. Here we describe and synthesize data sets and methodology to quantify the five major components of the global carbon budget and their uncertainties. Fossil CO2 emissions (EFOS) are based on energy statistics and cement production data, while emissions from land-use change (ELUC), mainly deforestation, are based on land-use and land-use change data and bookkeeping models. Atmospheric CO2 concentration is measured directly, and its growth rate (GATM) is computed from the annual changes in concentration. The ocean CO2 sink (SOCEAN) is estimated with global ocean biogeochemistry models and observation-based data-products. The terrestrial CO2 sink (SLAND) is estimated with dynamic global vegetation models. The resulting carbon budget imbalance (BIM), the difference between the estimated total emissions and the estimated changes in the atmosphere, ocean, and terrestrial biosphere, is a measure of imperfect data and understanding of the contemporary carbon cycle. All uncertainties are reported as ±1σ. For the first time, an approach is shown to reconcile the difference in our ELUC estimate with the one from national greenhouse gases inventories, supporting the assessment of collective countries’ climate progress. For the year 2020, EFOS declined by 5.4 % relative to 2019, with fossil emissions at 9.5 ± 0.5 GtC yr−1 (9.3 ± 0.5 GtC yr−1 when the cement carbonation sink is included), ELUC was 0.9 ± 0.7 GtC yr−1, for a total anthropogenic CO2 emission of 10.2 ± 0.8 GtC yr−1 (37.4 ± 2.9 GtCO2). Also, for 2020, GATM was 5.0 ± 0.2 GtC yr−1 (2.4 ± 0.1 ppm yr−1), SOCEAN was 3.0 ± 0.4 GtC yr−1 and SLAND was 2.9 ± 1 GtC yr−1, with a BIM of −0.8 GtC yr−1. The global atmospheric CO2 concentration averaged over 2020 reached 412.45 ± 0.1 ppm. Preliminary data for 2021, suggest a rebound in EFOS relative to 2020 of +4.9 % (4.1 % to 5.7 %) globally. Overall, the mean and trend in the components of the global carbon budget are consistently estimated over the period 1959–2020, but discrepancies of up to 1 GtC yr−1 persist for the representation of annual to semi-decadal variability in CO2 fluxes. Comparison of estimates from multiple approaches and observations shows: (1) a persistent large uncertainty in the estimate of land-use changes emissions, (2) a low agreement between the different methods on the magnitude of the land CO2 flux in the northern extra- tropics, and (3) a discrepancy between the different methods on the strength of the ocean sink over the last decade. This living data update documents changes in the methods and data sets used in this new global carbon budget and the progress in understanding of the global carbon cycle compared with previous publications of this data set (Friedlingstein et al., 2020; Friedlingstein et al., 2019; Le Quéré et al., 2018b, 2018a, 2016, 2015b, 2015a, 2014, 2013). The data presented in this work are available at https://doi.org/10.18160/gcp-2021 (Friedlingstein et al., 2021).

