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  • Hindawi  (13,560)
  • American Meteorological Society
  • Leipzig : Akad. Verlagsges.
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  • 1
    Publication Date: 2020-11-18
    Description: A realistic representation of the North Atlantic tropical cyclone tracks is crucial as it allows, for example, explaining potential changes in U.S. landfalling systems. Here, the authors present a tentative study that examines the ability of recent climate models to represent North Atlantic tropical cyclone tracks. Tracks from two types of climate models are evaluated: explicit tracks are obtained from tropical cyclones simulated in regional or global climate models with moderate to high horizontal resolution (1°–0.25°), and downscaled tracks are obtained using a downscaling technique with large-scale environmental fields from a subset of these models. For both configurations, tracks are objectively separated into four groups using a cluster technique, leading to a zonal and a meridional separation of the tracks. The meridional separation largely captures the separation between deep tropical and subtropical, hybrid or baroclinic cyclones, while the zonal separation segregates Gulf of Mexico and Cape Verde storms. The properties of the tracks’ seasonality, intensity, and power dissipation index in each cluster are documented for both configurations. The authors’ results show that, except for the seasonality, the downscaled tracks better capture the observed characteristics of the clusters. The authors also use three different idealized scenarios to examine the possible future changes of tropical cyclone tracks under 1) warming sea surface temperature, 2) increasing carbon dioxide, and 3) a combination of the two. The response to each scenario is highly variable depending on the simulation considered. Finally, the authors examine the role of each cluster in these future changes and find no preponderant contribution of any single cluster over the others.
    Description: Published
    Description: 1333–1361
    Description: 4A. Clima e Oceani
    Description: JCR Journal
    Description: restricted
    Keywords: tropical cyclones ; atlantic basin ; 01. Atmosphere::01.01. Atmosphere::01.01.02. Climate
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 2
    Publication Date: 2021-06-22
    Description: This work explores the impact of orbital parameters and greenhouse gas concentrations on the climate of marine isotope stage (MIS) 7 glacial inception and compares it to that of MIS 5. The authors use a coupled atmosphere-ocean general circulation model to simulate the mean climate state of six time slices at 115, 122, 125, 229, 236, and 239 kyr, representative of a climate evolution from interglacial to glacial inception conditions. The simulations are designed to separate the effects of orbital parameters from those of greenhouse gas (GHG). Their results show that, in all the time slices considered, MIS 7 boreal lands mean annual climate is colder than the MIS 5 one. This difference is explained at 70% by the impact of the MIS 7 GHG. While the impact of GHG over Northern Hemisphere is homogeneous, the difference in temperature between MIS 7 and MIS 5 due to orbital parameters differs regionally and is linked with the Arctic Oscillation. The perennial snow cover is larger in all the MIS 7 experiments compared to MIS 5, as a result of MIS 7 orbital parameters, strengthened by GHG. At regional scale, Eurasia exhibits the strongest response to MIS 7 cold climate with a perennial snow area 3 times larger than in MIS 5 experiments. This suggests that MIS 7 glacial inception is more favorable over this area than over North America. Furthermore, at 239 kyr, the perennial snow covers an area equivalent to that of MIS 5 glacial inception (115 kyr). The authors suggest that MIS 7 glacial inception is more extensive than MIS 5 glacial inception over the high latitudes.
    Description: Italian Ministry of Education, University and Research Ministry for Environment, Land and Sea through the project GEMINA
    Description: Published
    Description: 8918-8933
    Description: 4A. Clima e Oceani
    Description: JCR Journal
    Description: open
    Keywords: Arctic Oscillation ; Teleconnections ; Greenhouse gases ; Glaciation ; Paleoclimate ; 02. Cryosphere::02.03. Ice cores::02.03.05. Paleoclimate
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
    Publication Date: 2016-10-06
    Description: Heavy precipitation is a major hazard over Europe. It is well established that climate model projections indicate a tendency towards more extreme daily rainfall events. It is still uncertain, however, how this changing intensity translates at the sub-daily time scales. The main goal of the present study is to examine possible differences in projected changes in intense precipitation events over Europe at the daily and sub-daily (3-hourly) time scales using a state-of-the-science climate model. The focus will be on one Representative Concentration Pathway (RCP 8.5), considered as illustrative of a high rate of increase in greenhouse gas concentrations over this century. There are statistically significant differences in intense precipitation projections (up to 40%) when comparing the results at the daily and sub-daily time scales. Over north-eastern Europe, projected precipitation intensification at the 3-hour scale is lower than at the daily scale. On the other hand, Spain and the western seaboard exhibit an opposite behaviour, with stronger intensification at the 3-hour scale rather than daily scale. While the mean properties of the precipitation distributions are independent of the analysed frequency, projected precipitation intensification exhibits regional differences. This finding has implications on the extrapolation of impacts of intense precipitation events, given the daily time scale the analyses are usually performed at.
    Description: Published
    Description: 6193–6203
    Description: 4A. Clima e Oceani
    Description: JCR Journal
    Description: restricted
    Keywords: rainfall ; extreme events ; heavy precipitation ; snow ; europe ; 01. Atmosphere::01.01. Atmosphere::01.01.02. Climate
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
    Publication Date: 2017-04-04
    Description: Climate model simulations are currently the main tool to provide information about possible future climates. Apart from scenario uncertainties and model error, internal variability is a major source of uncertainty, complicating predictions of future changes. Here, a suite of statistical tests is proposed to determine the shortest time window necessary to capture the internal precipitation variability in a stationary climate. The length of this shortest window thus expresses internal variability in terms of years. The method is applied globally to daily precipitation in a 200-yr preindustrial climate simulation with the CMCC-CM coupled general circulation model. The two-sample Cramér–von Mises test is used to assess differences in precipitation distribution, the Walker test accounts for multiple testing at grid cell level, and field significance is determined by calculating the Bejamini–Hochberg false-discovery rate. Results for the investigated simulation show that internal variability of daily precipitation is regionally and seasonally dependent and that regions requiring long time windows do not necessarily coincide with areas with large standard deviation. The estimated time scales are longer over sea than over land, in the tropics than in midlatitudes, and in the transitional seasons than in winter and summer. For many land grid cells, 30 seasons suffice to capture the internal variability of daily precipitation. There exist regions, however, where even 50 years do not suffice to sample the internal variability. The results show that diagnosing daily precipitation change at different times based on fixed global snapshots of one climate simulation might not be a robust detection method.
    Description: Published
    Description: 3624–3630
    Description: 4A. Clima e Oceani
    Description: JCR Journal
    Description: restricted
    Keywords: precipitation ; internal variability ; 01. Atmosphere::01.01. Atmosphere::01.01.02. Climate
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
    Publication Date: 2017-04-04
    Description: We acknowledge the World Climate Research Programme's Working Group on Coupled Modeling, which is responsible for CMIP, and we thank the climate modeling groups (listed in Table 1 of this paper) for producing and making available their model outputs. For CMIP the U.S. Department of Energy's Program for Climate Model Diagnosis and Intercomparison provides coordinating support and led development of software infrastructure in partnership with the Global Organization for Earth System Science Portals. The financial support of the Italian Ministry of Education, University and Research, and Ministry for Environment, Land and Sea through the project GEMINA and that of INDO-MARECLIM (Project 295092) is gratefully acknowledged. A. Cherchi thankfully acknowledges the generous hospitality of the International Pacific Research Center at UH Manoa, Honolulu. Jan Hafner is thanked for providing the moist static energy budget code used here and Matthew Windlansky is thanked for comments and proof reading. H. Annamalai acknowledges the partial support by the Office of Science (BER) U.S. Department of Energy, Grant DE-FG02-07ER6445, and also by the three institutional grants (JAMSTEC, NASA, NOAA) of the IPRC. Dr. Chen and an anonymous reviewer are acknowledged for the instructive and helpful comments given.
    Description: Dry summers over the eastern Mediterranean are characterized by strong descent anchored by long Rossby waves, which are forced by diabatic heating associated with summer monsoon rainfall over South Asia. The large-scale teleconnection between rising and subsiding air masses is referred to as the "monsoon-desert mechanism.'' This study evaluates the ability of the phase 5 of the Coupled Model Intercomparison Project (CMIP5) models in representing the physical processes involved in this mechanism. An evaluation of statistics between summer climatologies of monsoon diabatic heating and that of vertical velocity over the eastern Mediterranean suggests a linear relationship. Despite large spatial diversity in monsoon heating, descent over the Mediterranean is coherently located and realistic in intensity. To measure the sensitivity of descent to the diversity in the horizontal and vertical distribution of monsoon heating, a series of linear atmosphere model experiments are performed. It is shown that column-integrated heating over both the Bay of Bengal and the Arabian Sea provides the largest descent with a more realistic spatial pattern. In the vertical, CMIP5 models underestimate the diabatic heating at upper levels, while they overestimate it at lower levels, resulting in a weaker forced response and weaker associated descent over the Mediterranean. A moist static energy budget analysis applied to CMIP5 suggests that most models capture the dominant role of horizontal temperature advection and radiative fluxes in balancing descent over the Mediterranean. Based on the objective analysis herein, a subset of models is identified that captures the teleconnection for reasons consistent with observations. The recognized processes vary at interannual time scales as well, with imprints of severe weak/strong monsoons noticeable over the Mediterranean.
    Description: Italian Ministry of Education, University and Research Ministry for Environment, Land and Sea through the project GEMINA INDO-MARECLIM 295092 Office of Science (BER) U.S. Department of Energy DE-FG02-07ER6445 (JAMSTEC) of the IPRC (NASA) of the IPRC (NOAA) of the IPRC
    Description: Published
    Description: 6877-6903
    Description: 4A. Clima e Oceani
    Description: JCR Journal
    Description: open
    Keywords: Rossby waves ; Teleconnections ; Diabatic heating ; Coupled models ; Model evaluation/performance ; Interannual variability ; 03. Hydrosphere::03.01. General::03.01.03. Global climate models
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
    Publication Date: 2017-04-04
    Description: Optimally modeling background-error horizontal correlations is crucial in ocean data assimilation. This paper investigates the impact of releasing the assumption of uniform background-error correlations in a global ocean variational analysis system. Spatially varying horizontal correlations are introduced in the recursive filter operator, which is used for modeling horizontal covariances in the Centro Euro-Mediterraneo sui Cambiamenti Climatici (CMCC) analysis system. The horizontal correlation length scales (HCLSs) were defined on the full three-dimensional model space and computed from both a dataset of monthly anomalies with respect to the monthly climatology and through the so-called National Meteorological Center (NMC) method. Different formulas for estimating the correlation length scale are also discussed and applied to the two forecast error datasets. The new formulation is tested within a 12-yr period (2000–11) in the ½° resolution system. The comparison with the data assimilation system using uniform background-error horizontal correlations indicates the superiority of the former, especially in eddy-dominated areas. Verification skill scores report a significant reduction of RMSE, and the use of nonuniform length scales improves the representation of the eddy kinetic energy at midlatitudes, suggesting that uniform, latitude, or Rossby radius-dependent formulations are insufficient to represent the geographical variations of the background-error correlations. Furthermore, a small tuning of the globally uniform value of the length scale was found to have a small impact on the analysis system. The use of either anomalies or NMC-derived correlation length scales also has a marginal effect with respect to the use of nonuniform HCLSs. On the other hand, the application of overestimated length scales has proved to be detrimental to the analysis system in all areas and for all parameters.
    Description: This work has received funding from the Italian Ministry of Education, University and Research and the Italian Ministry for the Environment, Land and Sea under the GEMINA project and from the European Commission's Copernicus program, previously known as the GMES program, under the MyOcean and MyOcean2 projects.
    Description: Published
    Description: 2330-2349
    Description: 4A. Clima e Oceani
    Description: JCR Journal
    Description: open
    Keywords: DATA ASSIMILATION SCHEME ; TROPICAL PACIFIC-OCEAN ; PART I ; VARIATIONAL ASSIMILATION ; COVARIANCE FUNCTIONS ; DIFFUSION EQUATION ; SYSTEM ; TEMPERATURE ; IMPLEMENTATION ; MODEL ; 03. Hydrosphere::03.01. General::03.01.04. Ocean data assimilation and reanalysis
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 7
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    American Meteorological Society
    In:  EPIC3Journal of Atmospheric and Oceanic Technology, American Meteorological Society, 32, pp. 591-602
    Publication Date: 2015-06-19
    Description: Iron in the vicinity of compasses results in magnetic deviations. ADCPs mounted on steel buoyancy devices and deployed on seven moorings on the East Greenland outer shelf and upper slope from 2007 to 2008 suffered from severe magnetic deviations of $〉$90$^\circ$ rendering the ADCP data useless without a compass correction. The effects on the measured velocities, which may also be present in other oceanic velocity measurements, are explained. On each of the moorings, velocity measurements from a different instrument which was assumed not to be affected by magnetic deviation are overlapping in space and time with the compromised ones. A method is described to determine the magnetic compass deviation from the compromised and uncompromised velocity measurements and the compromised compass headings. The method depends on the assumption that at least one instrument per mooring is not compromised. With this method, the magnetic deviation as well as the originally compromised velocity records can be corrected. The method is described in detail and a MATLAB(R) script implementing the method is supplied. The success of the method is demonstrated for one of the moorings.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 8
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 Atmospheric and Oceanic Technology 32 (2015): 842–854, doi:10.1175/JTECH-D-14-00215.1.
    Description: The time and space variability of wave transformation through a tidal inlet is investigated with radar remote sensing. The frequency of wave breaking and the net wave breaking dissipation at high spatial resolution is estimated using image sequences acquired with a land-based X-band marine radar. Using the radar intensity data, transformed to normalized radar cross section σ0, the temporal and spatial distributions of wave breaking are identified using a threshold developed via the data probability density function. In addition, the inlet bathymetry is determined via depth inversion of the radar-derived frequencies and wavenumbers of the surface waves using a preexisting algorithm (cBathy). Wave height transformation is calculated through the 1D cross-shore energy flux equation incorporating the radar-estimated breaking distribution and bathymetry. The accuracy of the methodology is tested by comparison with in situ wave height observations over a 9-day period, obtaining correlation values R = 0.68 to 0.96, and root-mean-square errors from 0.05 to 0.19 m. Predicted wave forcing, computed as the along-inlet gradient of the cross-shore radiation stress was onshore during high-wave conditions, in good agreement (R = 0.95) with observations.
    Description: These data were collected as part of a joint field program, Data Assimilation and Remote Sensing for Littoral Applications (DARLA) and Rivers and Inlets (RIVET-1), both funded by the Office of Naval Research. The authors were funded through the Office of Naval Research Grant N00014-10-1-0932 and the Office of the Assistant Secretary of Defense for Research and Engineering.
    Description: 2015-10-01
    Keywords: Wave breaking ; Waves, oceanic ; Wind waves ; In situ oceanic observations ; Radars/Radar observations ; Remote sensing
    Repository Name: Woods Hole Open Access Server
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  • 9
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015): 2006–2024, doi:10.1175/JPO-D-14-0234.1.
    Description: The effects of wind-driven whitecapping on the evolution of the ocean surface boundary layer are examined using an idealized one-dimensional Reynolds-averaged Navier–Stokes numerical model. Whitecapping is parameterized as a flux of turbulent kinetic energy through the sea surface and through an adjustment of the turbulent length scale. Simulations begin with a two-layer configuration and use a wind that ramps to a steady stress. This study finds that the boundary layer begins to thicken sooner in simulations with whitecapping than without because whitecapping introduces energy to the base of the boundary layer sooner than shear production does. Even in the presence of whitecapping, shear production becomes important for several hours, but then inertial oscillations cause shear production and whitecapping to alternate as the dominant energy sources for mixing. Details of these results are sensitive to initial and forcing conditions, particularly to the turbulent length scale imposed by breaking waves and the transfer velocity of energy from waves to turbulence. After 1–2 days of steady wind, the boundary layer in whitecapping simulations has thickened more than the boundary layer in simulations without whitecapping by about 10%–50%, depending on the forcing and initial conditions.
    Description: We thank Skidmore College for financial and infrastructure support, and Skidmore and the National Science Foundation for funding travel to meetings where early versions of this work were presented. We also thank the National Science Foundation, Oregon State University, Jonathan Nash, and Joe Jurisa for funding and hosting a workshop on River Plume Mixing in October, 2013, where ideas and context for this paper were developed.
    Description: 2016-02-01
    Keywords: Circulation/ Dynamics ; Mixing ; Turbulence ; Wave breaking ; Wind stress ; Atm/Ocean Structure/ Phenomena ; Mixed layer
    Repository Name: Woods Hole Open Access Server
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  • 10
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 Climate 28 (2015): 8574–8584, doi:10.1175/JCLI-D-14-00809.1.
