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Salmonella Typhimurium ST313 causes invasive nontyphoidal Salmonella (iNTS) disease in sub-Saharan Africa, targeting susceptible HIV + , malarial or malnourished individuals. An in-depth genomic comparison between the ST313 isolate D23580, and the well-characterized ST19 isolate 4/74 that causes gastroenteritis across the globe, revealed extensive synteny. To understand how the 856 nucleotide variations generated phenotypic differences, we devised a large-scale experimental approach that involved the global gene expression analysis of strains D23580 and 4/74 grown in sixteen infection-relevant growth conditions. Comparison of transcriptional patterns identified virulence and metabolic genes that were differentially expressed between D23580 versus 4/74, many of which were validated by proteomics. We also uncovered the S. Typhimurium D23580 and 4/74 genes that showed expression differences during infection of murine macrophages. Our comparative transcriptomic data are presented in a new enhanced version of the Salmonella expression compendium SalComD23580: bioinf.gen.tcd.ie/cgi-bin/salcom_v2.pl . We discovered that the ablation of melibiose utilization was caused by 3 independent SNP mutations in D23580 that are shared across ST313 lineage 2, suggesting that the ability to catabolise this carbon source has been negatively selected during ST313 evolution. The data revealed a novel plasmid maintenance system involving a plasmid-encoded CysS cysteinyl-tRNA synthetase, highlighting the power of large-scale comparative multi-condition analyses to pinpoint key phenotypic differences between bacterial pathovariants.

Streamflow in south-central Chile (SCC, ∼ 37–42∘ S) is vital for agriculture, forestry production, hydroelectricity, and human consumption. Recent drought episodes have generated hydrological deficits with damaging effects on these activities. This region is projected to undergo major reductions in water availability, concomitant with projected increases in water demand. However, the lack of long-term records hampers the development of accurate estimations of natural variability and trends. In order to provide more information on long-term streamflow variability and trends in SCC, here we report findings of an analysis of instrumental records and a tree-ring reconstruction of the summer streamflow of the Río Imperial (∼ 37∘ 40′ S–38∘ 50′ S). This is the first reconstruction in Chile targeted at this season. Results from the instrumental streamflow record (∼ 1940 onwards) indicated that the hydrological regime is fundamentally pluvial with a small snowmelt contribution during spring, and evidenced a decreasing trend, both for the summer and the full annual record. The reconstruction showed that streamflow below the average characterized the post-1980 period, with more frequent, but not more intense, drought episodes. We additionally found that the recent positive phase of the Southern Annular Mode has significantly influenced streamflow. These findings agree with previous studies, suggesting a robust regional signal and a shift to a new hydrological scenario. In this paper, we also discuss implications of these results for water managers and stakeholders; we provide rationale and examples that support the need for the incorporation of tree-ring reconstructions into water resources management.

The Stratosphere–troposphere Processes And their Role in Climate (SPARC) Quasi-Biennial Oscillation initiative (QBOi) aims to improve the fidelity of tropical stratospheric variability in general circulation and Earth system models by conducting coordinated numerical experiments and analysis. In the equatorial stratosphere, the QBO is the most conspicuous mode of variability. Five coordinated experiments have therefore been designed to (i) evaluate and compare the verisimilitude of modelled QBOs under present-day conditions, (ii) identify robustness (or alternatively the spread and uncertainty) in the simulated QBO response to commonly imposed changes in model climate forcings (e.g. a doubling of CO2 amounts), and (iii) examine model dependence of QBO predictability. This paper documents these experiments and the recommended output diagnostics. The rationale behind the experimental design and choice of diagnostics is presented. To facilitate scientific interpretation of the results in other planned QBOi studies, consistent descriptions of the models performing each experiment set are given, with those aspects particularly relevant for simulating the QBO tabulated for easy comparison.

Genome-wide association studies (GWAS) have identified hundreds of loci associated with Crohns disease (CD), however, as with all complex diseases, deriving pathogenic mechanisms from these non-coding GWAS discoveries has been challenging. To complement GWAS and better define actionable biological targets, we analysed sequenced data from more than 30,000 CD patients and 80,000 population controls. We observe rare coding variants in established CD susceptibility genes as well as ten genes where coding variation directly implicates the gene in disease risk for the first time.