Results: Soil temperature is a crucial variable in Land Surface Models (LSMs) because it affects the fractions of frozen and unfrozen water content in the soil. For example, getting the coupling between below-ground heat- and water transfer correct in LSMs is very important in permafrost regions because these are particularly sensitive to climate change. Poor predictions of the energy- and water balance in these regions will lead to large uncertainties in predicted carbon fluxes, and related land-atmosphere feedbacks. Also, simulated near-surface soil temperatures can be used to diagnose and explain model differences in skin temperatures and soil heat fluxes, both of which are pivotal in the prediction of the surface energy balance.Soil temperature is generally under-researched as part of LSM intercomparisons. Here we present an analysis of the spatial distribution (including the vertical distribution along the soil profile) and seasonal evolution of soil temperature simulated by eight LSMs as part of the Soil Parameter Model Intercomparison Project (SP-MIP). We found large inter-model differences in key metrics of the annual soil temperature wave, including the amplitude, phase shift and damping depth, which were partly attributed to diversity in hydraulic as well as thermal soil properties. Soil layer discretisation also played a role.Methods: Via manipulation of model soil hydraulic properties, and the soil texture inputs required to calculate these properties, controlled multi-model experiments have been conducted as part of SP-MIP, this MIP was originally proposed at the GEWEX-SoilWat workshop held in Leipzig (June 2016).The model experiments closely followed the LS3MIP protocol (van den Hurk et al. 2016). Eight land models (CLM5, ISBA, JSBACH, JULES, MATSIRO, MATSIRO-GW, NOAH-MP and ORCHIDEE) were run globally on 0.5° with GSWP3 forcing, from 1980-2010, for vertically homogeneous soil columns. There were 4 model experiments, leading to 7 model runs: Experiment 1. Global soil hydraulic parameter maps provided by SP-MIP; Experiment 2. Soil-hydraulic parameters derived from common soil textural properties, provided by SP-MIP, using model-specific pedotransfer functions (PTFs); Experiment 3. Reference run with all models applying their default soil hydraulic settings (including their own soil maps to derive the parameters); Experiment 4: four runs using spatially uniform soil hydraulic parameters for the whole globe (loamy sand, loam, clay and silt) provided by SP-MIP.Differences between the model experiments will allow the assessment of the inter-model variability that is introduced by the different stages of preparing model parameters. Soil parameters for Experiments 1 and soil textures for Experiment 2 at 0.5° resolution were prepared from dominant soil classes of the 0-5 cm layer of SoilGrids (Hengl et al. 2014) at 5 km resolution. Brooks and Corey hydraulic parameters come from Table 2 of Clapp and Hornberger (1978), Mualem-Van Genuchten hydraulic parameters are ROSETTA class average hydraulic parameters (Schaap et al. 2001), and soil textures are from Table 2 of Cosby et al. (1984). Experiments 4 a-d use the USDA soil classes, using the same PTFs for Brooks and Corey and Mualem-van Genuchten parameters as in Experiment 1.

Previous studies showed that high-resolution GCMs overestimate land precipitation when compared against observation-based data. Particularly, high-resolution HadGEM3-GC3.1 shows a significant precipitation increase in mountainous regions, where the scarcity of gauge stations increases the uncertainty of gridded observations and reanalyses. This work evaluates such precipitation uncertainties indirectly through the assessment of river discharge, considering that an increase of ~10% in land precipitation produces ~28% more runoff when the resolution is enhanced from 1° to 0.25°, and ~50% of the global runoff is produced in 27% of global land dominated by mountains. We diagnosed the river flow by routing the runoff generated by HadGEM3-GC3.1 low- and high-resolution simulations. The river flow is evaluated using a set of 344 monitored catchments distributed around the world. We also infer the global discharge by constraining the simulations with observations following a novel approach that implies bias correction in monitored rivers with two methods, and extension of the correction to the river mouth, and along the coast. Our global discharge estimate is 47.4±1.6×103km3yr−1, which is closer to the original high-resolution estimate (50.5 × 103km3yr−1) than to the low-resolution (39.6 × 103km3yr−1). The assessment suggests that high-resolution simulations performbetter in mountainous regions, either because the better-defined orography favours the placement of precipitation in the correct catchment, leading to a more accurate distribution of runoff, or the orographic precipitation increases, reducing the dry runoff bias of coarse resolution simulations. However, high-resolution slightly increases wet biases in catchments dominated by flat terrain. The improvement of model parameterizations and tuning may reduce the remaining errors in high-resolution simulations.

Year-to-year variability in CO2 fluxes can yield insight into climate-carbon cycle relationships, a fundamental yet uncertain aspect of the terrestrial carbon cycle. In this study, we use global observations from NASA’s Orbiting Carbon Observatory-2 (OCO-2) satellite for years 2015–2019 and a geostatistical inverse model to evaluate 5 years of interannual variability (IAV) in CO2 fluxes and its relationships with environmental drivers. OCO-2 launched in late 2014, and we specifically evaluate IAV during the time period when OCO-2 observations are available. We then compare inferences from OCO-2 with state-of-the-art process-based models (terrestrial biosphere model, TBMs). Results from OCO-2 suggest that the tropical grasslands biome (including grasslands, savanna, and agricultural lands within the tropics) makes contributions to global IAV during the 5 year study period that are comparable to tropical forests, a result that differs from a majority of TBMs. Furthermore, existing studies disagree on the environmental variables that drive IAV during this time period, and the analysis using OCO-2 suggests that both temperature and precipitation make comparable contributions. TBMs, by contrast, tend to estimate larger IAV during this time and usually estimate larger relative contributions from the extra-tropics. With that said, TBMs show little consensus on both the magnitude and the contributions of different regions to IAV. We further find that TBMs show a wide range of responses on the relationships of CO2 fluxes with annual anomalies in temperature and precipitation, and these relationships across most of the TBMs have a larger magnitude than inferred from OCO-2. Overall, the findings of this study highlight large uncertainties in process-based estimates of IAV during recent years and provide an avenue for evaluating these processes against inferences from OCO-2.