    Description: The subsurface ocean response to anthropogenic climate forcing remains poorly characterized. From the Coupled Model Intercomparison Project (CMIP), a robust response of the lower thermocline is identified, where the warming is considerably weaker in the subtropics than in the tropics and high latitudes. The lower thermocline change is inversely proportional to the thermocline depth in the present climatology. Ocean general circulation model (OGCM) experiments show that sea surface warming is the dominant forcing for the subtropical gyre change in contrast to natural variability for which wind dominates, and the ocean response is insensitive to the spatial pattern of surface warming. An analysis based on a ventilated thermocline model shows that the pattern of the lower thermocline change can be interpreted in terms of the dynamic response to the strengthened stratification and downward heat mixing. Consequently, the subtropical gyres become intensified at the surface but weakened in the lower thermcline, consistent with results from CMIP experiments.
    Description: The work was supported by the National Basic Research Program of China (2012CB955600), the National Natural Science Foundation of China (41125019, 41206021), and the U.S. National Science Foundation (AGS 1249145, 1305719).
    Description: 2016-05-01
    Keywords: Circulation/ Dynamics ; Ocean circulation ; Physical Meteorology and Climatology ; Climate change
    Repository Name: Woods Hole Open Access Server
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  • 11
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    American Meteorological Society
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015): 546–561, doi:10.1175/JPO-D-14-0082.1.
    Description: Model studies and observations in the Hudson River estuary indicate that frontogenesis occurs as a result of topographic forcing. Bottom fronts form just downstream of lateral constrictions, where the width of the estuary increases in the down-estuary (i.e., seaward) direction. The front forms during the last several hours of the ebb, when the combination of adverse pressure gradient in the expansion and baroclinicity cause a stagnation of near-bottom velocity. Frontogenesis is observed in two dynamical regimes: one in which the front develops at a transition from subcritical to supercritical flow and the other in which the flow is everywhere supercritical. The supercritical front formation appears to be associated with lateral flow separation. Both types of fronts are three-dimensional, with strong lateral gradients along the flanks of the channel. During spring tide conditions, the fronts dissipate during the flood, whereas during neap tides the fronts are advected landward during the flood. The zone of enhanced density gradient initiates frontogenesis at multiple constrictions along the estuary as it propagates landward more than 60 km during several days of neap tides. Frontogenesis and frontal propagation may thus be essential elements of the spring-to-neap transition to stratified conditions in partially mixed estuaries.
    Description: Support for this research was provided by NSF Grant OCE 0926427.
    Description: 2015-08-01
    Keywords: Circulation/ Dynamics ; Baroclinic flows ; Coastal flows ; Frontogenesis/frontolysis ; Fronts
    Repository Name: Woods Hole Open Access Server
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  • 12
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    American Meteorological Society
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015): 606–612, doi:10.1175/JPO-D-14-0221.1.
    Description: Mesoscale intrathermocline lenses are observed throughout the World Ocean and are commonly attributed to water mass anomalies advected from a distant origin. An alternative mechanism of local generation is offered herein, in which eddy–wind interaction can create lens-shaped disturbances in the thermocline. Numerical simulations illustrate how eddy–wind-driven upwelling in anticyclones can yield a convex lens reminiscent of a mode water eddy, whereas eddy–wind-driven downwelling in cyclones produces a concave lens that thins the mode water layer (a cyclonic “thinny”). Such transformations should be observable with long-term time series in the interiors of mesoscale eddies.
    Description: Support of this research by the National Science Foundation and National Aeronautics and Space Administration is gratefully acknowledged.
    Description: 2015-08-01
    Keywords: Circulation/ Dynamics ; Eddies ; Ekman pumping/transport ; Mesoscale processes ; Models and modeling ; Ocean models ; Primitive equations model
    Repository Name: Woods Hole Open Access Server
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  • 13
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 Climate 28 (2015): 1126–1147, doi:10.1175/JCLI-D-14-00285.1.
    Description: The local atmospheric response to a realistic shift of the Oyashio Extension SST front in the western North Pacific is analyzed using a high-resolution (HR; 0.25°) version of the global Community Atmosphere Model, version 5 (CAM5). A northward shift in the SST front causes an atmospheric response consisting of a weak surface wind anomaly but a strong vertical circulation extending throughout the troposphere. In the lower troposphere, most of the SST anomaly–induced diabatic heating is balanced by poleward transient eddy heat and moisture fluxes. Collectively, this response differs from the circulation suggested by linear dynamics, where extratropical SST forcing produces shallow anomalous heating balanced by strong equatorward cold air advection driven by an anomalous, stationary surface low to the east. This latter response, however, is obtained by repeating the same experiment except using a relatively low-resolution (LR; 1°) version of CAM5. Comparison to observations suggests that the HR response is closer to nature than the LR response. Strikingly, HR and LR experiments have almost identical vertical profiles of . However, diagnosis of the diabatic quasigeostrophic vertical pressure velocity (ω) budget reveals that HR has a substantially stronger response, which together with upper-level mean differential thermal advection balances stronger vertical motion. The results herein suggest that changes in transient eddy heat and moisture fluxes are critical to the overall local atmospheric response to Oyashio Front anomalies, which may consequently yield a stronger downstream response. These changes may require the high resolution to be fully reproduced, warranting further experiments of this type with other high-resolution atmosphere-only and fully coupled GCMs.
    Description: We gratefully acknowledge funding provided by NSF to DS and MN (AGS CLD 1035325) and Y-OK and CF (AGS CLD 1035423) and by DOE to Y-OK (DE-SC0007052).
    Description: 2015-08-01
    Keywords: Atmosphere-ocean interaction ; Atmospheric circulation ; Boundary layer ; Cyclogenesis/cyclolysis ; Diabatic heating ; Extratropical cyclones
    Repository Name: Woods Hole Open Access Server
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  • 14
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015): 966–987, doi:10.1175/JPO-D-14-0110.1.
    Description: A key remaining challenge in oceanography is the understanding and parameterization of small-scale mixing. Evidence suggests that topographic features play a significant role in enhancing mixing in the Southern Ocean. This study uses 914 high-resolution hydrographic profiles from novel EM-APEX profiling floats to investigate turbulent mixing north of the Kerguelen Plateau, a major topographic feature in the Southern Ocean. A shear–strain finescale parameterization is applied to estimate diapycnal diffusivity in the upper 1600 m of the ocean. The indirect estimates of mixing match direct microstructure profiler observations made simultaneously. It is found that mixing intensities have strong spatial and temporal variability, ranging from O(10−6) to O(10−3) m2 s−1. This study identifies topographic roughness, current speed, and wind speed as the main factors controlling mixing intensity. Additionally, the authors find strong regional variability in mixing dynamics and enhanced mixing in the Antarctic Circumpolar Current frontal region. This enhanced mixing is attributed to dissipating internal waves generated by the interaction of the Antarctic Circumpolar Current and the topography of the Kerguelen Plateau. Extending the mixing observations from the Kerguelen region to the entire Southern Ocean, this study infers a large water mass transformation rate of 17 Sverdrups (Sv; 1 Sv ≡ 106 m3 s−1) across the boundary of Antarctic Intermediate Water and Upper Circumpolar Deep Water in the Antarctic Circumpolar Current. This work suggests that the contribution of mixing to the Southern Ocean overturning circulation budget is particularly significant in fronts.
    Description: AM was supported by the joint CSIRO–University of Tasmania Quantitative Marine Science (QMS) program and the 2009 CSIRO Wealth from Ocean Flagship Collaborative Fund. BMS was supported by the Australian Climate Change Science Program, jointly funded by the Department of the Environment and CSIRO. KLPs salary support was provided by Woods Hole Oceanographic Institution bridge support funds.
    Description: 2015-10-01
    Keywords: Geographic location/entity ; Southern Ocean ; Circulation/ Dynamics ; Diapycnal mixing ; Fronts ; Ocean circulation ; Topographic effects ; Atm/Ocean Structure/ Phenomena ; Mixing
    Repository Name: Woods Hole Open Access Server
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  • 15
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015): 1610–1631, doi:10.1175/JPO-D-14-0047.1.
    Description: The use of a measure to diagnose submesoscale isopycnal diffusivity by determining the best match between observations of a tracer and simulations with varying small-scale diffusivities is tested. Specifically, the robustness of a “roughness” measure to discriminate between tracer fields experiencing different submesoscale isopycnal diffusivities and advected by scaled altimetric velocity fields is investigated. This measure is used to compare numerical simulations of the tracer released at a depth of about 1.5 km in the Pacific sector of the Southern Ocean during the Diapycnal and Isopycnal Mixing Experiment in the Southern Ocean (DIMES) field campaign with observations of the tracer taken on DIMES cruises. The authors find that simulations with an isopycnal diffusivity of ~20 m2 s−1 best match observations in the Pacific sector of the Antarctic Circumpolar Current (ACC), rising to ~20–50 m2 s−1 through Drake Passage, representing submesoscale processes and any mesoscale processes unresolved by the advecting altimetry fields. The roughness measure is demonstrated to be a statistically robust way to estimate a small-scale diffusivity when measurements are relatively sparse in space and time, although it does not work if there are too few measurements overall. The planning of tracer measurements during a cruise in order to maximize the robustness of the roughness measure is also considered. It is found that the robustness is increased if the spatial resolution of tracer measurements is increased with the time since tracer release.
    Description: We thank the U.K. Natural Environment Research Council and the U.S. National Science Foundation for funding the DIMES project.
    Description: 2015-12-01
    Keywords: Geographic location/entity ; Southern Ocean ; Circulation/ Dynamics ; Diffusion ; Physical Meteorology and Climatology ; Isopycnal mixing ; Observational techniques and algorithms ; Tracers ; Models and modeling ; Model comparison ; Tracers
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  • 16
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 the Atmospheric Sciences 72 (2015): 2786–2805, doi:10.1175/JAS-D-14-0257.1.
    Description: In Ammassalik, in southeast Greenland, downslope winds can reach hurricane intensity and represent a hazard for the local population and environment. They advect cold air down the ice sheet and over the Irminger Sea, where they drive large ocean–atmosphere heat fluxes over an important ocean convection region. Earlier studies have found them to be associated with a strong katabatic acceleration over the steep coastal slopes, flow convergence inside the valley of Ammassalik, and—in one instance—mountain wave breaking. Yet, for the general occurrence of strong downslope wind events, the importance of mesoscale processes is largely unknown. Here, two wind events—one weak and one strong—are simulated with the atmospheric Weather Research and Forecasting (WRF) Model with different model and topography resolutions, ranging from 1.67 to 60 km. For both events, but especially for the strong one, it is found that lower resolutions underestimate the wind speed because they misrepresent the steepness of the topography and do not account for the underlying wave dynamics. If a 5-km model instead of a 60-km model resolution in Ammassalik is used, the flow associated with the strong wind event is faster by up to 20 m s−1. The effects extend far downstream over the Irminger Sea, resulting in a diverging spatial distribution and temporal evolution of the heat fluxes. Local differences in the heat fluxes amount to 20%, with potential implications for ocean convection.
    Description: This study was supported by grants of the National Science Foundation (OCE- 0751554 and OCE-1130008) as well as the Natural Sciences and Engineering Research Council of Canada.
    Description: 2016-01-01
    Keywords: Katabatic winds ; Severe storms ; Air-sea interaction ; Mesoscale processes ; Orographic effects ; Model evaluation/performance
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  • 17
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 Climate 28 (2015): 6489–6502, doi:10.1175/JCLI-D-15-0143.1.
    Description: The global water cycle is predicted to intensify under various greenhouse gas emissions scenarios. Here the nature and strength of the expected changes for the ocean in the coming century are assessed by examining the output of several CMIP5 model runs for the periods 1990–2000 and 2090–2100 and comparing them to a dataset built from modern observations. Key elements of the water cycle, such as the atmospheric vapor transport, the evaporation minus precipitation over the ocean, and the surface salinity, show significant changes over the coming century. The intensification of the water cycle leads to increased salinity contrasts in the ocean, both within and between basins. Regional projections for several areas important to large-scale ocean circulation are presented, including the export of atmospheric moisture across the tropical Americas from Atlantic to Pacific Ocean, the freshwater gain of high-latitude deep water formation sites, and the basin averaged evaporation minus precipitation with implications for interbasin mass transports.
    Description: This research was supported by NASA Grant NNX12AF59GS03.
    Description: 2016-02-15
    Keywords: Climate change ; Climate prediction ; Hydrologic cycle ; Salinity ; Water budget ; Water vapor
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  • 18
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 Climate 28 (2015): 5885–5907, doi:10.1175/JCLI-D-14-00635.1.
    Description: The structure, variability, and regional connectivity of the Tokar Gap jet (TGJ) are described using WRF Model analyses and supporting atmospheric datasets from the East African–Red Sea–Arabian Peninsula (EARSAP) region during summer 2008. Sources of the TGJ’s unique quasi-diurnal nature and association with atypically high atmospheric moisture transport are traced back to larger-scale atmospheric dynamics influencing its forcing. These include seasonal shifts in the intertropical convergence zone (ITCZ), variability of the monsoon and North African wind regimes, and ties to other orographic flow patterns. Strong modulation of the TGJ by regional processes such as the desert heating cycle, wind convergence at the ITCZ surface front, and the local land–sea breeze cycle are described. Two case studies present the interplay of these influences in detail. The first of these was an “extreme” gap wind event on 12 July, in which horizontal velocities in the Tokar Gap exceeded 26 m s−1 and the flow from the jet extended the full width of the Red Sea basin. This event coincided with development of a large mesoscale convective complex (MCC) and precipitation at the entrance of the Tokar Gap as well as smaller gaps downstream along the Arabian Peninsula. More typical behavior of the TGJ during the 2008 summer is discussed using a second case study on 19 July. Downwind impact of the TGJ is evaluated using Lagrangian model trajectories and analysis of the lateral moisture fluxes (LMFs) during jet events. These results suggest means by which TGJ contributes to large LMFs and has potential bearing upon Sahelian rainfall and MCC development.
    Description: This work was supported by a grant from the King Abdullah University of Science and Technology (KAUST) as well as National Science Foundation Grant OCE0927017 and from DOD (MURI) Grant N000141110087, administered by the Office of Naval Research.
    Description: 2016-02-01
    Keywords: Africa ; Orographic effects ; Monsoons ; Atmosphere-land interaction ; Atmosphere-ocean interaction ; Hydrometeorology
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  • 19
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015): 2598–2620, doi:10.1175/JPO-D-14-0249.1.
    Description: Through combining analytical arguments and numerical models, this study investigates the finite-amplitude meanders of shelfbreak fronts characterized by sloping isopycnals outcropping at both the surface and the shelfbreak bottom. The objective is to provide a formula for the meander length scale that can explain observed frontal length scale variability and also be verified with observations. Considering the frontal instability to be a mixture of barotropic and baroclinic instability, the derived along-shelf meander length scale formula is [b1/(1 + a1S1/2)]NH/f, where N is the buoyancy frequency; H is the depth of the front; f is the Coriolis parameter; S is the Burger number measuring the ratio of energy conversion associated with barotropic and baroclinic instability; and a1 and b1 are empirical constants. Initial growth rate of the frontal instability is formulated as [b2(1 + a1S1/2)/(1 + a2αS1/2)]NH/L, where α is the bottom slope at the foot of the front, and a2 and b2 are empirical constants. The formulas are verified using numerical sensitivity simulations, and fitting of the simulated and formulated results gives a1 = 2.69, b1 = 14.65, a2 = 5.1 × 103, and b2 = 6.2 × 10−2. The numerical simulations also show development of fast-growing frontal symmetric instability when the minimum initial potential vorticity is negative. Although frontal symmetric instability leads to faster development of barotropic and baroclinic instability at later times, it does not significantly influence the meander length scale. The derived meander length scale provides a framework for future studies of the influences of external forces on shelfbreak frontal circulation and cross-frontal exchange.
    Description: WGZ and GGG were supported by the National Science Foundation through Grant OCE-1129125.
    Description: 2016-04-01
    Keywords: Circulation/ Dynamics ; Instability ; Ocean circulation ; Topographic effects ; Atm/Ocean Structure/ Phenomena ; Fronts ; Models and modeling ; Numerical analysis/modeling
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  • 20
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    American Meteorological Society
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015): 2820–2835, doi:10.1175/JPO-D-15-0101.1.
    Description: The response of a convective ocean basin to variations in atmospheric temperature is explored using numerical models and theory. The results indicate that the general behavior depends strongly on the frequency at which the atmosphere changes relative to the local response time to air–sea heat flux. For high-frequency forcing, the convective region in the basin interior is essentially one-dimensional and responds to the integrated local surface heat flux anomalies. For low-frequency forcing, eddy fluxes from the boundary current into the basin interior become important and act to suppress variability forced by the atmosphere. A theory is developed to quantify this time-dependent response and its influence on various oceanic quantities. The amplitude and phase of the temperature and salinity of the convective water mass, the meridional overturning circulation, the meridional heat flux, and the air–sea heat flux predicted by the theory compare well with that diagnosed from a series of numerical model calculations in both strongly eddying and weakly eddying regimes. Linearized analytic solutions provide direct estimates of each of these quantities and demonstrate their dependence on the nondimensional numbers that characterize the domain and atmospheric forcing. These results highlight the importance of mesoscale eddies in modulating the mean and time-dependent ocean response to atmospheric variability and provide a dynamical framework with which to connect ocean observations with changes in the atmosphere and surface heat flux.