Ocean reanalyses combine ocean models, atmospheric forcing fluxes, and observations using data assimilation to give a four-dimensional description of the ocean. Metrics assessing their reliability have improved over time, allowing reanalyses to become an important tool in climate services that provide a more complete picture of the changing ocean to end users. Besides climate monitoring and research, ocean reanalyses are used to initialize sub-seasonal to multi-annual predictions, to support observational network monitoring, and to evaluate climate model simulations. These applications demand robust uncertainty estimates and fit-for-purpose assessments, achievable through sustained advances in data assimilation and coordinated inter-comparison activities. Ocean reanalyses face specific challenges: i) dealing with intermittent or discontinued observing networks, ii) reproducing inter-annual variability and trends of integrated diagnostics for climate monitoring, iii) accounting for drift and bias due e.g. to air-sea flux or ocean mixing errors, iv) optimizing initialization and improving performances during periods and in regions with sparse data. Other challenges such as multi-scale data assimilation to reconcile mesoscale and large-scale variability and flow-dependent error characterization for rapidly evolving processes, are amplified in long-term reanalyses. The demand to extend reanalyses backward in time requires tackling all these challenges, especially in the emerging context of earth system reanalyses and coupled data assimilation. This mini-review aims at documenting recent advances from the ocean reanalysis community, discussing unsolved challenges that require sustained activities for maximizing the utility of ocean observations, supporting data rescue and advancing specific research and development requirements for reanalyses. © 2019 Storto, Alvera Azcarate, Balmaseda, Barth, Chevallier, Counillon, Domingues, Drévillon, Drillet, Forget, Garric, Haines, Hernandez, Iovino, Jackson, Lellouche, Masina, Mayer, Oke, Penny, Peterson, Yang and Zuo.

The Integrated Carbon Observation System is a Pan-European distributed research infrastructure that has as its main goal to monitor the greenhouse gas balance of Europe. The ecosystem component of Integrated Carbon Observation System consists of a multitude of stations where the net greenhouse gas exchange is monitored continuously by eddy covariance measurements while, in addition many other measurements are carried out that are a key to an understanding of the greenhouse gas balance. Amongst them are the continuous meteorological measurements and a set of non-continuous measurements related to vegetation. The latter include Green Area Index, aboveground biomass and litter biomass. The standardized methodology that is used at the Integrated Carbon Observation System ecosystem stations to monitor these vegetation related variables differs between the ecosystem types that are represented within the network, whereby in this paper we focus on forests, grasslands, croplands and mires. For each of the variables and ecosystems a spatial and temporal sampling design was developed so that the variables can be monitored in a consistent way within the ICOS network. The standardisation of the methodology to collect Green Area Index, above ground biomass and litter biomass and the methods to evaluate the quality of the collected data ensures that all stations within the ICOS ecosystem network produce data sets with small and similar errors, which allows for inter-comparison comparisons across the Integrated Carbon Observation System ecosystem network.

The data set reported here includes the part of a Hot Serial Cereal Experiment (HSC) experiment recently used in the AgMIP-Wheat project to analyze the uncertainty of 30 wheat models and quantify their response to temperature. The HSC experiment was conducted in an open-field in a semiarid environment in the southwest USA. The data reported herewith include one hard red spring wheat cultivar (Yecora Rojo) sown approximately every six weeks from December to August for a two-year period for a total of 11 planting dates out of the 15 of the entire HSC experiment. The treatments were chosen to avoid any effect of frost on grain yields. On late fall, winter and early spring plantings temperature free-air controlled enhancement (T-FACE) apparatus utilizing infrared heaters with supplemental irrigation were used to increase air temperature by 1.3°C/2.7°C (day/night) with conditions equivalent to raising air temperature at constant relative humidity (i.e. as expected with global warming) during the whole crop growth cycle. Experimental data include local daily weather data, soil characteristics and initial conditions, detailed crop measurements taken at three growth stages during the growth cycle, and cultivar information. Simulations include both daily in-season and end-of-season results from 30 wheat models.

