Zoonotic orthopoxviruses encode a high-affinity antagonist of NKG2D

NK and T lymphocytes express both activating and inhibiting receptors for various members of the major histocompatibility complex class I superfamily (MHCISF). To evade immunologic cytotoxicity, many viruses interfere with the function of these receptors, generally by altering the displayed profile of MHCISF proteins on host cells. Using a structurally constrained hidden Markov model, we discovered an orthopoxvirus protein, itself distantly class I–like, that acts as a competitive antagonist of the NKG2D activating receptor. This orthopoxvirus MHC class I–like protein (OMCP) is conserved among cowpox and monkeypox viruses, secreted by infected cells, and bound with high affinity by NKG2D of rodents and humans (KD ∼ 30 and 0.2 nM, respectively). OMCP blocks recognition of host-encoded ligands and inhibits NKG2D-dependent killing by NK cells. This finding represents a novel mechanism for viral interference with NKG2D and sheds light on intercellular recognition events underlying innate immunity against emerging orthopoxviruses

Internal lee wave closures: Parameter sensitivity and comparison to observations

This is the final version. Available from AGU via the DOI in this recordThe SOFine and DIMES data analyzed in this paper can be obtained through the British Oceanographic Data Centre (BODC) by navigating the following links, respectively: http://archive.noc.ac.uk/SOFINE/and http://dimes.ucsd.edu/en/data/This paper examines two internal lee wave closures that have been used together with ocean models to predict the time‐averaged global energy conversion rate into lee waves and dissipation rate associated with lee waves and topographic blocking: the Garner (2005) scheme and the Bell (1975) theory. The closure predictions in two Southern Ocean regions where geostrophic flows dominate over tides are examined and compared to microstructure profiler observations of the turbulent kinetic energy dissipation rate, where the latter are assumed to reflect the dissipation associated with topographic blocking and generated lee wave energy. It is shown that when applied to these Southern Ocean regions, the two closures differ most in their treatment of topographic blocking. For several reasons, pointwise validation of the closures is not possible using existing observations, but horizontally averaged comparisons between closure predictions and observations are made. When anisotropy of the underlying topography is accounted for, the two horizontally averaged closure predictions near the seafloor are approximately equal. The dissipation associated with topographic blocking is predicted by the Garner (2005) scheme to account for the majority of the depth‐integrated dissipation over the bottom 1000 m of the water column, where the horizontally averaged predictions lie well within the spatial variability of the horizontally averaged observations. Simplifications made by the Garner (2005) scheme that are inappropriate for the oceanic context, together with imperfect observational information, can partially account for the prediction‐observation disagreement, particularly in the upper water column.D. S. Trossman and B. K. Arbic gratefully acknowledge support from National Science Foundation (NSF) grant OCE‐0960820 and Office of Naval Research (ONR) grant N00014‐11‐1‐0487. S. Waterman gratefully acknowledges support from the Australian Research Council (grants DE120102927 and CE110001028) and the National Science and Engineering Research Council of Canada (grant 22R23085)

On the formation, ventilation, and erosion of mode waters in the North Atlantic and Southern Oceans

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/94834/1/jgrc12564.pd

Internal lee wave closures : parameter sensitivity and comparison to observations