    Description: This study was supported by the National Science Foundation under Grant OCE-1232389.
    Description: 2016-05-01
    Keywords: Circulation/ Dynamics ; Atmosphere-ocean interaction ; Deep convection ; Eddies ; Meridional overturning circulation
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  • 21
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2014. 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 Atmospheric and Oceanic Technology 31 (2014): 2844–2857, doi:10.1175/JTECH-D-14-00108.1.
    Description: A fiber optic–based spectrometry system was developed to enable automated, long-term measurements of spectral irradiance in sea ice environments. This system utilizes a single spectrometer module that measures the irradiance transmitted by multiple optical fibers, each coupled to the input fiber of the module via a mechanical rotary multiplexer. Small custom-printed optical diffusers, fixed to the input end of each fiber, allow these probes to be frozen into ice auger holes as small as 5 cm in diameter. Temperature-dependent biases in the spectrometer module and associated electronics were examined down to −40°C using an environmental chamber to identify any artifacts that might arise when operating these electronic and optical components below their vendor-defined lower temperature limits. The optical performance of the entire system was assessed by freezing multiple fiber probes in a 1.2-m-tall ice column, illuminating from above with a light source, and measuring spectral irradiance distributions at different depths within the ice column. Results indicated that the radiometric sensitivity of this fiber-based system is comparable to that of commercially available oceanographic spectroradiometers.
    Description: This research was supported by the Joint Initiative Awards Fund from the Andrew W. Mellon Foundation, through Woods Hole Oceanographic Institution’s internal Interdisciplinary Study Award program (S. R. L. and T. M.), and by a China scholarship council (CSC) scholarship and the Program for Zhejiang Leading Team of S&T Innovation (Grant 2010R50036) provided to H. W.
    Description: 2015-06-01
    Keywords: Sea ice ; In situ oceanic observations
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  • 22
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 Atmospheric and Oceanic Technology 32 (2015): 412–433, doi:10.1175/JTECH-D-14-00080.1.
    Description: A near-surface specific humidity (Qa) and air temperature (Ta) climatology on daily and 0.25° grids was constructed by the objectively analyzed air–sea fluxes (OAFlux) project by objectively merging two recent satellite-derived high-resolution analyses, the OAFlux existing 1° analysis, and atmospheric reanalyses. The two satellite products include the multi-instrument microwave regression (MIMR) Qa and Ta analysis and the Goddard Satellite-Based Surface Turbulent Fluxes, version 3 (GSSTF3), Qa analysis. This study assesses the degree of improvement made by OAFlux using buoy time series measurements at 137 locations and a global empirical orthogonal function (EOF) analysis. There are a total of 130 855 collocated daily values for Qa and 283 012 collocated daily values for Ta in the buoy evaluation. It is found that OAFlux Qa has a mean difference close to 0 and a root-mean-square (RMS) difference of 0.73 g kg−1, and Ta has a mean difference of −0.03°C and an RMS difference of 0.45°C. OAFlux shows no major systematic bias with respect to buoy measurements over all buoy locations except for the vicinity of the Gulf Stream boundary current, where the RMS difference exceeds 1.8°C in Ta and 1.2 g kg−1 in Qa. The buoy evaluation indicates that OAFlux represents an improvement over MIMR and GSSTF3. The global EOF-based intercomparison analysis indicates that OAFlux has a similar spatial–temporal variability pattern with that of three atmospheric reanalyses including MERRA, NCEP-1, and ERA-Interim, but that it differs from GSSTF3 and the Climate Forecast System Reanalysis (CFSR).
    Description: This study was supported by the NOAA Ocean Climate Observation (OCO) program under Grant NA09OAR4320129.
    Description: 2015-09-01
    Keywords: Data processing ; Databases ; In situ oceanic observations ; Satellite observations
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  • 23
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015):1189–1204, doi:10.1175/JPO-D-14-0122.1.
    Description: Winter outcropping of the Eighteen Degree Water (EDW) and its subsequent dispersion are studied using a ° eddy-resolving simulation of the Family of Linked Atlantic Modeling Experiments (FLAME). Outcropped EDW columns in the model simulations are detected in each winter from 1990 to 1999, and particles are deployed in the center of each outcropped EDW column. Subsequently, the trajectories of these particles are calculated for the following 5 yr. The particles slowly spread away from the outcropping region into the nonoutcropping/subducted EDW region south of ~30°N and eventually to the non-EDW region in the greater subtropical gyre. Approximately 30% of the particles are found in non-EDW waters 1 yr after deployment; after 5 yr, only 25% of the particles are found within EDW. The reoutcropping time is defined as the number of years between when a particle is originally deployed in an outcropping EDW column and when that particle is next found in an outcropping EDW column. Of the particles, 66% are found to reoutcrop as EDW in 1 yr, and less than 5% of the particles outcrop in each of the subsequent 4 yr. While the individual trajectories exhibit significant eddy-like motions, the time scale of reoutcropping is primarily set by the mean circulation. The dominance of reoutcropping in 1 yr suggests that EDW outcropping contributes considerably to the persistence of surface temperature anomalies from one winter to the next, that is, the reemergence of winter sea surface temperature anomalies.
    Description: We gratefully acknowledge the support from the NSF OCE Physical Oceanography program (NSF OCE-0961090 to Y-OK and J-JP; NSF OCE-0960776 to MSL and SFG; and NSF OCE-1242989 to Y-OK).
    Description: 2015-10-01
    Keywords: Circulation/ Dynamics ; Ocean circulation ; Atm/Ocean Structure/ Phenomena ; Water masses
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  • 24
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 Climate 28 (2015): 3004–3023, doi:10.1175/JCLI-D-14-00591.1.
    Description: Time series of surface meteorology and air–sea exchanges of heat, freshwater, and momentum collected from a long-term surface mooring located 1600 km west of the coast of northern Chile are analyzed. The observations, spanning 2000–10, have been withheld from assimilation into numerical weather prediction models. As such, they provide a unique in situ record of atmosphere–ocean coupling in a trade wind region characterized by persistent stratocumulus clouds. The annual cycle is described, as is the interannual variability. Annual variability in the air–sea heat flux is dominated by the annual cycle in net shortwave radiation. In austral summer, the ocean is heated; the 9-yr mean annual heating of the ocean is 38 W m−2. Ocean cooling is seen in 2006–08, coincident with La Niña events. Over the full record, significant trends were found. Increases in wind speed, wind stress, and latent heat flux over 9 yr were 0.8 m s−1, 0.022 N m−2, and 20 W m−2 or 13%, 29%, and 20% of the respective 9-yr means. The decrease in the annual mean net heat flux was 39 W m−2 or 104% of the mean. These changes were found to be largely associated with spring and fall. If this change persists, the annual mean net air–sea heat flux will change sign by 2016, when the magnitude of the wind stress will have increased by close to 60%.
    Description: This work is supported by the NOAA Climate Observation Division (NA09OAR4320129).
    Keywords: Climate variability ; Trends
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  • 25
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015): 1410–1425, doi:10.1175/JPO-D-14-0192.1.
    Description: The west-to-east crossover of boundary currents has been seen in mean circulation schemes from several past models of the Red Sea. This study investigates the mechanisms that produce and control the crossover in an idealized, eddy-resolving numerical model of the Red Sea. The authors also review the observational evidence and derive an analytical estimate for the crossover latitude. The surface buoyancy loss increases northward in the idealized model, and the resultant mean circulation consists of an anticyclonic gyre in the south and a cyclonic gyre in the north. In the midbasin, the northward surface flow crosses from the western boundary to the eastern boundary. Numerical experiments with different parameters indicate that the crossover latitude of the boundary currents changes with f0, β, and the meridional gradient of surface buoyancy forcing. In the analytical estimate, which is based on quasigeostrophic, β-plane dynamics, the crossover is predicted to lie at the latitude where the net potential vorticity advection (including an eddy component) is zero. Various terms in the potential vorticity budget can be estimated using a buoyancy budget, a thermal wind balance, and a parameterization of baroclinic instability.
    Description: This work is supported by Award USA 00002, KSA 00011, and KSA 00011/02 made by King Abdullah University of Science and Technology (KAUST), by National Science Foundation Grants OCE0927017, OCE1154641, and OCE85464100, and by the Woods Hole Oceanographic Institution Academic Program Office.
    Description: 2015-11-01
    Keywords: Circulation/ Dynamics ; Boundary currents ; Buoyancy ; Ocean circulation ; Ocean dynamics
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  • 26
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015): 1822–1842, doi:10.1175/JPO-D-14-0147.1.
    Description: Influences of time-dependent precipitation on water mass transformation and heat budgets in an idealized marginal sea are examined using theoretical and numerical models. The equations proposed by Spall in 2012 are extended to cases with time-dependent precipitation whose form is either a step function or a sinusoidal function. The theory predicts the differences in temperature and salinity between the convective water and the boundary current as well as the magnitudes of heat fluxes into the marginal sea and across the sea surface. Moreover, the theory reveals that there are three inherent time scales: relaxation time scales for temperature and salinity and a precipitation time scale. The relaxation time scales are determined by a steady solution of the theoretical model with steady precipitation. The relaxation time scale for temperature is always smaller than that for salinity as a result of not only the difference in the form of fluxes at the surface but also the variation in the eddy transport from the boundary current. These three time scales and the precipitation amplitude determine the strength of the ocean response to changes in precipitation and the phase relation between precipitation, changes in salinity and temperature, and changes in heat fluxes. It is demonstrated that the theoretical predictions agree qualitatively well with results from the eddy-resolving numerical model. This demonstrates the fundamental role of mesoscale eddies in the ocean response to time-dependent forcing and provides a framework with which to assess the extent to which observed variability in marginal sea convection and water mass transformation are consistent with an external forcing by variations in precipitation.
    Description: This work was initiated at the 2013 WHOI Geophysical Fluid Dynamics Summer Program, which was supported by the National Science Foundation and the Office of Naval Research. This work was also supported by Grant-in-Aid for Research Fellow (25·8466) of the Ministry of Education, Culture, Sports and Technology (MEXT), Japan, the Program for Leading Graduate Schools, MEXT, Japan (YY), and by the National Science Foundation Grant OCE-1232389 (MAS).
    Description: 2016-01-01
    Keywords: Circulation/ Dynamics ; Boundary currents ; Deep convection ; Eddies ; Ocean dynamics ; Atm/Ocean Structure/ Phenomena ; Precipitation
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  • 27
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015): 2806–2819, doi:10.1175/JPO-D-15-0061.1.
    Description: An eastward-flowing current of a homogeneous fluid with velocity U, contained in a channel of width L, impinges on an island of width of O(L), and the resulting interaction and dynamics are studied for values of the supercriticality parameter, b = βL2/U, both larger and smaller than π2. The former case is subcritical with respect to Rossby waves, and the latter is supercritical. The nature of the flow field depends strongly on b, and in particular, the nature of the flow around the island and the proportion of the flow passing to the north or south of the island are sensitive to b and to the position of the island in the channel. The problem is studied analytically in a relatively simple, nonlinear quasigeostrophic and adiabatic framework and numerically with a shallow-water model that allows a qualitative extension of the results to the equator. Although the issues involved are motivated by the interaction of the Equatorial Undercurrent and the Galapagos Islands, the analysis presented here focuses on the fundamental issue of the distinctive nature of the flow as a function of Rossby wave criticality.
    Description: Supported by the National Science Foundation Grant OCE-0959381.
    Description: 2016-05-01
    Keywords: Circulation/ Dynamics ; Ocean circulation ; Ocean dynamics ; Waves, oceanic
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  • 28
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015): 2773–2789, doi:10.1175/JPO-D-15-0031.1.
    Description: Tidal oscillatory salt transport, induced by the correlation between tidal variations in salinity and velocity, is an important term for the subtidal salt balance under the commonly used Eulerian method of salt transport decomposition. In this paper, its mechanisms in a partially stratified estuary are investigated with a numerical model of the Hudson estuary. During neap tides, when the estuary is strongly stratified, the tidal oscillatory salt transport is mainly due to the hydraulic response of the halocline to the longitudinal variation of topography. This mechanism does not involve vertical mixing, so it should not be regarded as oscillatory shear dispersion, but instead it should be regarded as advective transport of salt, which results from the vertical distortion of exchange flow obtained in the Eulerian decomposition by vertical fluctuations of the halocline. During spring tides, the estuary is weakly stratified, and vertical mixing plays a significant role in the tidal variation of salinity. In the spring tide regime, the tidal oscillatory salt transport is mainly due to oscillatory shear dispersion. In addition, the transient lateral circulation near large channel curvature causes the transverse tilt of the halocline. This mechanism has little effect on the cross-sectionally integrated tidal oscillatory salt transport, but it results in an apparent left–right cross-channel asymmetry of tidal oscillatory salt transport. With the isohaline framework, tidal oscillatory salt transport can be regarded as a part of the net estuarine salt transport, and the Lagrangian advective mechanism and dispersive mechanism can be distinguished.
    Description: Tao Wang was supported by the Open Research Fund of State Key Laboratory of Estuarine and Coastal Research (Grant SKLEC-KF201509) and Chinese Scholarship Council. Geyer was supported by by NSF Grant OCE 0926427. Wensheng Jiang was supported by NSFC-Shandong Joint Fund for Marine Science Research Centers (Grant U1406401).
    Description: 2016-05-01
    Keywords: Geographic location/entity ; Estuaries ; Circulation/ Dynamics ; Baroclinic flows ; Dispersion ; Shear structure/flows ; Atm/Ocean Structure/ Phenomena ; Diapycnal mixing ; Models and modeling ; Regional models
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  • 29
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2014. 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 44 (2014): 3033–3053, doi:10.1175/JPO-D-13-0227.1.
    Description: The East Greenland Current (EGC) had long been considered the main pathway for the Denmark Strait overflow (DSO). Recent observations, however, indicate that the north Icelandic jet (NIJ), which flows westward along the north coast of Iceland, is a major separate pathway for the DSO. In this study a two-layer numerical model and complementary integral constraints are used to examine various pathways that lead to the DSO and to explore plausible mechanisms for the NIJ’s existence. In these simulations, a westward and NIJ-like current emerges as a robust feature and a main pathway for the Denmark Strait overflow. Its existence can be explained through circulation integrals around advantageous contours. One such constraint spells out the consequences of overflow water as a source of low potential vorticity. A stronger constraint can be added when the outflow occurs through two outlets: it takes the form of a circulation integral around the Iceland–Faroe Ridge. In either case, the direction of overall circulation about the contour can be deduced from the required frictional torques. Some effects of wind stress forcing are also examined. The overall positive curl of the wind forces cyclonic gyres in both layers, enhancing the East Greenland Current. The wind stress forcing weakens but does not eliminate the NIJ. It also modifies the sign of the deep circulation in various subbasins and alters the path by which overflow water is brought to the Faroe Bank Channel, all in ways that bring the idealized model more in line with observations. The sequence of numerical experiments separates the effects of wind and buoyancy forcing and shows how each is important.
    Description: This study has been supported by National Science Foundation (OCE0927017 and ARC1107412).
    Description: 2015-06-01
    Keywords: Circulation/ Dynamics ; Boundary currents ; Channel flows ; Meridional overturning circulation ; Ocean circulation ; Topographic effects
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  • 30
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015): 1356–1375, doi:10.1175/JPO-D-13-0259.1.
    Description: Eddy–mean flow interactions along the Kuroshio Extension (KE) jet are investigated using a vorticity budget of a high-resolution ocean model simulation, averaged over a 13-yr period. The simulation explicitly resolves mesoscale eddies in the KE and is forced with air–sea fluxes representing the years 1995–2007. A mean-eddy decomposition in a jet-following coordinate system removes the variability of the jet path from the eddy components of velocity; thus, eddy kinetic energy in the jet reference frame is substantially lower than in geographic coordinates and exhibits a cross-jet asymmetry that is consistent with the baroclinic instability criterion of the long-term mean field. The vorticity budget is computed in both geographic (i.e., Eulerian) and jet reference frames; the jet frame budget reveals several patterns of eddy forcing that are largely attributed to varicose modes of variability. Eddies tend to diffuse the relative vorticity minima/maxima that flank the jet, removing momentum from the fast-moving jet core and reinforcing the quasi-permanent meridional meanders in the mean jet. A pattern associated with the vertical stretching of relative vorticity in eddies indicates a deceleration (acceleration) of the jet coincident with northward (southward) quasi-permanent meanders. Eddy relative vorticity advection outside of the eastward jet core is balanced mostly by vertical stretching of the mean flow, which through baroclinic adjustment helps to drive the flanking recirculation gyres. The jet frame vorticity budget presents a well-defined picture of eddy activity, illustrating along-jet variations in eddy–mean flow interaction that may have implications for the jet’s dynamics and cross-frontal tracer fluxes.