We have updated the soil properties used in JULES (Joint UK Land Environment Simulator), which is the land-surface component of the UM (Unified Model, the UK Met Office’s climate model). JULES models the interaction of the land surface with the atmosphere, and simulates the energy, water, and carbon fluxes. JULES allows either: (i) the Brooks & Corey (BC) model for estimating soil hydraulic properties, or (ii) the van Genuchten (VG) model but using hydraulic parameters translated from the BC model. One advantage of the VG model over the BC model is the smoother dependence of water retention upon matric potential for nearly saturated soils. Herein, we report on our work towards fully implementing the VG model in JULES and in the UM, through the implementation and evaluation of several VG pedotransfer functions (PTFs) for estimating the soil hydraulic parameters used in the hydraulic functions. We have tested three VG PTFs in global offline JULES runs (driven with WFDEI data over 1979-2012): the combination of Tóth et al. PTFs 17 & 20, the Weynants et al. PTF, and the Zhang & Schaap ROSETTA3 H1 PTF (modified for sandy soils). We also modernized the soil basic properties that are conventionally used for JULES and the UM, from the UM version of the Harmonized World Soil Database (HWSD) to the SoilGrids database. Evaluation of JULES simulations shows (i) that the modified version of the Zhang & Schaap ROSETTA3 H1 PTF is the best VG option, and (ii) that it compares favorably with the BC control model (which uses the Cosby et al. PTF and the UM/HWSD soils), in terms of the surface energy balance and the mitigation of near-surface temperature biases over mid-latitude continental regions. This modified version of the Zhang & Schaap ROSETTA3 H1 PTF with SoilGrids soils is also currently being used in coupled land-atmosphere UM runs.

Capturing soil moisture-atmosphere feedbacks in a weather or climate model requires realistic simulation of various land surface processes. However, irrigation and other water management methods are still missing in most global climate models today, despite irrigated agriculture being the dominant land use in parts of Asia. In this study, we test the irrigation scheme available in the land model JULES (Joint UK Land Environment Simulator) by running land-only simulations over South and East Asia driven by WFDEI (WATCH Forcing Data ERA-Interim) forcing data. Irrigation in JULES is applied on a daily basis by replenishing soil moisture in the upper soil layers to field capacity, and we use a version of the irrigation scheme that extracts water for irrigation from groundwater and rivers, which physically limits the amount of irrigation that can be applied. We prescribe irrigation for C3 grasses in order to simulate the effects of agriculture, albeit retaining the simpler, widely used 5-PFT (plant functional type) configuration in JULES. Irrigation generally increases soil moisture and evapotranspiration, which results in increasing latent heat fluxes and decreasing sensible heat fluxes. Comparison with combined observational/machine-learning products for turbulent fluxes shows that while irrigation can reduce biases, other biases in JULES, unrelated to irrigation, are larger than improvements due to the inclusion of irrigation. Irrigation also affects water fluxes within the soil, e.g. runoff and drainage into the groundwater level, as well as soil moisture outside of the irrigation season. We find that the irrigation scheme, at least in the uncoupled land-atmosphere setting, can rapidly deplete groundwater to the point that river flow becomes the main source of irrigation (over the North China Plain and the Indus region) and can have the counterintuitive effect of decreasing annual average soil moisture (over the Ganges plain). Subsequently, we will explore the impact of irrigation on regional climate by conducting coupled land-atmosphere simulations.