Author Posting. © American Geophysical Union, 2015. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 120 (2015): 7997–8019, doi:10.1002/2015JC010892.This paper examines two internal lee wave closures that have been used together with ocean models to predict the time-averaged global energy conversion rate into lee waves and dissipation rate associated with lee waves and topographic blocking: the Garner (2005) scheme and the Bell (1975) theory. The closure predictions in two Southern Ocean regions where geostrophic flows dominate over tides are examined and compared to microstructure profiler observations of the turbulent kinetic energy dissipation rate, where the latter are assumed to reflect the dissipation associated with topographic blocking and generated lee wave energy. It is shown that when applied to these Southern Ocean regions, the two closures differ most in their treatment of topographic blocking. For several reasons, pointwise validation of the closures is not possible using existing observations, but horizontally averaged comparisons between closure predictions and observations are made. When anisotropy of the underlying topography is accounted for, the two horizontally averaged closure predictions near the seafloor are approximately equal. The dissipation associated with topographic blocking is predicted by the Garner (2005) scheme to account for the majority of the depth-integrated dissipation over the bottom 1000 m of the water column, where the horizontally averaged predictions lie well within the spatial variability of the horizontally averaged observations. Simplifications made by the Garner (2005) scheme that are inappropriate for the oceanic context, together with imperfect observational information, can partially account for the prediction-observation disagreement, particularly in the upper water column.National Science Foundation Grant Number: OCE-0960820; Office of Naval Research (ONR) Grant Number: N00014-11-1-0487; Australian Research Council Grant Number: (DE120102927 and CE110001028); National Science and Engineering Research Council of Canada Grant Number: (22R23085)2016-06-1

Respiration Patterns in the Dark Ocean

In the dark ocean, respiring organisms are the main sink for dissolved oxygen. The respiration rate in a given seawater volume can be quantified through dissolved oxygen drawdown or organic matter consumption as a function of time. Estimates of dissolved oxygen utilization rates (OUR) abound in the literature, but are typically obtained using proxies of questionable accuracy, often with low vertical resolution, and neglecting key regions such as the Southern and Indian oceans. Respiration rates based on particulate (POC) or dissolved (DOC) organic carbon are also sparsely observed and for DOC are unavailable in many regions. Consequently, the relative contributions of POC or DOC as a respiration substrate in the dark ocean are unknown. Here, we use recent datasets of true oxygen utilization, seawater age, and DOC to derive OUR and DOC consumption-rate profiles in 10 oceanic regions. We demonstrate that although DOC and POC consumption rates are globally consistent with OUR, they underestimate OUR in the deep, suggesting strong oxygen utilization at the seafloor. In the abyss, we find a negative correlation of the DOC consumption rate with seawater age, suggesting that DOC reactivity decreases along the deep branch of the conveyor circulation. Our results highlight that benthic organisms are sensitive to perturbations in the surface production of organic matter and to large-scale circulation changes that affect its supply to the abyss

Ocean mass, sterodynamic effects, and vertical land motion largely explain US coast relative sea level rise

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Harvey, T., Hamlington, B. D., Frederikse, T., Nerem, R. S., Piecuch, C. G., Hammond, W. C., Blewitt, G., Thompson, P. R., Bekaert, D. P. S., Landerer, F. W., Reager, J. T., Kopp, R. E., Chandanpurkar, H., Fenty, I., Trossman, D. S., Walker, J. S., & Boening, C. W. Ocean mass, sterodynamic effects, and vertical land motion largely explain US coast relative sea level rise. Communications Earth & Environment, 2(1), (2021): 233, https://doi.org/10.1038/s43247-021-00300-w.Regional sea-level changes are caused by several physical processes that vary both in space and time. As a result of these processes, large regional departures from the long-term rate of global mean sea-level rise can occur. Identifying and understanding these processes at particular locations is the first step toward generating reliable projections and assisting in improved decision making. Here we quantify to what degree contemporary ocean mass change, sterodynamic effects, and vertical land motion influence sea-level rise observed by tide-gauge locations around the contiguous U.S. from 1993 to 2018. We are able to explain tide gauge-observed relative sea-level trends at 47 of 55 sampled locations. Locations where we cannot explain observed trends are potentially indicative of shortcomings in our coastal sea-level observational network or estimates of uncertainty.The research was carried out in part at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration. C.G.P. was supported by NASA grant 80NSSC20K1241. B.D.H., T.C.H., and T.F. were supported by NASA JPL Task 105393.281945.02.25.04.59. R.E.K. and J.S.W. were supported by U.S. National Aeronautics and Space Administration (grants 80NSSC17K0698, 80NSSC20K1724 and JPL task 105393.509496.02.08.13.31) and U.S. National Science Foundation (grant ICER-1663807). P.R.T. acknowledges financial support from the NOAA Global Ocean Monitoring and Observing program in support of the University of Hawaii Sea Level Center (NA11NMF4320128). The ECCO project is funded by the NASA Physical Oceanography; Modeling, Analysis, and Prediction; and Cryosphere Programs