    Description: A. S. Delman (ASD) and J. L. McClean (JLM) were supported by NSF Grant OCE-0850463 and Office of Science (BER), U.S. Department of Energy, Grant DE-FG02-05ER64119. ASD and J. Sprintall were also supported by a NASA Earth and Space Science Fellowship (NESSF), Grant NNX13AM93H. JLM was also supported by U.S. DOE Office of Science grant entitled “Ultra-High Resolution Global Climate Simulation” via a Los Alamos National Laboratory subcontract. S. R. Jayne was supported by NSF Grant OCE-0849808. Computational resources for the model run were provided by NSF Resource Grants TG-OCE110013 and TG-OCE130010.
    Description: 2015-11-01
    Keywords: Geographic location/entity ; North Pacific Ocean ; Circulation/ Dynamics ; Forcing ; Instability ; Mesoscale processes ; Atm/Ocean Structure/ Phenomena ; Jets ; Models and modeling ; General circulation models
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  • 31
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 Atmospheric and Oceanic Technology 32 (2015): 1042–1057, doi:10.1175/JTECH-D-14-00161.1.
    Description: A 1-yr experiment using a pressure-sensor-equipped inverted echo sounder (PIES) was conducted in Sermilik Fjord in southeastern Greenland (66°N, 38°E) from August 2011 to September 2012. Based on these high-latitude data, the interpretation of PIESs’ acoustic travel-time records from regions that are periodically ice covered were refined. In addition, new methods using PIESs for detecting icebergs and sea ice and for estimating iceberg drafts and drift speeds were developed and tested. During winter months, the PIES in Sermilik Fjord logged about 300 iceberg detections and recorded a 2-week period in early March of land-fast ice cover over the instrument site, consistent with satellite synthetic aperture radar (SAR) imagery. The deepest icebergs in the fjord were found to have keel depths greater than approximately 350 m. Average and maximum iceberg speeds were approximately 0.2 and 0.5 m s−1, respectively. The maximum tidal range at the site was ±1.8 m and during neap tides the range was ±0.3 m, as shown by the PIES’s pressure record.
    Description: This work was supported by the National Science Foundation through the Divisions of Ocean Science and Polar Programs under Grant PLR-1332911. A. Silvano was supported as a WHOI guest student through a Gori Fellowship.
    Keywords: Glaciers ; Sea ice ; Ice thickness ; Data processing ; In situ oceanic observations ; Instrumentation/sensors
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  • 32
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015): 1735–1756, doi:10.1175/JPO-D-14-0238.1.
    Description: The Lofoten basin of the Nordic Seas is recognized as a crucial component of the meridional overturning circulation in the North Atlantic because of the large horizontal extent of Atlantic Water and winter surface buoyancy loss. In this study, hydrographic and current measurements collected from a mooring deployed in the Lofoten basin from July 2010 to September 2012 are used to describe water mass transformation and the mesoscale eddy field. Winter mixed layer depths (MLDs) are observed to reach approximately 400 m, with larger MLDs and denser properties resulting from the colder 2010 winter. A heat budget of the upper water column requires lateral input, which balances the net annual heat loss of ~80 W m−2. The lateral flux is a result of mesoscale eddies, which dominate the velocity variability. Eddy velocities are enhanced in the upper 1000 m, with a barotropic component that reaches the bottom. Detailed examination of two eddies, from April and August 2012, highlights the variability of the eddy field and eddy properties. Temperature and salinity properties of the April eddy suggest that it originated from the slope current but was ventilated by surface fluxes. The properties within the eddy were similar to those of the mode water, indicating that convection within the eddies may make an important contribution to water mass transformation. A rough estimate of eddy flux per unit boundary current length suggests that fluxes in the Lofoten basin are larger than in the Labrador Sea because of the enhanced boundary current–interior density difference.
    Description: The work was supported by NSF OCE 0850416.
    Description: 2015-12-01
    Keywords: Circulation/ Dynamics ; Atmosphere-ocean interaction ; Boundary currents ; Eddies ; Fluxes ; Mesoscale processes ; Atm/Ocean Structure/ Phenomena ; Thermohaline circulation
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  • 33
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 Climate 28 (2015): 4653–4687, doi:10.1175/JCLI-D-13-00326.1.
    Description: Downscaled climate model projections from phase 5 of the Coupled Model Intercomparison Project (CMIP5) were used to force a dynamic vegetation agricultural model (Agro-IBIS) and simulate yield responses to historical climate and two future emissions scenarios for maize in the U.S. Midwest and wheat in southeastern Australia. In addition to mean changes in yield, the frequency of high- and low-yield years was related to changing local hydroclimatic conditions. Particular emphasis was on the seasonal cycle of climatic variables during extreme-yield years and links to crop growth. While historically high (low) yields in Iowa tend to occur during years with anomalous wet (dry) growing season, this is exacerbated in the future. By the end of the twenty-first century, the multimodel mean (MMM) of growing season temperatures in Iowa is projected to increase by more than 5°C, and maize yield is projected to decrease by 18%. For southeastern Australia, the frequency of low-yield years rises dramatically in the twenty-first century because of significant projected drying during the growing season. By the late twenty-first century, MMM growing season precipitation in southeastern Australia is projected to decrease by 15%, temperatures are projected to increase by 2.8°–4.5°C, and wheat yields are projected to decline by 70%. Results highlight the sensitivity of yield projections to the nature of hydroclimatic changes. Where future changes are uncertain, the sign of the yield change simulated by Agro-IBIS is uncertain as well. In contrast, broad agreement in projected drying over southern Australia across models is reflected in consistent yield decreases for the twenty-first century. Climatic changes of the order projected can be expected to pose serious challenges for continued staple grain production in some current centers of production, especially in marginal areas.
    Description: This work was initiated at the Dissertations Initiative for the Advancement of Climate Change Research (DISCCRS) V Symposium, supported by the U.S. National Science Foundation through collaborative Grants SES-0932916 and SES-0931402. CCU was supported by a University of New South Wales Vice-Chancellor Fellowship and the Penzance Endowed Fund and John P. Chase Memorial Endowed Fund at WHOI. TET was supported by the U.S. Department of Energy Award DE-EE0004397. NC was funded by NSF Grant EAR-1204774. We are indebted to the FORMAS-funded Land Use Today and Tomorrow (LUsTT) project (Grant 211-2009-1682) for financial support.
    Keywords: Australia ; North America ; Climate change ; Climate models ; Climate variability ; Agriculture
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  • 34
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 96 (2015): 921–938, doi:10.1175/BAMS-D-13-00117.1.
    Description: El Niño–Southern Oscillation (ENSO) is a naturally occurring mode of tropical Pacific variability, with global impacts on society and natural ecosystems. While it has long been known that El Niño events display a diverse range of amplitudes, triggers, spatial patterns, and life cycles, the realization that ENSO’s impacts can be highly sensitive to this event-to-event diversity is driving a renewed interest in the subject. This paper surveys our current state of knowledge of ENSO diversity, identifies key gaps in understanding, and outlines some promising future research directions.
    Description: AC acknowledges support from the National Science Foundation for this study.
    Description: 2015-12-01
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  • 35
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015): 2381–2406, doi:10.1175/JPO-D-14-0086.1.
    Description: While near-inertial waves are known to be generated by atmospheric storms, recent observations in the Kuroshio Front find intense near-inertial internal-wave shear along sloping isopycnals, even during calm weather. Recent literature suggests that spontaneous generation of near-inertial waves by frontal instabilities could represent a major sink for the subinertial quasigeostrophic circulation. An unforced three-dimensional 1-km-resolution model, initialized with the observed cross-Kuroshio structure, is used to explore this mechanism. After several weeks, the model exhibits growth of 10–100-km-scale frontal meanders, accompanied by O(10) mW m−2 spontaneous generation of near-inertial waves associated with readjustment of submesoscale fronts forced out of balance by mesoscale confluent flows. These waves have properties resembling those in the observations. However, they are reabsorbed into the model Kuroshio Front with no more than 15% dissipating or radiating away. Thus, spontaneous generation of near-inertial waves represents a redistribution of quasigeostrophic energy rather than a significant sink.
    Description: “The Study of Kuroshio Ecosystem Dynamics for Sustainable Fisheries (SKED)” supported by MEXT, MIT-Hayashi Seed Fund, ONR (Awards N000140910196 and N000141210101), NSF (Award OCE 0928617, 0928138) for support.
    Description: 2016-03-01
    Keywords: Circulation/ Dynamics ; Frontogenesis/frontolysis ; Fronts ; Internal waves ; Turbulence ; Upwelling/downwelling ; Atm/Ocean Structure/ Phenomena ; Jets
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  • 36
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 Climate 28 (2015): 7659–7677, doi:10.1175/JCLI-D-15-0007.1.
    Description: Maximum covariance analysis of a preindustrial control simulation of the NCAR Community Climate System Model, version 4 (CCSM4), shows that a barotropic signal in winter broadly resembling a negative phase of the North Atlantic Oscillation (NAO) follows an intensification of the Atlantic meridional overturning circulation (AMOC) by about 7 yr. The delay is due to the cyclonic propagation along the North Atlantic Current (NAC) and the subpolar gyre of a SST warming linked to a northward shift and intensification of the NAC, together with an increasing SST cooling linked to increasing southward advection of subpolar water along the western boundary and a southward shift of the Gulf Stream (GS). These changes result in a meridional SST dipole, which follows the AMOC intensification after 6 or 7 yr. The SST changes were initiated by the strengthening of the western subpolar gyre and by bottom torque at the crossover of the deep branches of the AMOC with the NAC on the western flank of the Mid-Atlantic Ridge and the GS near the Tail of the Grand Banks, respectively. The heat flux damping of the SST dipole shifts the region of maximum atmospheric transient eddy growth southward, leading to a negative NAO-like response. No significant atmospheric response is found to the Atlantic multidecadal oscillation (AMO), which is broadly realistic but shifted south and associated with a much weaker meridional SST gradient than the AMOC fingerprint. Nonetheless, the wintertime atmospheric response to the AMOC shows some similarity with the observed response to the AMO, suggesting that the ocean–atmosphere interactions are broadly realistic in CCSM4.
    Description: Support from the NOAA Climate Program Office (NA10OAR4310202 and NA13OAR4310139), NSF EaSM2 (OCE 1242989) and the European Community 7th framework programme (FP7 2007-2013) under Grant Agreement 308299 (NACLIM) is gratefully acknowledged. The analysis benefited from the IPSL Prodiguer-Ciclad facility, which is supported by CNRS, UPMC, Labex L-IPSL funded by the ANR (Grant ANR-10-LABX-0018) and by the European FP7 IS-ENES2 project (Grant 312979).
    Description: 2016-04-01
    Keywords: Meridional overturning circulation ; North Atlantic Oscillation ; Climate models ; Climate variability
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  • 37
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 Atmospheric and Oceanic Technology 32 (2015): 1945–1959, doi:10.1175/JTECH-D-14-00222.1.
    Description: Observations of waves and setup on a steep, sandy beach are used to identify and assess potential applications of spatially dense lidar measurements for studying inner-surf and swash-zone hydrodynamics. There is good agreement between lidar- and pressure-based estimates of water levels (r2 = 0.98, rmse = 0.05 m), setup (r2 = 0.92, rmse = 0.03 m), infragravity wave heights (r2 = 0.91, rmse = 0.03 m), swell–sea wave heights (r2 = 0.87, rmse = 0.07 m), and energy density spectra. Lidar observations did not degrade with range (up to 65 m offshore of the lidar) when there was sufficient foam present on the water surface to generate returns, suggesting that for narrow-beam 1550-nm light, spatially varying spot size, grazing angle affects, and linear interpolation (to estimate the water surface over areas without returns) are not large sources of error. Consistent with prior studies, the lidar and pressure observations indicate that standing infragravity waves dominate inner-surf and swash energy at low frequencies and progressive swell–sea waves dominate at higher frequencies. The spatially dense lidar measurements enable estimates of reflection coefficients from pairs of locations at a range of spatial lags (thus spanning a wide range of frequencies or wavelengths). Reflection is high at low frequencies, increases with beach slope, and decreases with increasing offshore wave height, consistent with prior studies. Lidar data also indicate that wave asymmetry increases rapidly across the inner surf and swash. The comparisons with pressure measurements and with theory demonstrate that lidar measures inner-surf waves and setup accurately, and can be used for studies of inner-surf and swash-zone hydrodynamics.
    Description: Funding was provided by the USACE Coastal Field Data Collection (CFDC) and Coastal Ocean Data Systems (CODS) programs, the Office of Naval Research, the National Science Foundation, and the Assistant Secretary of Defense (R&E).
    Description: 2016-04-01
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  • 38
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015): 2497–2521, doi:10.1175/JPO-D-14-0128.1.
    Description: Oceanic density overturns are commonly used to parameterize the dissipation rate of turbulent kinetic energy. This method assumes a linear scaling between the Thorpe length scale LT and the Ozmidov length scale LO. Historic evidence supporting LT ~ LO has been shown for relatively weak shear-driven turbulence of the thermocline; however, little support for the method exists in regions of turbulence driven by the convective collapse of topographically influenced overturns that are large by open-ocean standards. This study presents a direct comparison of LT and LO, using vertical profiles of temperature and microstructure shear collected in the Luzon Strait—a site characterized by topographically influenced overturns up to O(100) m in scale. The comparison is also done for open-ocean sites in the Brazil basin and North Atlantic where overturns are generally smaller and due to different processes. A key result is that LT/LO increases with overturn size in a fashion similar to that observed in numerical studies of Kelvin–Helmholtz (K–H) instabilities for all sites but is most clear in data from the Luzon Strait. Resultant bias in parameterized dissipation is mitigated by ensemble averaging; however, a positive bias appears when instantaneous observations are depth and time integrated. For a series of profiles taken during a spring tidal period in the Luzon Strait, the integrated value is nearly an order of magnitude larger than that based on the microstructure observations. Physical arguments supporting LT ~ LO are revisited, and conceptual regimes explaining the relationship between LT/LO and a nondimensional overturn size are proposed. In a companion paper, Scotti obtains similar conclusions from energetics arguments and simulations.
    Description: B.D.M. and S.K.V. gratefully acknowledge the support of the Office of Naval Research under Grants N00014-12-1-0279, N00014-12-1-0282, and N00014-12-1-0938 (Program Manager: Dr. Terri Paluszkiewicz). S.K.V. also acknowledges support of the National Science Foundation under Grant OCE-1151838. L.S.L. acknowledges support for BBTRE by the National Science Foundation by Contract OCE94-15589 and NATRE and IWISE by the Office of Naval Research by Contracts N00014-92-1323 and N00014-10-10315. J.N.M. was supported through Grant 1256620 from the National Science Foundation and the Office of Naval Research (IWISE Project).
    Description: 2016-04-01
    Keywords: Circulation/ Dynamics ; Diapycnal mixing ; Small scale processes ; Turbulence ; Atm/Ocean Structure/ Phenomena ; Mixing ; Observational techniques and algorithms ; Profilers, oceanic ; Models and modeling ; Parameterization
    Repository Name: Woods Hole Open Access Server
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  • 39
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015): 2621–2639, doi:10.1175/JPO-D-14-0239.1.
    Description: Measurements made as part of a large-scale experiment to examine wind-driven circulation and mixing in Chesapeake Bay demonstrate that circulations consistent with Langmuir circulation play an important role in surface boundary layer dynamics. Under conditions when the turbulent Langmuir number Lat is low (〈0.5), the surface mixed layer is characterized by 1) elevated vertical turbulent kinetic energy; 2) decreased anisotropy; 3) negative vertical velocity skewness indicative of strong/narrow downwelling and weak/broad upwelling; and 4) strong negative correlations between low-frequency vertical velocity and the velocity in the direction of wave propagation. These characteristics appear to be primarily the result of the vortex force associated with the surface wave field, but convection driven by a destabilizing heat flux is observed and appears to contribute significantly to the observed negative vertical velocity skewness. Conditions that favor convection usually also have strong Langmuir forcing, and these two processes probably both contribute to the surface mixed layer turbulence. Conditions in which traditional stress-driven turbulence is important are limited in this dataset. Unlike other shallow coastal systems where full water column Langmuir circulation has been observed, the salinity stratification in Chesapeake Bay is nearly always strong enough to prevent full-depth circulation from developing.
    Description: The funding for this research was provided by the National Science Foundation Grants OCE-1339032 and OCE-1338518.
    Description: 2016-04-01
    Keywords: Circulation/ Dynamics ; Convection ; Instability ; Mixing ; Turbulence ; Wave breaking ; Wind stress
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  • 40
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    American Meteorological Society
    In:  EPIC3Monthly Weather Review, American Meteorological Society, 143, pp. 1554-1567, ISSN: 0027-0644
    Publication Date: 2019-07-17
    Description: Ensemble square root filters can either assimilate all observations that are available at a given time at once, or assimilate the observations in batches or one at a time. For large-scale models, the filters are typically applied with a localized analysis step. This study demonstrates that the interaction of serial observation processing and localization can destabilize the analysis process and examines under which conditions the instability becomes significant. The instability results from a repeated inconsistent update of the state error covariance matrix that is caused by the localization. The inconsistency is present in all ensemble Kalman filters, except the classical ensemble Kalman filter with perturbed observations. With serial observation processing, its effect is small in cases when the assimilation changes the ensemble of model states only slightly. However, when the assimilation has a strong effect on the state estimates, the interaction of localization and serial observation processing can significantly deteriorate the filter performance. In realistic large-scale applications, when the assimilation changes the states only slightly and when the distribution of the observations is irregular and changing over time, the instability is likely not significant.