Extreme summer temperatures in western and central Europe have become more frequent and heatwaves more prolonged over the past decades. The summer of 2018 was one of the driest and hottest in the observational record and led to losses in vegetation productivity in central Europe by up to 50%. Legacy effects from such extreme summers can affect ecosystem functioning over several years, as vegetation slowly recovers. In 2019 an extremely dry and hot summer was registered again in the region, imposing stress conditions at a time when ecosystems were still recovering from summer 2018.Using Enhanced Vegetation Index (EVI) fields from MODIS, we evaluate how ecosystems in central Europe responded to the occurrence of two consecutive extreme summers. We find that only ca. 21% of the area negatively impacted by drought in summer 2018 fully recovered in 2019.We find that the strongest EVI anomalies in 2018/19 diverge from the long-term relationships between EVI and climate, indicating an increase in ecosystem vulnerability to heat and drought events. Furthermore, 18% of the area showed a worsening of plant status during summer 2019 in spite of drought alleviation, which could be explained by interannual legacy effects from 2018, such as impaired growth and increased biotic disturbances.Land-surface models do not simulate interannual legacy effects from summer 2018 and thereby underestimate the impact of drought in 2019 on ecosystems. The poor representation of drought-induced damage and mortality and lack of biotic disturbances in these models may result in an overestimation of the resilience and stability of temperate ecosystems in the future.

The potential effect of climate change on regional suitability for cocoa cultivation is a serious economic concern for West Africa—especially for Ghana and Côte d’Ivoire, whose cocoa cultivation accounts for respectively ∼19% and ∼45% of world production. Here, we present a modelling and observational study of cocoa net primary productivity (NPP) in present day and future West African climates. Our analysis uses a data assimilation technique to parameterise a process-based land-surface model. The parameterisation is based on laboratory observations of cocoa, grown under both ambient and elevated CO2. Present day and end of 21st century cocoa cultivation scenarios are produced by driving the parameterised land-surface model with output from a high-resolution climate model. This represents a significant advance on previous work, because unlike the CMIP5 models, the high-resolution model used in this study accurately captures the observed precipitation seasonality in the cocoa-growing regions of West Africa—a key sensitivity for perennials like cocoa. We find that temperature is projected to increase significantly and precipitation is projected to increase slightly, although not in all parts of the region of interest. We find, furthermore, that the physiological effect of higher atmospheric CO2 concentration ameliorates the impacts of high temperature and variation in precipitation thereby reducing some of the negative impacts of climate change and maintaining NPP in West Africa, for the whole 21st Century, even under a high emissions scenario. Although NPP is an indicator of general vegetation condition, it is not equivalent to yield or bean quality. The study presented here is, nevertheless, a strong basis for further field and modelling studies of cultivation under elevated CO2 conditions.

Two urban schemes within the Joint UK Land Environment Simulator\ud (JULES) are evaluated offline against multi-year flux observations in the densely\ud built-up city centre of London and in suburban Swindon (UK): (i) the 1-tile slab\ud model, used in climate simulations, (ii) the 2-tile canopy model MORUSES (Met\ud Office–Reading Urban Surface Exchange Scheme), used for numerical weather pre-\ud diction over the UK. Offline, both models perform better at the suburban site,\ud where differences between the urban schemes are less pronounced due to larger\ud vegetation fractions. At both sites, the outgoing short- and longwave radiation is\ud more accurately represented than the turbulent heat fluxes. The seasonal varia-\ud tions of model skill are large in London, where the sensible heat flux in autumn and\ud winter is strongly under-predicted if the large city-centre magnitudes of anthro-\ud pogenic heat emissions are not represented. The delayed timing of the sensible heat flux in the 1-tile model in London results in large negative bias in the morning.\ud The partitioning of the urban surface into canyon and roof in MORUSES improves\ud this as the roof-tile is modelled with a very low thermal inertia, but phase and\ud amplitude of the gridbox-averaged flux critically depend on accurate knowledge of\ud the plan-area fractions of streets and buildings. Not representing non-urban land-\ud cover (e.g. vegetation, inland water) in London results in severely under-predicted\ud latent heat fluxes. Control runs demonstrate that the skill of both models can be\ud greatly improved by providing accurate land-cover and morphology information\ud and using representative anthropogenic heat emissions, which is essential if the\ud model output is intended to inform integrated urban services.