We analyse aerosol particle composition measurements from five research missions between 2014 and 2018 to assess the meridional extent of particles containing meteoric material in the upper troposphere and lower stratosphere (UTLS). Measurements from the Jungfraujoch mountaintop site and a low-altitude aircraft mission show that meteoric material is also present within middle- and lower-tropospheric aerosol but within only a very small proportion of particles. For both the UTLS campaigns and the lower- and mid-troposphere observations, the measurements were conducted with single-particle laser ablation mass spectrometers with bipolar-ion detection, which enabled us to measure the chemical composition of particles in a diameter range of approximately 150 nm to 3 µm. The five UTLS aircraft missions cover a latitude range from 15 to 68∘ N, altitudes up to 21 km, and a potential temperature range from 280 to 480 K. In total, 338 363 single particles were analysed, of which 147 338 were measured in the stratosphere. Of these total particles, 50 688 were characterized by high abundances of magnesium and iron, together with sulfuric ions, the vast majority (48 610) in the stratosphere, and are interpreted as meteoric material immersed or dissolved within sulfuric acid. It must be noted that the relative abundance of such meteoric particles may be overestimated by about 10 % to 30 % due to the presence of pure sulfuric acid particles in the stratosphere which are not detected by the instruments used here. Below the tropopause, the observed fraction of the meteoric particle type decreased sharply with 0.2 %–1 % abundance at Jungfraujoch, and smaller abundances (0.025 %–0.05 %) were observed during the lower-altitude Canadian Arctic aircraft measurements. The size distribution of the meteoric sulfuric particles measured in the UTLS campaigns is consistent with earlier aircraft-based mass-spectrometric measurements, with only 5 %–10 % fractions in the smallest particles detected (200–300 nm diameter) but with substantial (> 40 %) abundance fractions for particles from 300–350 up to 900 nm in diameter, suggesting sedimentation is the primary loss mechanism. In the tropical lower stratosphere, only a small fraction (< 10 %) of the analysed particles contained meteoric material. In contrast, in the extratropics the observed fraction of meteoric particles reached 20 %–40 % directly above the tropopause. At potential temperature levels of more than 40 K above the thermal tropopause, particles containing meteoric material were observed in much higher relative abundances than near the tropopause, and, at these altitudes, they occurred at a similar abundance fraction across all latitudes and seasons measured. Above 440 K, the observed fraction of meteoric particles is above 60 % at latitudes between 20 and 42∘ N. Meteoric smoke particles are transported from the mesosphere into the stratosphere within the winter polar vortex and are subsequently distributed towards low latitudes by isentropic mixing, typically below a potential temperature of 440 K. By contrast, the findings from the UTLS measurements show that meteoric material is found in stratospheric aerosol particles at all latitudes and seasons, which suggests that either isentropic mixing is effective also above 440 K or that meteoric fragments may be the source of a substantial proportion of the observed meteoric material.

As part of the Model Intercomparison Project on the climatic response to Volcanic forcing (VolMIP), several climate modeling centers performed a coordinated pre-study experiment with interactive stratospheric aerosol models simulating the volcanic aerosol cloud from an eruption resembling the 1815 Mt. Tambora eruption (VolMIP-Tambora ISA ensemble). The pre-study provided the ancillary ability to assess intermodel diversity in the radiative forcing for a large stratospheric-injecting equatorial eruption when the volcanic aerosol cloud is simulated interactively. An initial analysis of the VolMIP-Tambora ISA ensemble showed large disparities between models in the stratospheric global mean aerosol optical depth (AOD). In this study, we now show that stratospheric global mean AOD differences among the participating models are primarily due to differences in aerosol size, which we track here by effective radius. We identify specific physical and chemical processes that are missing in some models and/or parameterized differently between models, which are together causing the differences in effective radius. In particular, our analysis indicates that interactively tracking hydroxyl radical (OH) chemistry following a large volcanic injection of sulfur dioxide (SO2) is an important factor in allowing for the timescale for sulfate formation to be properly simulated. In addition, depending on the timescale of sulfate formation, there can be a large difference in effective radius and subsequently AOD that results from whether the SO2 is injected in a single model grid cell near the location of the volcanic eruption, or whether it is injected as a longitudinally averaged band around the Earth.