    Repository Name: EPIC Alfred Wegener Institut
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  • 41
    Publication Date: 2021-11-09
    Description: Ensembles of retrospective 2-month dynamical forecasts initiated on 1May are used to predict the onset of the Indian summer monsoon (ISM) for the period 1989–2005. The subseasonal predictions (SSPs) are based on a coupled general circulation model and recently they have been upgraded by the realistic initialization of the atmosphere with initial conditions taken from reanalysis. Two objective large-scale methods based on dynamical circulation and hydrological indices are applied to detect the ISM onset. The SSPs show some skill in forecasting earlier-than-normal ISM onsets, while they have difficulty in predicting late onsets. It is shown that significant contribution to the skill in forecasting early ISM onsets comes from the newly developed initialization of the atmosphere from reanalysis. On one hand, atmospheric initialization produces a better representation of the atmospheric mean state in the initial conditions, leading to a systematically improved monsoon onset sequence. On the other hand, the initialization of the atmosphere allows some skill in forecasting the northward propagating intraseasonal wind and precipitation anomalies over the tropical Indian Ocean. The northward propagating intraseasonal modes trigger the monsoon in some early-onset years. The realistic phase initialization of these modes improves the forecasts of the associated earlier-than-normal monsoon onsets. The prediction of late onsets is not noticeably improved by the initialization of the atmosphere. It is suggested that late onsets of the monsoon are too far away from the start date of the forecasts to conserve enough memory of the intraseasonal oscillation (ISO) anomalies and of the improved representation of the mean state in the initial conditions.
    Description: Published
    Description: 778-793
    Description: 4A. Clima e Oceani
    Description: JCR Journal
    Description: restricted
    Keywords: indian summer monsoon ; onset ; seasonal predictions ; 01. Atmosphere::01.01. Atmosphere::01.01.02. Climate ; 01. Atmosphere::01.01. Atmosphere::01.01.04. Processes and Dynamics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 42
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Monthly Weather Review 143 (2015): 195–211, doi:10.1175/MWR-D-14-00051.1.
    Description: Lagrangian measurements from passive ocean instruments provide a useful source of data for estimating and forecasting the ocean’s state (velocity field, salinity field, etc.). However, trajectories from these instruments are often highly nonlinear, leading to difficulties with widely used data assimilation algorithms such as the ensemble Kalman filter (EnKF). Additionally, the velocity field is often modeled as a high-dimensional variable, which precludes the use of more accurate methods such as the particle filter (PF). Here, a hybrid particle–ensemble Kalman filter is developed that applies the EnKF update to the potentially high-dimensional velocity variables, and the PF update to the relatively low-dimensional, highly nonlinear drifter position variable. This algorithm is tested with twin experiments on the linear shallow water equations. In experiments with infrequent observations, the hybrid filter consistently outperformed the EnKF, both by better capturing the Bayesian posterior and by better tracking the truth.
    Description: The work of Apte benefited from the support of the AIRBUS Group Corporate Foundation Chair in Mathematics of Complex Systems established in ICTS-TIFR. Spiller would like to acknowledge support by NSF Grant DMS-1228265 and ONR Grant N00014-11-1-0087. Sandstede gratefully acknowledges support by the NSF through Grant DMS-0907904. Slivinski was supported by the NSF through Grants DMS-0907904 and DMS-1148284.
    Description: 2015-07-01
    Keywords: Bayesian methods ; Filtering techniques ; Kalman filters ; Statistical techniques ; Data assimilation
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  • 43
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    Unknown
    American Meteorological Society
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2014. 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 Atmospheric and Oceanic Technology 31 (2014): 2871, doi:10.1175/JTECH-D-14-00187.1.
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  • 44
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015): 778–791, doi:10.1175/JPO-D-14-0164.1.
    Description: This study examines anisotropic transport properties of the eddying North Atlantic flow, using an idealized model of the double-gyre oceanic circulation and altimetry-derived velocities. The material transport by the time-dependent flow (quantified by the eddy diffusivity tensor) varies geographically and is anisotropic, that is, it has a well-defined direction of the maximum transport. One component of the time-dependent flow, zonally elongated large-scale transients, is particularly important for the anisotropy, as it corresponds to primarily zonal material transport and long correlation time scales. The importance of these large-scale zonal transients in the material distribution is further confirmed with simulations of idealized color dye tracers, which has implications for parameterizations of the eddy transport in non-eddy-resolving models.
    Description: IK would like to acknowledge support through the NSF Grant OCE-1154923. IR was supported by the NSF OCE-1154641 and NASA Grant NNX14AH29G.
    Description: 2015-09-01
    Keywords: Circulation/ Dynamics ; Eddies ; Lagrangian circulation/transport ; Mesoscale processes ; Ocean circulation ; Models and modeling ; Tracers
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  • 45
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2015. 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 Climate 28 (2015): 8289–8318, doi:10.1175/JCLI-D-14-00555.1.
    Description: This study quantifies mean annual and monthly fluxes of Earth’s water cycle over continents and ocean basins during the first decade of the millennium. To the extent possible, the flux estimates are based on satellite measurements first and data-integrating models second. A careful accounting of uncertainty in the estimates is included. It is applied within a routine that enforces multiple water and energy budget constraints simultaneously in a variational framework in order to produce objectively determined optimized flux estimates. In the majority of cases, the observed annual surface and atmospheric water budgets over the continents and oceans close with much less than 10% residual. Observed residuals and optimized uncertainty estimates are considerably larger for monthly surface and atmospheric water budget closure, often nearing or exceeding 20% in North America, Eurasia, Australia and neighboring islands, and the Arctic and South Atlantic Oceans. The residuals in South America and Africa tend to be smaller, possibly because cold land processes are negligible. Fluxes were poorly observed over the Arctic Ocean, certain seas, Antarctica, and the Australasian and Indonesian islands, leading to reliance on atmospheric analysis estimates. Many of the satellite systems that contributed data have been or will soon be lost or replaced. Models that integrate ground-based and remote observations will be critical for ameliorating gaps and discontinuities in the data records caused by these transitions. Continued development of such models is essential for maximizing the value of the observations. Next-generation observing systems are the best hope for significantly improving global water budget accounting.
    Description: This research was funded by multiple grants from NASA’s Energy and Water Cycle Study (NEWS) program.
    Description: 2016-05-01
    Keywords: Physical Meteorology and Climatology ; Water budget ; Observational techniques and algorithms ; Remote sensing ; Mathematical and statistical techniques ; Numerical analysis/modeling
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  • 46
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2015. 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 96 (2015): 1257–1279, doi:10.1175/BAMS-D-14-00015.1.
    Description: Lateral stirring is a basic oceanographic phenomenon affecting the distribution of physical, chemical, and biological fields. Eddy stirring at scales on the order of 100 km (the mesoscale) is fairly well understood and explicitly represented in modern eddy-resolving numerical models of global ocean circulation. The same cannot be said for smaller-scale stirring processes. Here, the authors describe a major oceanographic field experiment aimed at observing and understanding the processes responsible for stirring at scales of 0.1–10 km. Stirring processes of varying intensity were studied in the Sargasso Sea eddy field approximately 250 km southeast of Cape Hatteras. Lateral variability of water-mass properties, the distribution of microscale turbulence, and the evolution of several patches of inert dye were studied with an array of shipboard, autonomous, and airborne instruments. Observations were made at two sites, characterized by weak and moderate background mesoscale straining, to contrast different regimes of lateral stirring. Analyses to date suggest that, in both cases, the lateral dispersion of natural and deliberately released tracers was O(1) m2 s–1 as found elsewhere, which is faster than might be expected from traditional shear dispersion by persistent mesoscale flow and linear internal waves. These findings point to the possible importance of kilometer-scale stirring by submesoscale eddies and nonlinear internal-wave processes or the need to modify the traditional shear-dispersion paradigm to include higher-order effects. A unique aspect of the Scalable Lateral Mixing and Coherent Turbulence (LatMix) field experiment is the combination of direct measurements of dye dispersion with the concurrent multiscale hydrographic and turbulence observations, enabling evaluation of the underlying mechanisms responsible for the observed dispersion at a new level.
    Description: The bulk of this work was funded under the Scalable Lateral Mixing and Coherent Turbulence Departmental Research Initiative and the Physical Oceanography Program. The dye experiments were supported jointly by the Office of Naval Research and the National Science Foundation Physical Oceanography Program (Grants OCE-0751653 and OCE-0751734).
    Description: 2016-02-01
    Repository Name: Woods Hole Open Access Server
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  • 47
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2015. 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 Climate 28 (2015): 8319-8346, doi:10.1175/JCLI-D-14-00556.1.
    Description: New objectively balanced observation-based reconstructions of global and continental energy budgets and their seasonal variability are presented that span the golden decade of Earth-observing satellites at the start of the twenty-first century. In the absence of balance constraints, various combinations of modern flux datasets reveal that current estimates of net radiation into Earth’s surface exceed corresponding turbulent heat fluxes by 13–24 W m−2. The largest imbalances occur over oceanic regions where the component algorithms operate independent of closure constraints. Recent uncertainty assessments suggest that these imbalances fall within anticipated error bounds for each dataset, but the systematic nature of required adjustments across different regions confirm the existence of biases in the component fluxes. To reintroduce energy and water cycle closure information lost in the development of independent flux datasets, a variational method is introduced that explicitly accounts for the relative accuracies in all component fluxes. Applying the technique to a 10-yr record of satellite observations yields new energy budget estimates that simultaneously satisfy all energy and water cycle balance constraints. Globally, 180 W m−2 of atmospheric longwave cooling is balanced by 74 W m−2 of shortwave absorption and 106 W m−2 of latent and sensible heat release. At the surface, 106 W m−2 of downwelling radiation is balanced by turbulent heat transfer to within a residual heat flux into the oceans of 0.45 W m−2, consistent with recent observations of changes in ocean heat content. Annual mean energy budgets and their seasonal cycles for each of seven continents and nine ocean basins are also presented.
    Description: This study is the result of a collaboration of multiple investigators each supported by the NEWS program.
    Keywords: Climatology ; Energy budget/balance ; Heat budgets/fluxes ; Radiative fluxes ; Surface fluxes ; Satellite observations
    Repository Name: Woods Hole Open Access Server
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  • 48
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2014. 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 Climate 27 (2014): 9359–9376, doi:10.1175/JCLI-D-14-00228.1.
    Description: Multidecadal variability of the Atlantic meridional overturning circulation (AMOC) is examined based on a comparison of the AMOC streamfunctions in depth and in density space, in a 700-yr present-day control integration of the fully coupled Community Climate System Model, version 3. The commonly used depth-coordinate AMOC primarily exhibits the variability associated with the deep equatorward transport that follows the changes in the Labrador Sea deep water formation. On the other hand, the density-based AMOC emphasizes the variability associated with the subpolar gyre circulation in the upper ocean leading to the changes in the Labrador Sea convection. Combining the two representations indicates that the ~20-yr periodicity of the AMOC variability in the first half of the simulation is primarily due to an ocean-only mode resulting from the coupling of the deep equatorward flow and the upper ocean gyre circulation near the Gulf Stream and North Atlantic Current. In addition, the density-based AMOC reveals a gradual change in the deep ocean associated with cooling and increased density, which is likely responsible for the transition of AMOC variability from strong ~20-yr oscillations to a weaker red noise–like multidecadal variability.
    Description: Support from the NOAA Climate Program Office (Grant NA10OAR4310202 and NA13OAR4310139) and NSF EaSM2 (OCE1242989) is gratefully acknowledged.
    Description: 2015-06-15
    Keywords: North Atlantic Ocean ; Meridional overturning circulation ; Ocean circulation ; Thermocline circulation ; Climate variability ; Multidecadal variability
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  • 49
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2014. 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 Climate 27 (2014): 8981–9005, doi:10.1175/JCLI-D-12-00565.1.
    Description: Version 1 of the Community Earth System Model, in the configuration where its full carbon cycle is enabled, is introduced and documented. In this configuration, the terrestrial biogeochemical model, which includes carbon–nitrogen dynamics and is present in earlier model versions, is coupled to an ocean biogeochemical model and atmospheric CO2 tracers. The authors provide a description of the model, detail how preindustrial-control and twentieth-century experiments were initialized and forced, and examine the behavior of the carbon cycle in those experiments. They examine how sea- and land-to-air CO2 fluxes contribute to the increase of atmospheric CO2 in the twentieth century, analyze how atmospheric CO2 and its surface fluxes vary on interannual time scales, including how they respond to ENSO, and describe the seasonal cycle of atmospheric CO2 and its surface fluxes. While the model broadly reproduces observed aspects of the carbon cycle, there are several notable biases, including having too large of an increase in atmospheric CO2 over the twentieth century and too small of a seasonal cycle of atmospheric CO2 in the Northern Hemisphere. The biases are related to a weak response of the carbon cycle to climatic variations on interannual and seasonal time scales and to twentieth-century anthropogenic forcings, including rising CO2, land-use change, and atmospheric deposition of nitrogen.
    Description: The CESM project is supported by the National Science Foundation and the Office of Science (BER) of the U.S. Department of Energy. Computing resources were provided by the Climate Simulation Laboratory at NCAR’s Computational and Information Systems Laboratory (CISL), sponsored by the National Science Foundation and other agencies. This research was enabled by CISL compute and storage resources. SCD acknowledges support from the National Science Foundation (NSF AGS-1048827). This research is supported in part by the U.S. Department of Energy (DOE), Office of Science, Biological and Environmental Research. Oak Ridge National Laboratory is managed by UT-BATTELLE for DOE under contract DE-AC05-00OR22725.
    Description: 2015-06-15
    Keywords: Carbon cycle ; Climate models ; Coupled models ; Model evaluation/performance
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  • 50
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015): 294–312, doi:10.1175/JPO-D-14-0104.1.
    Description: Model analyses of an alongshelf flow over a continental shelf and slope reveal upwelling near the shelf break. A stratified, initially uniform, alongshelf flow undergoes a rapid adjustment with notable differences onshore and offshore of the shelf break. Over the shelf, a bottom boundary layer and an offshore bottom Ekman transport develop within an inertial period. Over the slope, the bottom offshore transport is reduced from the shelf’s bottom transport by two processes. First, advection of buoyancy downslope induces vertical mixing, destratifying, and thickening the bottom boundary layer. The downward-tilting isopycnals reduce the geostrophic speed near the bottom. The reduced bottom stress weakens the offshore Ekman transport, a process known as buoyancy shutdown of the Ekman transport. Second, the thickening bottom boundary layer and weakening near-bottom speeds are balanced by an upslope ageostrophic transport. The convergence in the bottom transport induces adiabatic upwelling offshore of the shelf break. For a time period after the initial adjustment, scalings are identified for the upwelling speed and the length scale over which it occurs. Numerical experiments are used to test the scalings for a range of initial speeds and stratifications. Upwelling occurs within an inertial period, reaching values of up to 10 m day−1 within 2 to 7 km offshore of the shelf break. Upwelling drives an interior secondary circulation that accelerates the alongshelf flow over the slope, forming a shelfbreak jet. The model results are compared with upwelling estimates from other models and observations near the Middle Atlantic Bight shelf break.
    Description: J. Benthuysen acknowledges support from the ARC Centre of Excellence for Climate System Science (CE110001028) and the MIT/WHOI Joint Program, where this work was initiated.
    Description: 2015-07-01
    Keywords: Circulation/ Dynamics ; Boundary currents ; Diapycnal mixing ; Ekman pumping/transport ; Mixing ; Topographic effects ; Upwelling/downwelling
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  • 51
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015): 104–132, doi:10.1175/JPO-D-14-0032.1.
    Description: Three mechanisms for self-induced Ekman pumping in the interiors of mesoscale ocean eddies are investigated. The first arises from the surface stress that occurs because of differences between surface wind and ocean velocities, resulting in Ekman upwelling and downwelling in the cores of anticyclones and cyclones, respectively. The second mechanism arises from the interaction of the surface stress with the surface current vorticity gradient, resulting in dipoles of Ekman upwelling and downwelling. The third mechanism arises from eddy-induced spatial variability of sea surface temperature (SST), which generates a curl of the stress and therefore Ekman pumping in regions of crosswind SST gradients. The spatial structures and relative magnitudes of the three contributions to eddy-induced Ekman pumping are investigated by collocating satellite-based measurements of SST, geostrophic velocity, and surface winds to the interiors of eddies identified from their sea surface height signatures. On average, eddy-induced Ekman pumping velocities approach O(10) cm day−1. SST-induced Ekman pumping is usually secondary to the two current-induced mechanisms for Ekman pumping. Notable exceptions are the midlatitude extensions of western boundary currents and the Antarctic Circumpolar Current, where SST gradients are strong and all three mechanisms for eddy-induced Ekman pumping are comparable in magnitude. Because the polarity of current-induced curl of the surface stress opposes that of the eddy, the associated Ekman pumping attenuates the eddies. The decay time scale of this attenuation is proportional to the vertical scale of the eddy and inversely proportional to the wind speed. For typical values of these parameters, the decay time scale is about 1.3 yr.