SummarySingle cell RNA sequencing is an evolving field to elucidate cellular architecture of adult organs. Using normal breast tissues from healthy volunteers and a rapid procurement/processing/sequencing protocol, 13 breast epithelial cell clusters were identified. Approximately 90% of breast cancers were enriched for cell-of-origin signatures derived from differentiated luminal clusters and two minor luminal progenitor clusters. Expression of cell cycle and chromosome segregation-related genes were higher in one of the minor clusters and breast tumors with this cluster signature displayed the highest mutation rate and poor outcome. We identified TBX3 and PDK4 as genes co-expressed with estrogen receptor (ER) in the normal breasts and their expression analyses in >550 breast cancers enabled prognostically relevant cell-of-origin based subclassification of ER+ breast cancers.SignificanceThis study elucidates different epithelial cell types of the normal breasts and identifies a minor subpopulation of cells from which the majority of breast cancers may originate. This observation should help to develop methods to characterize breast tumors based on cell-of-origin. Although it was suggested that intrinsic subtypes of breast cancers have distinct cells of origins, this study suggests multiple cell-of-origin for an intrinsic subtype of breast cancer, including for hormone responsive breast cancers. Cell-of-origin signatures allowed survival-associated subclassification of intrinsic subtypes. Critically, this normal breast cell atlas would allow for the classification of genes differentially expressed in a breast tumor compared to normal breast due to the cell-of-origin of tumor and those that are acquired due to genomic aberrations.

Previous studies showed that high resolution GCMs overestimate land precipitation when compared against gridded observations or reanalysis (Demory et al. 2014, Vannière et al. 2019). In particular, grid point models (eg. HadGEM3) show a significant increase of precipitation on regions dominated by complex orography, where the scarcity of gauge stations increase the uncertainty of gridded observations. The goal of this work is to assess the effect of such differences in precipitation on river discharge, considering it as an integrator of the water balance at catchment scale. A set of JULES and CLM simulations have been conducted turning rivers on with Total Runoff Integrating Pathways (TRIP) and the River Transport Model (RTM) respectively. The simulations form three ensembles for each land surface model (LSM) which main difference is given by the forcing dataset. The forcings are WFDEI (reanalysis), LR (~1° resolution in meteorological data from GCMs) and HR (~0.25° resolution in meteorological data from GCMs). These ensembles are evaluated in a set of 280 catchments distributed around the world.In terms of correlation between simulated and observed river discharge observations, the results show that LSMs forced by reanalysis have higher performance than LSMs forced by GCMs as expected. In terms of biases, the river discharge is underestimated in eight out of eleven major basins when LSMs are forced by reanalysis. On those basins, the extra precipitation estimated by GCMs help to simulate an amount of river discharge closer to observations (Eg. Yenisey and Lena). Moreover, 37 small basins with a strong component of orographic precipitation over the Andes, the Rocky Mountains, the Alps and in the Maritime Continent were evaluated. In most cases HR offers notably better results than LR and WFDEI, suggesting that high resolution models produce orographic precipitation in the correct place and time.In future works offline TRIP simulations will be carried out directly forced by runoff and subsurface runoff from GCMs. It will allow to discard errors in evapotranspiration produced by JULES or CLM when they are used to simulate river discharge. This work is part of the European Process-based climate sIMulation: AdVances in high resolution modelling and European climate Risk Assessment (PRIMAVERA) Project. PRIMAVERA is a collaboration between 19 funded by the European Union’s Horizon 2020 Research & Innovation Programme.Demory, M. E., Vidale, P. L., Roberts, M. J., Berrisford, P., Strachan, J., Schiemann, R., & Mizielinski, M. S. (2014). The role of horizontal resolution in simulating drivers of the global hydrological cycle. CLIM DYNAM, 42(7-8), 2201-2225.Vannière, B., Demory, M. E., Vidale, P. L., Schiemann, R., Roberts, M. J., Roberts, C. D., ... & Senan, R. (2018). Multi-model evaluation of the sensitivity of the global energy budget and hydrological cycle to resolution. CLIM DYNAM, 1-30.