Estimates of North Atlantic ventilation and mode water formation for winters 2002–06

Author Posting. © American Meteorological Society, 2009. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 39 (2009): 2600-2617, doi:10.1175/2009JPO3930.1.Lagrangian estimates for ventilation rates in the Gulf Stream Extension using Argo and World Ocean Circulation Experiment/Atlantic Climate and Circulation Experiment (WOCE/ACCE) float data, scatterometer (QuikSCAT) wind stress satellite observations, and altimetric [Archiving, Validation, and Interpretation of Satellite Oceanographic data (AVISO)] sea surface height (SSH) satellite observations from 2002 to 2006 are presented. Satellite winds and estimates of surface geostrophic currents allow the inclusion of the effects of currents on wind stress as well as their impact on the Ekman pumping. The presence of large surface geostrophic currents decreases the total Ekman pumping, contributing up to 20% where the Gulf Stream makes its two sharpest turns, and increases the total Ekman pumping by 10% or less everywhere else. The ageostrophic currents may be as large as 15% of the geostrophic currents, but only in proximity of the Gulf Stream. Using currents and mixed layer depths (MLDs) that are either climatological or vary from year to year, obducted water tends to originate along the Gulf Stream, while subducted water tends to originate to its south. However, using time-varying MLDs for each year, subduction varies significantly, sometimes oppositely from obduction. The 18° Water (EDW) subducts in different locations and is distributed differently each year but tends to be located in the Sargasso Sea. Vertical pumping is the only dominant factor in ventilation closer to the coast where MLDs are shallower and lighter parcels are subducted. Vertical pumping contributes up to 20% of the several hundreds of ventilated meters per year around the Gulf Stream and less elsewhere. Using a temperature- or density-based criterion for estimating the MLDs, especially along the coasts and north of 45°N, obduction estimates differ by up to 25%. The horizontal and temporal structure of the MLDs is the primary factor that controls the tens of sverdrups of ventilation (and a few sverdrups of EDW subduction)

Climate Process Team on internal wave–driven ocean mixing

Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Bulletin of the American Meteorological Society 98 (2017): 2429-2454, doi:10.1175/BAMS-D-16-0030.1.Diapycnal mixing plays a primary role in the thermodynamic balance of the ocean and, consequently, in oceanic heat and carbon uptake and storage. Though observed mixing rates are on average consistent with values required by inverse models, recent attention has focused on the dramatic spatial variability, spanning several orders of magnitude, of mixing rates in both the upper and deep ocean. Away from ocean boundaries, the spatiotemporal patterns of mixing are largely driven by the geography of generation, propagation, and dissipation of internal waves, which supply much of the power for turbulent mixing. Over the last 5 years and under the auspices of U.S. Climate Variability and Predictability Program (CLIVAR), a National Science Foundation (NSF)- and National Oceanic and Atmospheric Administration (NOAA)-supported Climate Process Team has been engaged in developing, implementing, and testing dynamics-based parameterizations for internal wave–driven turbulent mixing in global ocean models. The work has primarily focused on turbulence 1) near sites of internal tide generation, 2) in the upper ocean related to wind-generated near inertial motions, 3) due to internal lee waves generated by low-frequency mesoscale flows over topography, and 4) at ocean margins. Here, we review recent progress, describe the tools developed, and discuss future directions.We are grateful to U.S. CLIVAR for their leadership in instigating and facilitating the Climate Process Team program. We are indebted to NSF and NOAA for sponsoring the CPT series.2018-06-0

Climate Process Team On Internal Wave-Driven Ocean Mixing

The study summarizes recent advances in our understanding of internal wave–driven turbulent mixing in the ocean interior and introduces new parameterizations for global climate ocean models and their climate impacts