    Description: This work was funded by NASA Grants NNX08AI80G, NNX08AR37G, NNX13AD78G, NNX10AE91G, NNX13AE47G, and NNX10AO98G.
    Description: 2015-07-01
    Keywords: Circulation/ Dynamics ; Atmosphere-ocean interaction ; Eddies ; Ekman pumping/transport ; Atm/Ocean Structure/ Phenomena ; Eddies ; Ekman pumping ; Observational techniques and algorithms ; Satellite observations
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  • 52
    Publication Date: 2015-05-11
    Description: Disruption of circadian rhythmicity is associated with obesity and related disorders, including type 2 diabetes and cardiovascular disease. Specifically, prolonged artificial light exposure associates with obesity in humans, although the underlying mechanism is unclear. Here, we report that increasing the daily hours of light exposure increases body adiposity through attenuation of brown adipose tissue (BAT) activity, a major contributor of energy expenditure. Mice exposed to a prolonged day length of 16- and 24-h light, compared with regular 12-h light, showed increased adiposity without affecting food intake or locomotor activity. Mechanistically, we demonstrated that prolonged day length decreases sympathetic input into BAT and reduces β3-adrenergic intracellular signaling. Concomitantly, prolonging day length decreased the uptake of fatty acids from triglyceride-rich lipoproteins, as well as of glucose from plasma selectively by BAT. We conclude that impaired BAT activity is an important mediator in the association between disturbed circadian rhythm and adiposity, and anticipate that activation of BAT may overcome the adverse metabolic consequences of disturbed circadian rhythmicity.
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  • 53
    Publication Date: 2015-10-26
    Description: The autoactivation of an initiating serine protease upon binding of pattern recognition proteins to pathogen surfaces is a crucial step in eliciting insect immune responses such as the activation of Toll and prophenoloxidase pathways. However, the molecular mechanisms responsible for autoactivation of the initiating protease remains poorly understood. Here, we investigated the molecular basis for the autoactivation of hemolymph protease 14 (HP14), an initiating protease in hemolymph of Manduca sexta, upon the binding of β-1,3-glucan by its recognition protein, βGRP2. Biochemical analysis using HP14 zymogen (proHP14), βGRP2, and the recombinant proteins as truncated forms showed that the amino-terminal modular low-density lipoprotein receptor class A (LA) domains within HP14 are required for proHP14 autoactivation that is stimulated by its interaction with βGRP2. Consistent with this result, recombinant LA domains inhibit the activation of proHP14 and prophenoloxidase, likely by competing with the interaction between βGRP2 and LA domains within proHP14. Using surface plasmon resonance, we demonstrated that immobilized LA domains directly interact with βGRP2 in a calcium-dependent manner and that high-affinity interaction requires the C-terminal glucanase-like domain of βGRP2. Importantly, the affinity of LA domains for βGRP2 increases nearly 100-fold in the presence of β-1,3-glucan. Taken together, these results present the first experimental evidence to our knowledge that LA domains of an insect modular protease and glucanase-like domains of a βGRP mediate their interaction, and that this binding is essential for the protease autoactivation. Thus, our study provides important insight into the molecular basis underlying the initiation of protease cascade in insect immune responses.
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  • 54
    Publication Date: 2015-12-29
    Description: Synaptic depression is prominent among synapses, but the underlying mechanisms remain uncertain. Here, we use paired patch clamp recording to study neuromuscular transmission between the caudal primary motor neuron and target skeletal muscle in zebrafish. This synapse has an unusually low number of release sites, all with high probabilities of release in response to low-frequency stimulation. During high-frequency stimulation, the synapse undergoes short-term depression and reaches steady-state levels of transmission that sustain the swimming behavior. To determine the release parameters underlying this steady state, we applied variance analysis. Our analysis revealed two functionally distinct subclasses of release sites differing by over 60-fold in rates of vesicle reloading. A slow reloading class requires seconds to recover and contributes to depression onset but not the steady-state transmission. By contrast, a fast reloading class recovers within tens of milliseconds and is solely responsible for steady-state transmission. Thus, in contrast to most current models that assign levels of steady-state depression to vesicle availability, our findings instead assign this function to nonuniform release site kinetics. The duality of active-site properties accounts for the highly nonlinear dependence of steady-state depression levels on frequency.
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  • 55
    Publication Date: 2015-12-23
    Description: Two specific genetic variants of the apolipoprotein L1 (APOL1) gene are responsible for the high rate of kidney disease in people of recent African ancestry. Expression in cultured cells of these APOL1 risk variants, commonly referred to as G1 and G2, results in significant cytotoxicity. The underlying mechanism of this cytotoxicity is poorly understood. We hypothesized that this cytotoxicity is mediated by APOL1 risk variant-induced dysregulation of intracellular signaling relevant for cell survival. To test this hypothesis, we conditionally expressed WT human APOL1 (G0), the APOL1 G1 variant, or the APOL1 G2 variant in human embryonic kidney cells (T-REx-293) using a tetracycline-mediated (Tet-On) system. We found that expression of either G1 or G2 APOL1 variants increased apparent cell swelling and cell death compared with G0-expressing cells. These manifestations of cytotoxicity were preceded by G1 or G2 APOL1-induced net efflux of intracellular potassium as measured by X-ray fluorescence, resulting in the activation of stress-activated protein kinases (SAPKs), p38 MAPK, and JNK. Prevention of net K+ efflux inhibited activation of these SAPKs by APOL1 G1 or G2. Furthermore, inhibition of SAPK signaling and inhibition of net K+ efflux abrogated cytotoxicity associated with expression of APOL1 risk variants. These findings in cell culture raise the possibility that nephrotoxicity of APOL1 risk variants may be mediated by APOL1 risk variant-induced net loss of intracellular K+ and subsequent induction of stress-activated protein kinase pathways.
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  • 56
    Publication Date: 2015-01-26
    Description: G protein-coupled receptor 17 (GPR17) was recently reported to be a Foxo1 target in agouti-related peptide (AGRP) neurons. Intracerebroventricular injection of GPR17 agonists induced food intake, whereas administration of an antagonist to the receptor reduced feeding. These data lead to the conclusion that pharmacological modulation of GPR17 has therapeutic potential to treat obesity. Here we report that mice deficient in Gpr17 (Gpr17−/−) have similar food intake and body weight compared with their wild-type littermates. Gpr17−/− mice have normal hypothalamic Agrp mRNA expression, AGRP plasma levels, and metabolic rate. GPR17 deficiency in mice did not affect glucose homeostasis or prevent fat-induced insulin resistance. These data do not support a role for GPR17 in the control of food intake, body weight, or glycemic control.
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  • 57
    Publication Date: 2015-04-06
    Description: Major changes in bacterial physiology including biofilm and spore formation involve signaling by the cyclic dinucleotides c-di-GMP and c-di-AMP. Recently, another second messenger dinucleotide, c-AMP-GMP, was found to control chemotaxis and colonization by Vibrio cholerae. We have identified a superregulon of genes controlled by c-AMP-GMP in numerous Deltaproteobacteria, including Geobacter species that use extracellular insoluble metal oxides as terminal electron acceptors. This exoelectrogenic process has been studied for its possible utility in energy production and bioremediation. Many genes involved in adhesion, pilin formation, and others that are important for exoelectrogenesis are controlled by members of a variant riboswitch class that selectively bind c-AMP-GMP. These RNAs constitute, to our knowledge, the first known specific receptors for c-AMP-GMP and reveal that this molecule is used by many bacteria to control specialized physiological processes.
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  • 58
    Publication Date: 2015-04-27
    Description: Aminoacyl-tRNA synthetases (ARSs) establish the rules of the genetic code, whereby each amino acid is attached to a cognate tRNA. Errors in this process lead to mistranslation, which can be toxic to cells. The selective forces exerted by species-specific requirements and environmental conditions potentially shape quality-control mechanisms that serve to prevent mistranslation. A family of editing factors that are homologous to the editing domain of bacterial prolyl-tRNA synthetase includes the previously characterized trans-editing factors ProXp-ala and YbaK, which clear Ala-tRNAPro and Cys-tRNAPro, respectively, and three additional homologs of unknown function, ProXp-x, ProXp-y, and ProXp-z. We performed an in vivo screen of 230 conditions in which an Escherichia coli proXp-y deletion strain was grown in the presence of elevated levels of amino acids and specific ARSs. This screen, together with the results of in vitro deacylation assays, revealed Ser- and Thr-tRNA deacylase function for this homolog. A similar activity was demonstrated for Bordetella parapertussis ProXp-z in vitro. These proteins, now renamed “ProXp-ST1” and “ProXp-ST2,” respectively, recognize multiple tRNAs as substrates. Taken together, our data suggest that these free-standing editing domains have the ability to prevent mistranslation errors caused by a number of ARSs, including lysyl-tRNA synthetase, threonyl-tRNA synthetase, seryl-tRNA synthetase, and alanyl-tRNA synthetase. The expression of these multifunctional enzymes is likely to provide a selective growth advantage to organisms subjected to environmental stresses and other conditions that alter the amino acid pool.
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  • 59
    Publication Date: 2015-09-23
    Description: Host compatible rhizobia induce the formation of legume root nodules, symbiotic organs within which intracellular bacteria are present in plant-derived membrane compartments termed symbiosomes. In Medicago truncatula nodules, the Sinorhizobium microsymbionts undergo an irreversible differentiation process leading to the development of elongated polyploid noncultivable nitrogen fixing bacteroids that convert atmospheric dinitrogen into ammonia. This terminal differentiation is directed by the host plant and involves hundreds of nodule specific cysteine-rich peptides (NCRs). Except for certain in vitro activities of cationic peptides, the functional roles of individual NCR peptides in planta are not known. In this study, we demonstrate that the inability of M. truncatula dnf7 mutants to fix nitrogen is due to inactivation of a single NCR peptide, NCR169. In the absence of NCR169, bacterial differentiation was impaired and was associated with early senescence of the symbiotic cells. Introduction of the NCR169 gene into the dnf7-2/NCR169 deletion mutant restored symbiotic nitrogen fixation. Replacement of any of the cysteine residues in the NCR169 peptide with serine rendered it incapable of complementation, demonstrating an absolute requirement for all cysteines in planta. NCR169 was induced in the cell layers in which bacteroid elongation was most pronounced, and high expression persisted throughout the nitrogen-fixing nodule zone. Our results provide evidence for an essential role of NCR169 in the differentiation and persistence of nitrogen fixing bacteroids in M. truncatula.
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  • 60
    Publication Date: 2015-03-30
    Description: Polycystic ovary syndrome (PCOS) is one of the most common female endocrine disorders and a leading cause of female subfertility. The mechanism underlying the pathophysiology of PCOS remains to be illustrated. Here, we identify two alternative splice variants (ASVs) of the androgen receptor (AR), insertion and deletion isoforms, in granulosa cells (GCs) in ∼62% of patients with PCOS. AR ASVs are strongly associated with remarkable hyperandrogenism and abnormalities in folliculogenesis, and are absent from all control subjects without PCOS. Alternative splicing dramatically alters genome-wide AR recruitment and androgen-induced expression of genes related to androgen metabolism and folliculogenesis in human GCs. These findings establish alternative splicing of AR in GCs as the major pathogenic mechanism for hyperandrogenism and abnormal folliculogenesis in PCOS.
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  • 61
    Publication Date: 2015-05-20
    Description: After their endosymbiotic acquisition, plastids become intimately connected with the biology of their host. For example, genes essential for plastid function may be relocated from the genomes of plastids to the host nucleus, and pathways may evolve within the host to support the plastid. In this review, we consider the different degrees of integration observed in dinoflagellates and their associated plastids, which have been acquired through multiple different endosymbiotic events. Most dinoflagellate species possess plastids that contain the pigment peridinin and show extreme reduction and integration with the host biology. In some species, these plastids have been replaced through serial endosymbiosis with plastids derived from a different phylogenetic derivation, of which some have become intimately connected with the biology of the host whereas others have not. We discuss in particular the evolution of the fucoxanthin-containing dinoflagellates, which have adapted pathways retained from the ancestral peridinin plastid symbiosis for transcript processing in their current, serially acquired plastids. Finally, we consider why such a diversity of different degrees of integration between host and plastid is observed in different dinoflagellates and how dinoflagellates may thus inform our broader understanding of plastid evolution and function.
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  • 62
    Publication Date: 2015-04-13
    Description: Toll-like receptor (TLR) signaling is initiated by dimerization of intracellular Toll/IL-1 receptor resistance (TIR) domains. For all TLRs except TLR3, recruitment of the adapter, myeloid differentiation primary response gene 88 (MyD88), to TLR TIR domains results in downstream signaling culminating in proinflammatory cytokine production. Therefore, blocking TLR TIR dimerization may ameliorate TLR2-mediated hyperinflammatory states. The BB loop within the TLR TIR domain is critical for mediating certain protein–protein interactions. Examination of the human TLR2 TIR domain crystal structure revealed a pocket adjacent to the highly conserved P681 and G682 BB loop residues. Using computer-aided drug design (CADD), we sought to identify a small molecule inhibitor(s) that would fit within this pocket and potentially disrupt TLR2 signaling. In silico screening identified 149 compounds and 20 US Food and Drug Administration-approved drugs based on their predicted ability to bind in the BB loop pocket. These compounds were screened in HEK293T-TLR2 transfectants for the ability to inhibit TLR2-mediated IL-8 mRNA. C16H15NO4(C29) was identified as a potential TLR2 inhibitor. C29, and its derivative,ortho-vanillin (o-vanillin), inhibited TLR2/1 and TLR2/6 signaling induced by synthetic and bacterial TLR2 agonists in human HEK-TLR2 and THP-1 cells, but only TLR2/1 signaling in murine macrophages. C29 failed to inhibit signaling induced by other TLR agonists and TNF-α. Mutagenesis of BB loop pocket residues revealed an indispensable role for TLR2/1, but not TLR2/6, signaling, suggesting divergent roles. Mice treated witho-vanillin exhibited reduced TLR2-induced inflammation. Our data provide proof of principle that targeting the BB loop pocket is an effective approach for identification of TLR2 signaling inhibitors.
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  • 63
    Publication Date: 2015-01-20
    Description: The ability to predict the mechanisms and the associated rate constants of protein–ligand unbinding is of great practical importance in drug design. In this work we demonstrate how a recently introduced metadynamics-based approach allows exploration of the unbinding pathways, estimation of the rates, and determination of the rate-limiting steps in the paradigmatic case of the trypsin–benzamidine system. Protein, ligand, and solvent are described with full atomic resolution. Using metadynamics, multiple unbinding trajectories that start with the ligand in the crystallographic binding pose and end with the ligand in the fully solvated state are generated. The unbinding rate koff is computed from the mean residence time of the ligand. Using our previously computed binding affinity we also obtain the binding rate kon. Both rates are in agreement with reported experimental values. We uncover the complex pathways of unbinding trajectories and describe the critical rate-limiting steps with unprecedented detail. Our findings illuminate the role played by the coupling between subtle protein backbone fluctuations and the solvation by water molecules that enter the binding pocket and assist in the breaking of the shielded hydrogen bonds. We expect our approach to be useful in calculating rates for general protein–ligand systems and a valid support for drug design.
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  • 64
    Publication Date: 2015-08-05
    Description: Vitamin B12 (cobalamin) is required by humans and other organisms for diverse metabolic processes, although only a subset of prokaryotes is capable of synthesizing B12 and other cobamide cofactors. The complete aerobic and anaerobic pathways for the de novo biosynthesis of B12 are known, with the exception of the steps leading to the anaerobic biosynthesis of the lower ligand, 5,6-dimethylbenzimidazole (DMB). Here, we report the identification and characterization of the complete pathway for anaerobic DMB biosynthesis. This pathway, identified in the obligate anaerobic bacterium Eubacterium limosum, is composed of five previously uncharacterized genes, bzaABCDE, that together direct DMB production when expressed in anaerobically cultured Escherichia coli. Expression of different combinations of the bza genes revealed that 5-hydroxybenzimidazole, 5-methoxybenzimidazole, and 5-methoxy-6-methylbenzimidazole, all of which are lower ligands of cobamides produced by other organisms, are intermediates in the pathway. The bza gene content of several bacterial and archaeal genomes is consistent with experimentally determined structures of the benzimidazoles produced by these organisms, indicating that these genes can be used to predict cobamide structure. The identification of the bza genes thus represents the last remaining unknown component of the biosynthetic pathway for not only B12 itself, but also for three other cobamide lower ligands whose biosynthesis was previously unknown. Given the importance of cobamides in environmental, industrial, and human-associated microbial metabolism, the ability to predict cobamide structure may lead to an improved ability to understand and manipulate microbial metabolism.