Ecosystems responded asymmetrically to the 2018 European drought., In summer 2018, central and northern Europe were stricken by extreme drought and heat (DH2018). The DH2018 differed from previous events in being preceded by extreme spring warming and brightening, but moderate rainfall deficits, yet registering the fastest transition between wet winter conditions and extreme summer drought. Using 11 vegetation models, we show that spring conditions promoted increased vegetation growth, which, in turn, contributed to fast soil moisture depletion, amplifying the summer drought. We find regional asymmetries in summer ecosystem carbon fluxes: increased (reduced) sink in the northern (southern) areas affected by drought. These asymmetries can be explained by distinct legacy effects of spring growth and of water-use efficiency dynamics mediated by vegetation composition, rather than by distinct ecosystem responses to summer heat/drought. The asymmetries in carbon and water exchanges during spring and summer 2018 suggest that future land-management strategies could influence patterns of summer heat waves and droughts under long-term warming.

The Gulf of Cadiz is characterized by extensive active and inactive fluid escape structures which manifest as mud volcanoes, diapiric ridges, pockmarks and cold seeps. The high methane content and the presence of gas hydrates in the shallow sediments of the most active fluid escape structures indicate that these are areas of preferential migration and escape of fluids enriched in hydrocarbons and methane. Extensive fields of methane-derived authigenic carbonates are found at fluid escape structures along the upper and mid-continental slope, where the Mediterranean Outflow water is in direct contact with the seafloor, at water depths generally 1400 m) parts of the basin. The estimated U/Th ages of the authigenic carbonates, suggest that they were probably formed during discrete episodes of gas hydrate activity that may have occurred as a result of rapid climatic changes (such as the termination of the last glacial stage.) Numerical modelling indicates that seafloor temperature variations, associated with glacial/interglacial cycles and the changes of the Mediterranean Outflow pathway, could have restricted or eliminated the gas hydrate stability zone at the mud volcanoes shallower than 1400 m, resulting in intense fluxes of methane-rich fluids to the shallow sediments or even the seafloor. This fluid flux was recorded by the microbially mediated precipitation of authigenic carbonates. published

Summary Single-cell RNA sequencing (scRNA-seq) is an evolving technology used to elucidate the cellular architecture of adult organs. Previous scRNA-seq on breast tissue utilized reduction mammoplasty samples, which are often histologically abnormal. We report a rapid tissue collection/processing protocol to perform scRNA-seq of breast biopsies of healthy women and identify 23 breast epithelial cell clusters. Putative cell-of-origin signatures derived from these clusters are applied to analyze transcriptomes of ~3,000 breast cancers. Gene signatures derived from mature luminal cell clusters are enriched in ~68% of breast cancers, whereas a signature from a luminal progenitor cluster is enriched in ~20% of breast cancers. Overexpression of luminal progenitor cluster-derived signatures in HER2+, but not in other subtypes, is associated with unfavorable outcome. We identify TBX3 and PDK4 as genes co-expressed with estrogen receptor (ER) in the normal breasts, and their expression analyses in >550 breast cancers enable prognostically relevant subclassification of ER+ breast cancers., Graphical abstract, Highlights Healthy breast contains 23 subclusters of epithelial cells Breast cancers may originate from 3 luminal mature and 1 progenitor subclusters TBX3 and PDK4, co-expressed with estrogen receptor (ER), subclassify ER+ breast cancers, Bhat-Nakshatri et al. describe the single-cell atlas and document 23 epithelial cell subclusters in the healthy breast. Although experimentally validating cell of origin of a tumor is technically challenging, overlap analysis of subcluster-enriched gene signatures with breast tumor transcriptomes revealed dominant representation of differentiated luminal subclusters-derived signatures in breast cancers.

The empirical volcano-scan atmospheric correction is widely applied to Martian near infrared CRISM and OMEGA spectra between 1000 and 2600 nanometers to remove prominent atmospheric gas absorptions with minimal computational investment. This correction method employs division by a scaled empirically-derived atmospheric transmission spectrum that is generated from observations of the Martian surface in which different path lengths through the atmosphere were measured and transmission calculated using the Beer-Lambert Law. Identifying and characterizing both artifacts and residual atmospheric features left by the volcano-scan correction is important for robust interpretation of CRISM and OMEGA volcano scan corrected spectra. In order to identify and determine the cause of spectral artifacts introduced by the volcano-scan correction, we simulated this correction using a multiple scattering radiative transfer algorithm (DISORT). Simulated transmission spectra that are similar to actual CRISM- and OMEGA-derived transmission spectra were generated from modeled Olympus Mons base and summit spectra. Results from the simulations were used to investigate the validity of assumptions inherent in the volcano-scan correction and to identify artifacts introduced by this method of atmospheric correction. We found that the most prominent artifact, a bowl-shaped feature centered near 2000 nanometers, is caused by the inaccurate assumption that absorption coefficients of CO2 in the Martian atmosphere are independent of column density. In addition, spectral albedo and slope are modified by atmospheric aerosols. Residual atmospheric contributions that are caused by variable amounts of dust aerosols, ice aerosols, and water vapor are characterized by the analysis of CRISM volcano-scan corrected spectra from the same location acquired at different times under variable atmospheric conditions.

