This work documents the first version of the U.S. Department of Energy (DOE) new EnergyExascale Earth System Model (E3SMv1). We focus on the standard resolution of the fully coupled physical model designed to address DOE mission-relevant water cycle questions. Its components include atmosphere and land (110-km grid spacing), ocean and sea ice (60 km in the midlatitudes and 30 km at the equator and poles), and river transport (55 km) models. This base configuration will also serve as a foundation for additional configurations exploring higher horizontal resolution as well as augmented capabilities in the form of biogeochemistry and cryosphere configurations. The performance of E3SMv1 is evaluated by means of a standard set of Coupled Model Intercomparison Project Phase 6 (CMIP6) Diagnosis, Evaluation, and Characterization of Klima simulations consisting of a long preindustrial control, historical simulations (ensembles of fully coupled and prescribed SSTs) as well as idealized CO 2 forcing simulations. The model performs well overall with biases typical of other CMIP-class models, although the simulated Atlantic Meridional Overturning Circulation is weaker than many CMIP-class models. While the E3SMv1 historical ensemble captures the bulk of the observed warming between preindustrial (1850) and present day, the trajectory of the warming diverges from observations in the Key Points: • This work documents E3SMv1, the first version of the U.S. DOE Energy Exascale Earth System Model • The performance of E3SMv1 is documented with a set of standard CMIP6 DECK and historical simulations comprising nearly 3,000 years • E3SMv1 has a high equilibrium climate sensitivity (5.3 K) and strong aerosol-related effective radiative forcing (-1.65 W/m 2 ) Correspondence to: Chris Golaz, golaz1@llnl.gov Citation: Golaz, J.-C., Caldwell, P. M., Van Roekel, L. P., Petersen, M. R., Tang, Q., Wolfe, J. D., et al. (2019). The DOE E3SM coupled model version 1: Overview and evaluation at standard resolution. second half of the twentieth century with a period of delayed warming followed by an excessive warming trend. Using a two-layer energy balance model, we attribute this divergence to the model's strong aerosol-related effective radiative forcing (ERF ari+aci = −1.65 W/m 2 ) and high equilibrium climate sensitivity (ECS = 5.3 K). Plain Language Summary The U.S. Department of Energy funded the development of a new state-of-the-art Earth system model for research and applications relevant to its mission. The Energy Exascale Earth System Model version 1 (E3SMv1) consists of five interacting components for the global atmosphere, land surface, ocean, sea ice, and rivers. Three of these components (ocean, sea ice, and river) are new and have not been coupled into an Earth system model previously. The atmosphere and land surface components were created by extending existing components part of the Community Earth System Model, Version 1. E3SMv1's capabilities are demonstrated by performing a set of standardized simulation experiments described by...

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SummaryBurkholderia pseudomallei is the causative agent of melioidosis, a serious infectious disease of humans and animals that is endemic in subtropical areas. B. pseudomallei is a facultative intracellular pathogen that may invade and survive within eukaryotic cells for prolonged periods. After internalization, the bacteria escape from endocytic vacuoles into the cytoplasm of infected cells and form membrane protrusions by inducing actin polymerization at one pole. It is believed that survival within phagocytic cells and cell-to-cell spread via actin protrusions is required for full virulence. We have studied the role of a putative type III protein secretion apparatus (Bsa) in the interaction between B. pseudomallei and host cells. The Bsa system is very similar to the Inv/Mxi-Spa type III secretion systems of Salmonella and Shigella. Moreover, B. pseudomallei encodes proteins that are very similar to Salmonella and Shigella Inv/Mxi-Spa secreted proteins required for invasion, escape from endocytic vacuoles, intercellular spread and pathogenesis. Antibodies to putative Bsa-secreted proteins were detected in convalescent serum from a melioidosis patient, suggesting that the system is functionally expressed in vivo . B. pseudomallei mutant strains lacking components of the Bsa secretion and translocation apparatus were constructed. The mutant strains exhibited reduced replication in J774.2 murine macrophage-like cells, an inability to escape from endocytic vacuoles and a complete absence of formation of membrane protrusions and actin tails. These findings indicate that the Bsa type III secretion system plays an essential role in modulating the intracellular behaviour of B. pseudomallei .

Type III secreted Sop protein effectors are delivered into target eukaryotic cells and elicit cellular responses underlying Salmonella pathogenicity. In this work, we have identified another secreted protein, SopE2, and showed that SopE2 is an important invasion-associated effector. SopE2 is encoded by the sopE2 gene which is present and conserved in pathogenic strains of Salmonella. SopE2 is highly homologous to SopE, a protein encoded by a gene within a temperate bacteriophage and present in only some pathogenic strains.

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The Energy Exascale Earth System Model (E3SM) is a new coupled Earth system model sponsored by the U.S Department of Energy. Here we present E3SM global simulations using active ocean and sea ice that are driven by the Coordinated Ocean‐ice Reference Experiments II (CORE‐II) interannual atmospheric forcing data set. The E3SM ocean and sea ice components are MPAS‐Ocean and MPAS‐Seaice, which use the Model for Prediction Across Scales (MPAS) framework and run on unstructured horizontal meshes. For this study, grid cells vary from 30 to 60 km for the low‐resolution mesh and 6 to 18 km at high resolution. The vertical grid is a structured z‐star coordinate and uses 60 and 80 layers for low and high resolution, respectively. The lower‐resolution simulation was run for five CORE cycles (310 years) with little drift in sea surface temperature (SST) or heat content. The meridional heat transport (MHT) is within observational range, while the meridional overturning circulation at 26.5°N is low compared to observations. The largest temperature biases occur in the Labrador Sea and western boundary currents (WBCs), and the mixed layer is deeper than observations at northern high latitudes in the winter months. In the Antarctic, maximum mixed layer depths (MLD) compare well with observations, but the spatial MLD pattern is shifted relative to observations. Sea ice extent, volume, and concentration agree well with observations. At high resolution, the sea surface height compares well with satellite observations in mean and variability.

The relative levels of invasiveness of two bovine isolates each of Salmonella typhimurium and Salmonella dublin and of invH mutants of S. typhimurium were determined in MDCK and Int 407 cultured-cell assays and in bovine ileal loops. S. dublin was found to be significantly less invasive in cultured cells than S. typhimurium, but this difference was not observed in bovine intestines. The invH mutants exhibited a significant reduction in invasion in both cultured cells and bovine intestines. The invasive phenotypes of the strains were confirmed by fluorescent microscopy and scanning and transmission electron microscopy. The wild-type strains were observed in the laminae propriae of the intestinal villi, while in contrast the invH mutants were generally associated with the enterocyte layer. The degree of damage in the bovine ileum was related to the magnitude of the invasion. There was no difference in the amount of S. typhimurium or S. dublin recovered from the bovine ileum either with or without Peyer's patches 3 h after inoculation of the loop.