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  • 65
    Publication Date: 2015-12-07
    Description: Published estimates of methane emissions from atmospheric data (top-down approaches) exceed those from source-based inventories (bottom-up approaches), leading to conflicting claims about the climate implications of fuel switching from coal or petroleum to natural gas. Based on data from a coordinated campaign in the Barnett Shale oil and gas-producing region of Texas, we find that top-down and bottom-up estimates of both total and fossil methane emissions agree within statistical confidence intervals (relative differences are 10% for fossil methane and 0.1% for total methane). We reduced uncertainty in top-down estimates by using repeated mass balance measurements, as well as ethane as a fingerprint for source attribution. Similarly, our bottom-up estimate incorporates a more complete count of facilities than past inventories, which omitted a significant number of major sources, and more effectively accounts for the influence of large emission sources using a statistical estimator that integrates observations from multiple ground-based measurement datasets. Two percent of oil and gas facilities in the Barnett accounts for half of methane emissions at any given time, and high-emitting facilities appear to be spatiotemporally variable. Measured oil and gas methane emissions are 90% larger than estimates based on the US Environmental Protection Agency’s Greenhouse Gas Inventory and correspond to 1.5% of natural gas production. This rate of methane loss increases the 20-y climate impacts of natural gas consumed in the region by roughly 50%.
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  • 66
    Publication Date: 2015-04-09
    Description: Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-helical membrane proteins from sequence alignments alone, we developed an approach to predict the 3D structure of TMBs. The approach combines the maximum-entropy evolutionary coupling method for predicting residue contacts (EVfold) with a machine-learning approach (boctopus2) for predicting β-strands in the barrel. In a blinded test for 19 TMB proteins of known structure that have a sufficient number of diverse homologous sequences available, this combined method (EVfold_bb) predicts hydrogen-bonded residue pairs between adjacent β-strands at an accuracy of ∼70%. This accuracy is sufficient for the generation of all-atom 3D models. In the transmembrane barrel region, the average 3D structure accuracy [template-modeling (TM) score] of top-ranked models is 0.54 (ranging from 0.36 to 0.85), with a higher (44%) number of residue pairs in correct strand–strand registration than in earlier methods (18%). Although the nonbarrel regions are predicted less accurately overall, the evolutionary couplings identify some highly constrained loop residues and, for FecA protein, the barrel including the structure of a plug domain can be accurately modeled (TM score = 0.68). Lower prediction accuracy tends to be associated with insufficient sequence information and we therefore expect increasing numbers of β-barrel families to become accessible to accurate 3D structure prediction as the number of available sequences increases.
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  • 67
    Publication Date: 2015-12-11
    Description: Preeclampsia (PE) is a pregnancy-specific disorder characterized by hypertension and proteinuria after 20 wk gestation. Abnormal extravillous trophoblast (EVT) invasion and remodeling of uterine spiral arterioles is thought to contribute to PE development. Interleukin-11 (IL11) impedes human EVT invasion in vitro and is elevated in PE decidua in women. We demonstrate that IL11 administered to mice causes development of PE features. Immunohistochemistry shows IL11 compromises trophoblast invasion, spiral artery remodeling, and placentation, leading to increased systolic blood pressure (SBP), proteinuria, and intrauterine growth restriction, although nonpregnant mice were unaffected. Real-time PCR array analysis identified pregnancy-associated plasma protein A2 (PAPPA2), associated with PE in women, as an IL11 regulated target. IL11 increased PAPPA2 serum and placental tissue levels in mice. In vitro, IL11 compromised primary human EVT invasion, whereas siRNA knockdown of PAPPA2 alleviated the effect. Genes regulating uterine natural killer (uNK) recruitment and differentiation were down-regulated and uNK cells were reduced after IL11 treatment in mice. IL11 withdrawal in mice at onset of PE features reduced SBP and proteinuria to control levels and alleviated placental labyrinth defects. In women, placental IL11 immunostaining levels increased in PE pregnancies and in serum collected from women before development of early-onset PE, shown by ELISA. These results indicate that elevated IL11 levels result in physiological changes at the maternal–fetal interface, contribute to abnormal placentation, and lead to the development of PE. Targeting placental IL11 may provide a new treatment option for PE.
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  • 68
    Publication Date: 2015-09-23
    Description: We previously computed that genes with de novo (DN) likely gene-disruptive (LGD) mutations in children with autism spectrum disorders (ASD) have high vulnerability: disruptive mutations in many of these genes, the vulnerable autism genes, will have a high likelihood of resulting in ASD. Because individuals with ASD have lower fecundity, such mutations in autism genes would be under strong negative selection pressure. An immediate prediction is that these genes will have a lower LGD load than typical genes in the human gene pool. We confirm this hypothesis in an explicit test by measuring the load of disruptive mutations in whole-exome sequence databases from two cohorts. We use information about mutational load to show that lower and higher intelligence quotients (IQ) affected individuals can be distinguished by the mutational load in their respective gene targets, as well as to help prioritize gene targets by their likelihood of being autism genes. Moreover, we demonstrate that transmission of rare disruptions in genes with a lower LGD load occurs more often to affected offspring; we show transmission originates most often from the mother, and transmission of such variants is seen more often in offspring with lower IQ. A surprising proportion of transmission of these rare events comes from genes expressed in the embryonic brain that show sharply reduced expression shortly after birth.
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  • 69
    Publication Date: 2015-11-30
    Description: Dynamic particle-scale numerical simulations are used to show that the shear thickening observed in dense colloidal, or Brownian, suspensions is of a similar nature to that observed in noncolloidal suspensions, i.e., a stress-induced transition from a flow of lubricated near-contacting particles to a flow of a frictionally contacting network of particles. Abrupt (or discontinuous) shear thickening is found to be a geometric rather than hydrodynamic phenomenon; it stems from the strong sensitivity of the jamming volume fraction to the nature of contact forces between suspended particles. The thickening obtained in a colloidal suspension of purely hard frictional spheres is qualitatively similar to experimental observations. However, the agreement cannot be made quantitative with only hydrodynamics, frictional contacts, and Brownian forces. Therefore, the role of a short-range repulsive potential mimicking the stabilization of actual suspensions on the thickening is studied. The effects of Brownian and repulsive forces on the onset stress can be combined in an additive manner. The simulations including Brownian and stabilizing forces show excellent agreement with experimental data for the viscosity η and the second normal stress difference N2.
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  • 70
    Publication Date: 2015-10-02
    Description: Classical feed-forward inhibition involves an excitation–inhibition sequence that enhances the temporal precision of neuronal responses by narrowing the window for synaptic integration. In the input layer of the cerebellum, feed-forward inhibition is thought to preserve the temporal fidelity of granule cell spikes during mossy fiber stimulation. Although this classical feed-forward inhibitory circuit has been demonstrated in vitro, the extent to which inhibition shapes granule cell sensory responses in vivo remains unresolved. Here we combined whole-cell patch-clamp recordings in vivo and dynamic clamp recordings in vitro to directly assess the impact of Golgi cell inhibition on sensory information transmission in the granule cell layer of the cerebellum. We show that the majority of granule cells in Crus II of the cerebrocerebellum receive sensory-evoked phasic and spillover inhibition prior to mossy fiber excitation. This preceding inhibition reduces granule cell excitability and sensory-evoked spike precision, but enhances sensory response reproducibility across the granule cell population. Our findings suggest that neighboring granule cells and Golgi cells can receive segregated and functionally distinct mossy fiber inputs, enabling Golgi cells to regulate the size and reproducibility of sensory responses.
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  • 71
    Publication Date: 2015-04-20
    Description: Model projections indicate that climate change may dramatically restructure phytoplankton communities, with cascading consequences for marine food webs. It is currently not known whether evolutionary change is likely to be able to keep pace with the rate of climate change. For simplicity, and in the absence of evidence to the contrary, most model projections assume species have fixed environmental preferences and will not adapt to changing environmental conditions on the century scale. Using 15 y of observations from Station CARIACO (Carbon Retention in a Colored Ocean), we show that most of the dominant species from a marine phytoplankton community were able to adapt their realized niches to track average increases in water temperature and irradiance, but the majority of species exhibited a fixed niche for nitrate. We do not know the extent of this adaptive capacity, so we cannot conclude that phytoplankton will be able to adapt to the changes anticipated over the next century, but community ecosystem models can no longer assume that phytoplankton cannot adapt.
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  • 72
    Publication Date: 2015-05-18
    Description: Guiding behavior requires the brain to make predictions about the future values of sensory inputs. Here, we show that efficient predictive computation starts at the earliest stages of the visual system. We compute how much information groups of retinal ganglion cells carry about the future state of their visual inputs and show that nearly every cell in the retina participates in a group of cells for which this predictive information is close to the physical limit set by the statistical structure of the inputs themselves. Groups of cells in the retina carry information about the future state of their own activity, and we show that this information can be compressed further and encoded by downstream predictor neurons that exhibit feature selectivity that would support predictive computations. Efficient representation of predictive information is a candidate principle that can be applied at each stage of neural computation.
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  • 73
    Publication Date: 2015-09-08
    Description: Acanthamoeba species are infected by the largest known DNA viruses. These include icosahedral Mimiviruses, amphora-shaped Pandoraviruses, and Pithovirus sibericum, the latter one isolated from 30,000-y-old permafrost. Mollivirus sibericum, a fourth type of giant virus, was isolated from the same permafrost sample. Its approximately spherical virion (0.6-µm diameter) encloses a 651-kb GC-rich genome encoding 523 proteins of which 64% are ORFans; 16% have their closest homolog in Pandoraviruses and 10% in Acanthamoeba castellanii probably through horizontal gene transfer. The Mollivirus nucleocytoplasmic replication cycle was analyzed using a combination of “omic” approaches that revealed how the virus highjacks its host machinery to actively replicate. Surprisingly, the host’s ribosomal proteins are packaged in the virion. Metagenomic analysis of the permafrost sample uncovered the presence of both viruses, yet in very low amount. The fact that two different viruses retain their infectivity in prehistorical permafrost layers should be of concern in a context of global warming. Giant viruses’ diversity remains to be fully explored.
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  • 74
    Publication Date: 2015-04-14
    Description: Inositol 1,4,5-trisphosphate receptor (IP3R) binding protein released with IP3 (IRBIT) contributes to various physiological events (electrolyte transport and fluid secretion, mRNA polyadenylation, and the maintenance of genomic integrity) through its interaction with multiple targets. However, little is known about the physiological role of IRBIT in the brain. Here we identified calcium calmodulin-dependent kinase II alpha (CaMKIIα) as an IRBIT-interacting molecule in the central nervous system. IRBIT binds to and suppresses CaMKIIα kinase activity by inhibiting the binding of calmodulin to CaMKIIα. In addition, we show that mice lacking IRBIT present with elevated catecholamine levels, increased locomotor activity, and social abnormalities. The level of tyrosine hydroxylase (TH) phosphorylation by CaMKIIα, which affects TH activity, was significantly increased in the ventral tegmental area of IRBIT-deficient mice. We concluded that IRBIT suppresses CaMKIIα activity and contributes to catecholamine homeostasis through TH phosphorylation.
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  • 75
    Publication Date: 2015-01-05
    Description: The two products of the KRAS locus, K-Ras4A and K-Ras4B, are encoded by alternative fourth exons and therefore, possess distinct membrane-targeting sequences. The common activating mutations occur in exons 1 or 2 and therefore, render both splice variants oncogenic. K-Ras4A has been understudied, because it has been considered a minor splice variant. By priming off of the splice junction, we developed a quantitative RT-PCR assay for K-Ras4A and K-Ras4B message capable of measuring absolute amounts of the two transcripts. We found that K-Ras4A was widely expressed in 30 of 30 human cancer cell lines and amounts equal to K-Ras4B in 17 human colorectal tumors. Using splice variant-specific antibodies, we detected K-Ras4A protein in several tumor cell lines at a level equal to or greater than that of K-Ras4B. In addition to the CAAX motif, the C terminus of K-Ras4A contains a site of palmitoylation as well as a bipartite polybasic region. Although both were required for maximal efficiency, each of these could independently deliver K-Ras4A to the plasma membrane. Thus, among four Ras proteins, K-Ras4A is unique in possessing a dual membrane-targeting motif. We also found that, unlike K-Ras4B, K-Ras4A does not bind to the cytosolic chaperone δ-subunit of cGMP phosphodiesterase type 6 (PDE6δ). We conclude that efforts to develop anti–K-Ras drugs that interfere with membrane trafficking will have to take into account the distinct modes of targeting of the two K-Ras splice variants.
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  • 76
    Publication Date: 2015-11-20
    Description: Coherent laser radiation has enabled many scientific and technological breakthroughs including Bose–Einstein condensates, ultrafast spectroscopy, superresolution optical microscopy, photothermal therapy, and long-distance telecommunications. However, it has remained a challenge to refrigerate liquid media (including physiological buffers) during laser illumination due to significant background solvent absorption and the rapid (∼ps) nonradiative vibrational relaxation of molecular electronic excited states. Here we demonstrate that single-beam laser trapping can be used to induce and quantify the local refrigeration of physiological media by 〉10 °C following the emission of photoluminescence from upconverting yttrium lithium fluoride (YLF) nanocrystals. A simple, low-cost hydrothermal approach is used to synthesize polycrystalline particles with sizes ranging from 1 μm. A tunable, near-infrared continuous-wave laser is used to optically trap individual YLF crystals with an irradiance on the order of 1 MW/cm2. Heat is transported out of the crystal lattice (across the solid–liquid interface) by anti-Stokes (blue-shifted) photons following upconversion of Yb3+ electronic excited states mediated by the absorption of optical phonons. Temperatures are quantified through analysis of the cold Brownian dynamics of individual nanocrystals in an inhomogeneous temperature field via forward light scattering in the back focal plane. The cold Brownian motion (CBM) analysis of individual YLF crystals indicates local cooling by 〉21 °C below ambient conditions in D2O, suggesting a range of potential future applications including single-molecule biophysics and integrated photonic, electronic, and microfluidic devices.
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  • 77
    Publication Date: 2015-08-18
    Description: Functional connectivity between the hippocampus and prefrontal cortex (PFC) is essential for associative recognition memory and working memory. Disruption of hippocampal–PFC synchrony occurs in schizophrenia, which is characterized by hypofunction of NMDA receptor (NMDAR)-mediated transmission. We demonstrate that activity of dopamine D2-like receptors (D2Rs) leads selectively to long-term depression (LTD) of hippocampal–PFC NMDAR-mediated synaptic transmission. We show that dopamine-dependent LTD of NMDAR-mediated transmission profoundly disrupts normal synaptic transmission between hippocampus and PFC. These results show how dopaminergic activation induces long-term hypofunction of NMDARs, which can contribute to disordered functional connectivity, a characteristic that is a hallmark of psychiatric disorders such as schizophrenia.
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  • 78
    Publication Date: 2015-08-31
    Description: Although anatomy is often the first step in assigning functions to neural structures, it is not always clear whether architecturally distinct regions of the brain correspond to operational units. Whereas neuroarchitecture remains relatively static, functional connectivity may change almost instantaneously according to behavioral context. We imaged panneuronal responses to visual stimuli in a highly conserved central brain region in the fruit fly, Drosophila, during flight. In one substructure, the fan-shaped body, automated analysis revealed three layers that were unresponsive in quiescent flies but became responsive to visual stimuli when the animal was flying. The responses of these regions to a broad suite of visual stimuli suggest that they are involved in the regulation of flight heading. To identify the cell types that underlie these responses, we imaged activity in sets of genetically defined neurons with arborizations in the targeted layers. The responses of this collection during flight also segregated into three sets, confirming the existence of three layers, and they collectively accounted for the panneuronal activity. Our results provide an atlas of flight-gated visual responses in a central brain circuit.
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  • 79
    Publication Date: 2015-11-17
    Description: We surveyed the “dark” proteome–that is, regions of proteins never observed by experimental structure determination and inaccessible to homology modeling. For 546,000 Swiss-Prot proteins, we found that 44–54% of the proteome in eukaryotes and viruses was dark, compared with only ∼14% in archaea and bacteria. Surprisingly, most of the dark proteome could not be accounted for by conventional explanations, such as intrinsic disorder or transmembrane regions. Nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure. Dark proteins fulfill a wide variety of functions, but a subset showed distinct and largely unexpected features, such as association with secretion, specific tissues, the endoplasmic reticulum, disulfide bonding, and proteolytic cleavage. Dark proteins also had short sequence length, low evolutionary reuse, and few known interactions with other proteins. These results suggest new research directions in structural and computational biology.
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  • 80
    Publication Date: 2015-05-19
    Description: We predict by first-principles methods a phase transition in TiO2 at 6.5 Mbar from the Fe2P-type polymorph to a ten-coordinated structure with space group I4/mmm. This is the first report, to our knowledge, of the pressure-induced phase transition to the I4/mmm structure among all dioxide compounds. The I4/mmm structure was found to be up to 3.3% denser across all pressures investigated. Significant differences were found in the electronic properties of the two structures, and the metallization of TiO2 was calculated to occur concomitantly with the phase transition to I4/mmm. The implications of our findings were extended to SiO2, and an analogous Fe2P-type to I4/mmm transition was found to occur at 10 TPa. This is consistent with the lower-pressure phase transitions of TiO2, which are well-established models for the phase transitions in other AX2 compounds, including SiO2. As in TiO2, the transition to I4/mmm corresponds to the metallization of SiO2. This transformation is in the pressure range reached in the interiors of recently discovered extrasolar planets and calls for a reformulation of the equations of state used to model them.