Acid-sulfate minerals such as jarosite are often used as indicators of environmental conditions on Mars. These minerals form in a diverse set of environments on Earth; however, all known Martian jarosite deposits are most likely evaporative, from evaporation of either groundwater or ponded water. Here, we use the Compact Reconnaissance Imaging Spectrometer for Mars and High-Resolution Imaging Science Experiment to report a new jarosite deposit along the southern wall of Ius Chasma. The morphology and geologic context of the Ius deposit are unique on Mars, and difficult to explain with an evaporative or groundwater mechanism. We propose instead that it was deposited along the margins of a past glacier. Such acid-ice interactions would be similar to those reported along the margins of Svalbard glaciers (arctic Norway), and would represent a new style of acid-sulfate formation on Mars.

[1] There is ample evidence of both ancient and long-lasting fluvial activity and chemical alteration in the Libya Montes region south of Isidis Basin. The region hosts Noachian to Amazonian aged surface rocks with extensive outcrops of olivine- and pyroxene-bearing material. Libya Montes also features surface outcrops and/or deposits hosting Fe/Mg-smectite, Fe/Mg-smectite mixed with carbonate and/or other Fe/Mg-rich phyllosilicates, and Al-smectite. These units likely formed through chemical alteration connected with hydrothermal activity resulting from the formation of the Isidis Basin and/or the pervasive fluvial activity throughout this region. The morphology and stratigraphy of the aqueous and mafic minerals are described using High Resolution Imaging Science Experiment and High Resolution Stereo Camera derived digital terrain models. Analyses of the Compact Reconnaissance Imaging Spectrometer for Mars spectra show variations in the chemistry of the Fe/Mg-smectite from nontronite-like exposures with spectral features near 2.29 and 2.4 µm more consistent with Fe3+2OH groups in the mineral structure, and saponite-like outcrops with spectral features near 2.31 and 2.38 µm characteristic of Mg2+3OH groups. These Fe/Mg-smectite bearing materials also have bands near 1.9 µm due to H2O and near 2.5 µm that could be due to the smectite, other phyllosilicates, and carbonates. All regions exhibiting carbonate features near 3.4–3.5 µm also have features consistent with the presence of olivine and Fe/Mg-smectite, indicating that the carbonate signatures occur in rocks likely containing a mixture of these minerals. The Al-smectite-bearing rocks have bands near 1.41, 1.91, and 2.19 µm that are more consistent with beidellite than other Al-phyllosilicates, indicating a higher-temperature or diagenetically processed origin for this material. Our interpretation of the geologic history of this region is that ancient Noachian basaltic crustal materials experienced extensive aqueous alteration at the time of the Isidis impact, during which the montes were also formed, followed by emplacement of a rough olivine-rich lava or melt, and finally the smooth pyroxene-bearing caprock unit.

The High Resolution Stereo Camera (HRSC) of ESA׳s Mars Express is designed to map and investigate the topography of Mars. The camera, in particular its Super Resolution Channel (SRC), also obtains images of Phobos and Deimos on a regular basis. As HRSC is a push broom scanning instrument with nine CCD line detectors mounted in parallel, its unique feature is the ability to obtain along-track stereo images and four colors during a single orbital pass. The sub-pixel accuracy of 3D points derived from stereo analysis allows producing DTMs with grid size of up to 50 m and height accuracy on the order of one image ground pixel and better, as well as corresponding orthoimages. Such data products have been produced systematically for approximately 40% of the surface of Mars so far, while global shape models and a near-global orthoimage mosaic could be produced for Phobos. HRSC is also unique because it bridges between laser altimetry and topography data derived from other stereo imaging instruments, and provides geodetic reference data and geological context to a variety of non-stereo datasets. This paper, in addition to an overview of the status and evolution of the experiment, provides a review of relevant methods applied for 3D reconstruction and mapping, and respective achievements. We will also review the methodology of specific approaches to science analysis based on joint analysis of DTM and orthoimage information, or benefitting from high accuracy of co-registration between multiple datasets, such as studies using multi-temporal or multi-angular observations, from the fields of geomorphology, structural geology, compositional mapping, and atmospheric science. Related exemplary results from analysis of HRSC data will be discussed. After 10 years of operation, HRSC covered about 70% of the surface by panchromatic images at 10–20 m/pixel, and about 97% at better than 100 m/pixel. As the areas with contiguous coverage by stereo data are increasingly abundant, we also present original data related to the analysis of image blocks and address methodology aspects of newly established procedures for the generation of multi-orbit DTMs and image mosaics. The current results suggest that multi-orbit DTMs with grid spacing of 50 m can be feasible for large parts of the surface, as well as brightness-adjusted image mosaics with co-registration accuracy of adjacent strips on the order of one pixel, and at the highest image resolution available. These characteristics are demonstrated by regional multi-orbit data products covering the MC-11 (East) quadrangle of Mars, representing the first prototype of a new HRSC data product level.

Hydrated minerals have been detected in many martian chaos regions and chasmata, playing a major role in its past aqueous activity. Based on short wave infrared data from CRISM, imagery and elevation data, we identified and mapped hydrated minerals in Aureum Chaos to shed light on their stratigraphy and geological context. The Interior Layered Deposits (ILDs) display three stratigraphic units: The lowest unit shows massive and also layered, high-albedo monohydrated sulfate (MHS, best matching kieserite; 20–650 m thick) with intercalated hydroxylated ferric sulfates (HFSs, best matching jarosite) and ferric oxides. The overlying polyhydrated sulfate (PHS) is commonly layered (20–40 m thick), smooth to heavily fractured, of lower albedo and partially contains ferric oxides. Spectrally neutral, distinctly layered, and bumpy cap rock (40–300 m thick) forms the top. We found spectral and morphological similarities to Aram Chaos (PHS, MHS, ferric oxides; texture of ILD and cap rock) and Juventae Chasma (HFS). Besides, the phyllosilicate nontronite was found attributed to chaotic terrain as light toned fractured exposure and within dark, smooth mantling. The coexistence of sulfates and phyllosilicates indicates changes in the geochemistry of the aqueous environment. Since sulfates and phyllosilicates could be alteration products, the observed mineralogy presumably is not the original; conversions between PHS and MHS, MHS or PHS into jarosite, jarosite into iron oxides are considered. Due to its occurrence along mantling edges and on flat surfaces of MHS without textural differences, it appears that PHS is an alteration product of MHS, e.g. due to surface exposure. The facies and relative timing of sulfate formation remains undefined. However, two different formation models are considered. The first implies contemporaneous ILD and PHS deposition and diagenetic sulfate conversion (into MHS, iron oxides) due to overburden later on. This model is less conclusive than groundwater evaporation -the second model- due to the lack of a sharp PHS–MHS boundary that would indicate a diagenetic formation. Alternatively, the second model suggests subsequent sulfate formation. Groundwater would have penetrated into pre-existing sulfate-free ILD. The permeability and porosity of ILD material would have defined the rate of water absorption and sulfate precipitation (low in cap rock?), resulting in cementation of probably aeolian deposited ILDs. We think this model is more consistent and could explain ILD stratigraphy with the potential anhydrous cap rock on top. The surface age of chaotic terrain (late Hesperian) and mantling deposits (mid to late Amazonian) limit the ILD age and possibly the emplacement of sulfates. Phyllosilicates in the mantling are presumably allochthonous. Limiting the timing of in situ phyllosilicates is more complicated; they could be Noachian (excavated material, following the phyllosian era), or instead syn- or post-chaotic. A close spatial and temporal association of sulfates and phyllosilicates, in which nontronite represents the deep facies, and sulfates the evaporitic facies is known from Earth and is also possible and would combine groundwater alteration with the observed mineralogy. The preservation of nontronite, HFS and MHS probably reflects a relatively dry environment with intermittent aqueous activity since their emplacement.