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  • 81
    Publication Date: 2015-05-18
    Description: Decomposition of organic material by soil microbes generates an annual global release of 50–75 Pg carbon to the atmosphere, ∼7.5–9 times that of anthropogenic emissions worldwide. This process is sensitive to global change factors, which can drive carbon cycle–climate feedbacks with the potential to enhance atmospheric warming. Although the effects of interacting global change factors on soil microbial activity have been a widespread ecological focus, the regulatory effects of interspecific interactions are rarely considered in climate feedback studies. We explore the potential of soil animals to mediate microbial responses to warming and nitrogen enrichment within a long-term, field-based global change study. The combination of global change factors alleviated the bottom-up limitations on fungal growth, stimulating enzyme production and decomposition rates in the absence of soil animals. However, increased fungal biomass also stimulated consumption rates by soil invertebrates, restoring microbial process rates to levels observed under ambient conditions. Our results support the contemporary theory that top-down control in soil food webs is apparent only in the absence of bottom-up limitation. As such, when global change factors alleviate the bottom-up limitations on microbial activity, top-down control becomes an increasingly important regulatory force with the capacity to dampen the strength of positive carbon cycle–climate feedbacks.
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  • 82
    Publication Date: 2015-10-22
    Description: Glutamine synthetase (GS), a key enzyme in biological nitrogen assimilation, is regulated in multiple ways in response to varying nitrogen sources and levels. Here we show a small regulatory RNA, NsiR4 (nitrogen stress-induced RNA 4), which plays an important role in the regulation of GS in cyanobacteria. NsiR4 expression in the unicellularSynechocystissp. PCC 6803 and in the filamentous, nitrogen-fixingAnabaenasp. PCC 7120 is stimulated through nitrogen limitation via NtcA, the global transcriptional regulator of genes involved in nitrogen metabolism. NsiR4 is widely conserved throughout the cyanobacterial phylum, suggesting a conserved function. In silico target prediction, transcriptome profiling on pulse overexpression, and site-directed mutagenesis experiments using a heterologous reporter system showed that NsiR4 interacts with the 5′UTR ofgifAmRNA, which encodes glutamine synthetase inactivating factor (IF)7. InSynechocystis, we observed an inverse relationship between the levels of NsiR4 and the accumulation of IF7 in vivo. This NsiR4-dependent modulation ofgifA(IF7) mRNA accumulation influenced the glutamine pool and thusNH4+assimilation via GS. As a second target, we identifiedssr1528, a hitherto uncharacterized nitrogen-regulated gene. Competition experiments between WT and an ΔnsiR4KO mutant showed that the lack of NsiR4 led to decreased acclimation capabilities ofSynechocystistoward oscillating nitrogen levels. These results suggest a role for NsiR4 in the regulation of nitrogen metabolism in cyanobacteria, especially for the adaptation to rapid changes in available nitrogen sources and concentrations. NsiR4 is, to our knowledge, the first identified bacterial sRNA regulating the primary assimilation of a macronutrient.
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  • 83
    Publication Date: 2015-03-02
    Description: Bone mass is maintained by balanced activity of osteoblasts and osteoclasts. Lrp4 (low-density lipoprotein receptor related protein 4) is a member of the LDL receptor family, whose mutations have been identified in patients with high–bone-mass disorders, such as sclerosteosis and van Buchem diseases. However, it remains unknown whether and how Lrp4 regulates bone-mass homeostasis in vivo. Here we provide evidence that Lrp4-null mutation or specific mutation in osteoblast-lineage cells increased cortical and trabecular bone mass, which was associated with elevated bone formation and impaired bone resorption. This phenotype was not observed in osteoclast-selective Lrp4 knockout mice. Mechanistic studies indicate that loss of Lrp4 function in osteoblast-lineage cells increased serum levels of sclerostin, a key factor for bone-mass homeostasis that interacts with Lrp4, but abolished the inhibition of Wnt/β-catenin signaling and osteoblastic differentiation by sclerostin. Concomitantly, sclerostin induction of RANKL (receptor activator of nuclear kappa B ligand) was impaired, leading to a lower ratio of RANKL over OPG (osteoprotegerin) (a key factor for osteoclastogenesis). Taken together, these results support the view for Lrp4 as a receptor of sclerostin to inhibit Wnt/β-catenin signaling and bone formation and identify Lrp4 as a critical player in bone-mass homeostasis.
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  • 84
    Publication Date: 2015-01-23
    Description: Methane emissions from natural gas delivery and end use must be quantified to evaluate the environmental impacts of natural gas and to develop and assess the efficacy of emission reduction strategies. We report natural gas emission rates for 1 y in the urban region of Boston, using a comprehensive atmospheric measurement and modeling framework. Continuous methane observations from four stations are combined with a high-resolution transport model to quantify the regional average emission flux, 18.5 ± 3.7 (95% confidence interval) g CH4⋅m−2⋅y−1. Simultaneous observations of atmospheric ethane, compared with the ethane-to-methane ratio in the pipeline gas delivered to the region, demonstrate that natural gas accounted for ∼60–100% of methane emissions, depending on season. Using government statistics and geospatial data on natural gas use, we find the average fractional loss rate to the atmosphere from all downstream components of the natural gas system, including transmission, distribution, and end use, was 2.7 ± 0.6% in the Boston urban region, with little seasonal variability. This fraction is notably higher than the 1.1% implied by the most closely comparable emission inventory.
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  • 85
    Publication Date: 2015-11-16
    Description: microRNAs (miRNAs) can act as oncosuppressors or oncogenes, induce chemoresistance or chemosensitivity, and are major posttranscriptional gene regulators. Anaplastic lymphoma kinase (ALK), EGF receptor (EGFR), and V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) are major drivers of non-small cell lung cancer (NSCLC). The aim of this study was to assess the miRNA profiles of NSCLCs driven by translocated ALK, mutant EGFR, or mutant KRAS to find driver-specific diagnostic and prognostic miRNA signatures. A total of 85 formalin-fixed, paraffin-embedded samples were considered: 67 primary NSCLCs and 18 matched normal lung tissues. Of the 67 primary NSCLCs, 17 were echinoderm microtubule-associated protein-like 4–ALK translocated (ALK+) lung cancers; the remaining 50 were not (ALK−). Of the 50 ALK− primary NSCLCs, 24 were EGFR and KRAS mutation-negative (i.e., WT; triple negative); 11 were mutant EGFR (EGFR+), and 15 were mutant KRAS (KRAS+). We developed a diagnostic classifier that shows how miR-1253, miR-504, and miR-26a-5p expression levels can classify NSCLCs as ALK-translocated, mutant EGFR, or mutant KRAS versus mutation-free. We also generated a prognostic classifier based on miR-769-5p and Let-7d-5p expression levels that can predict overall survival. This classifier showed better performance than the commonly used classifiers based on mutational status. Although it has several limitations, this study shows that miRNA signatures and classifiers have great potential as powerful, cost-effective next-generation tools to improve and complement current genetic tests. Further studies of these miRNAs can help define their roles in NSCLC biology and in identifying best-performing chemotherapy regimens.
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  • 86
    Publication Date: 2015-04-13
    Description: Human pluripotent stem cells (PSCs) show epiblast-type pluripotency that is maintained with ACTIVIN/FGF2 signaling. Here, we report the acquisition of a unique stem cell phenotype by both human ES cells (hESCs) and induced pluripotent stem cells (iPSCs) in response to transient (24–36 h) exposure to bone morphogenetic protein 4 (BMP4) plus inhibitors of ACTIVIN signaling (A83-01) and FGF2 (PD173074), followed by trypsin dissociation and recovery of colonies capable of growing on a gelatin substratum in standard medium for human PSCs at low but not high FGF2 concentrations. The self-renewing cell lines stain weakly for CDX2 and strongly for NANOG, can be propagated clonally on either Matrigel or gelatin, and are morphologically distinct from human PSC progenitors on either substratum but still meet standard in vitro criteria for pluripotency. They form well-differentiated teratomas in immune-compromised mice that secrete human chorionic gonadotropin (hCG) into the host mouse and include small areas of trophoblast-like cells. The cells have a distinct transcriptome profile from the human PSCs from which they were derived (including higher expression of NANOG, LEFTY1, and LEFTY2). In nonconditioned medium lacking FGF2, the colonies spontaneously differentiated along multiple lineages, including trophoblast. They responded to PD173074 in the absence of both FGF2 and BMP4 by conversion to trophoblast, and especially syncytiotrophoblast, whereas an A83-01/PD173074 combination favored increased expression of HLA-G, a marker of extravillous trophoblast. Together, these data suggest that the cell lines exhibit totipotent potential and that BMP4 can prime human PSCs to a self-renewing alternative state permissive for trophoblast development. The results may have implications for regulation of lineage decisions in the early embryo.
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  • 87
    Publication Date: 2015-09-15
    Description: Light-induced material phase transitions enable the formation of shapes and patterns from the nano- to the macroscale. From lithographic techniques that enable high-density silicon circuit integration, to laser cutting and welding, light–matter interactions are pervasive in everyday materials fabrication and transformation. These noncontact patterning techniques are ideally suited to reshape soft materials of biological relevance. We present here the use of relatively low-energy (
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  • 88
    Publication Date: 2015-02-23
    Description: Even moderate doses of alcohol cause considerable impairment of motor coordination, an effect that substantially involves potentiation of GABAergic activity at δ subunit-containing GABAA receptors (δ-GABAARs). Here, we demonstrate that oxytocin selectively attenuates ethanol-induced motor impairment and ethanol-induced increases in GABAergic activity at δ-GABAARs and that this effect does not involve the oxytocin receptor. Specifically, oxytocin (1 µg i.c.v.) given before ethanol (1.5 g/kg i.p.) attenuated the sedation and ataxia induced by ethanol in the open-field locomotor test, wire-hanging test, and righting-reflex test in male rats. Using two-electrode voltage-clamp electrophysiology in Xenopus oocytes, oxytocin was found to completely block ethanol-enhanced activity at α4β1δ and α4β3δ recombinant GABAARs. Conversely, ethanol had no effect when applied to α4β1 or α4β3 cells, demonstrating the critical presence of the δ subunit in this effect. Oxytocin had no effect on the motor impairment or in vitro effects induced by the δ-selective GABAAR agonist 4,5,6,7-tetrahydroisoxazolo(5,4-c)pyridin-3-ol, which binds at a different site on δ-GABAARs than ethanol. Vasopressin, which is a nonapeptide with substantial structural similarity to oxytocin, did not alter ethanol effects at δ-GABAARs. This pattern of results confirms the specificity of the interaction between oxytocin and ethanol at δ-GABAARs. Finally, our in vitro constructs did not express any oxytocin receptors, meaning that the observed interactions occur directly at δ-GABAARs. The profound and direct interaction observed between oxytocin and ethanol at the behavioral and cellular level may have relevance for the development of novel therapeutics for alcohol intoxication and dependence.
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  • 89
    Publication Date: 2015-03-02
    Description: The uterine epithelium of mice and humans undergoes cyclical waves of cell proliferation and differentiation under the regulation of estradiol-17β (E2) and progesterone (P4). These epithelial cells respond to E2 with increased protein and DNA synthesis, whereas P4 inhibits only the E2-induced DNA synthetic response. Here we show that E2 regulates protein synthesis in these epithelial cells through activating PKC that in turn stimulates ERK1/2 to phosphorylate and thereby activate the central regulator of protein synthesis mechanistic target of rapamycin (mTOR). This mTOR pathway is not inhibited by P4. Inhibitor studies with an estrogen receptor (ESR1) antagonist showed the dependence of this mTOR pathway on ESR1 but that once activated, a phosphorylation cascade independent of ESR1 propagates the pathway. E2 also stimulates an IGF1 receptor (IGF1R) to PI3 kinase to AKT to GSK-3β pathway required for activation of the canonical cell cycle machinery that is inhibited by P4. PKC activation did not stimulate this pathway nor does inhibition of PKC or ERK1/2 affect it. These studies therefore indicate a mechanism whereby DNA and protein synthesis are regulated by two ESR1-activated pathways that run in parallel with only the one responsible for the initiation of DNA synthesis blocked by P4. Inhibition of mTOR by rapamycin in vivo resulted in inhibition of E2-induced protein and DNA synthesis. Proliferative diseases of the endometrium such as endometriosis and cancer are common and E2 dependent. Thus, defining this mTOR pathway suggests that local (intrauterine or peritoneal) rapamycin administration might be a therapeutic option for these diseases.
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  • 90
    Publication Date: 2015-05-26
    Description: Tumor-specific molecules are needed across diverse areas of oncology for use in early detection, diagnosis, prognosis and therapy. Large and growing public databases of transcriptome sequencing data (RNA-seq) derived from tumors and normal tissues hold the potential of yielding tumor-specific molecules, but because the data are new they have not been fully explored for this purpose. We have developed custom bioinformatic algorithms and used them with 296 high-grade serous ovarian (HGS-OvCa) tumor and 1,839 normal RNA-seq datasets to identify mRNA isoforms with tumor-specific expression. We rank prioritized isoforms by likelihood of being expressed in HGS-OvCa tumors and not in normal tissues and analyzed 671 top-ranked isoforms by high-throughput RT-qPCR. Six of these isoforms were expressed in a majority of the 12 tumors examined but not in 18 normal tissues. An additional 11 were expressed in most tumors and only one normal tissue, which in most cases was fallopian or colon. Of the 671 isoforms, the topmost 5% (n = 33) ranked based on having tumor-specific or highly restricted normal tissue expression by RT-qPCR analysis are enriched for oncogenic, stem cell/cancer stem cell, and early development loci—including ETV4, FOXM1, LSR, CD9, RAB11FIP4, and FGFRL1. Many of the 33 isoforms are predicted to encode proteins with unique amino acid sequences, which would allow them to be specifically targeted for one or more therapeutic strategies—including monoclonal antibodies and T-cell–based vaccines. The systematic process described herein is readily and rapidly applicable to the more than 30 additional tumor types for which sufficient amounts of RNA-seq already exist.
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  • 91
    Publication Date: 2015-01-26
    Description: Protein turnover can be achieved via the lysosome/vacuole and the autophagic degradation pathways. Evidence has accumulated revealing that efficient autophagic degradation requires functional endosomal sorting complex required for transport (ESCRT) machinery. However, the interplay between the ESCRT machinery and the autophagy regulator remains unclear. Here, we show that FYVE domain protein required for endosomal sorting 1 (FREE1), a recently identified plant-specific ESCRT component essential for multivesicular body (MVB) biogenesis and plant growth, plays roles both in vacuolar protein transport and autophagic degradation. FREE1 also regulates vacuole biogenesis in both seeds and vegetative cells of Arabidopsis. Additionally, FREE1 interacts directly with a unique plant autophagy regulator SH3 DOMAIN-CONTAINING PROTEIN2 and associates with the PI3K complex, to regulate the autophagic degradation in plants. Thus, FREE1 plays multiple functional roles in vacuolar protein trafficking and organelle biogenesis as well as in autophagic degradation via a previously unidentified regulatory mechanism of cross-talk between the ESCRT machinery and autophagy process.
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  • 92
    Publication Date: 2015-09-22
    Description: Adult T-cell leukemia (ATL) develops in individuals infected with human T-cell lymphotropic virus-1 (HTLV-1). Presently there is no curative therapy for ATL. HTLV-1–encoded protein Tax (transactivator from the X-gene region) up-regulates Bcl-xL (B-cell lymphoma-extra large) expression and activates interleukin-2 (IL-2), IL-9, and IL-15 autocrine/paracrine systems, resulting in amplified JAK/STAT signaling. Inhibition of JAK signaling reduces cytokine-dependent ex vivo proliferation of peripheral blood mononuclear cells (PBMCs) from ATL patients in smoldering/chronic stages. Currently, two JAK inhibitors are approved for human use. In this study, we examined activity of multiple JAK inhibitors in ATL cell lines. The selective JAK inhibitor ruxolitinib was examined in a high-throughput matrix screen combined with 〉450 potential therapeutic agents, and Bcl-2/Bcl-xL inhibitor navitoclax was identified as a strong candidate for multicomponent therapy. The combination was noted to strongly activate BAX (Bcl-2-associated X protein), effect mitochondrial depolarization, and increase caspase 3/7 activities that lead to cleavage of PARP (poly ADP ribose polymerase) and Mcl-1 (myeloid cell leukemia 1). Ruxolitinib and navitoclax independently demonstrated modest antitumor efficacy, whereas the combination dramatically lowered tumor burden and prolonged survival in an ATL murine model. This combination strongly blocked ex vivo proliferation of five ATL patients’ PBMCs. These studies provide support for a therapeutic trial in patients with smoldering/chronic ATL using a drug combination that inhibits JAK signaling and antiapoptotic protein Bcl-xL.
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  • 93
    Publication Date: 2015-02-23
    Description: Dendritic cells (DCs) are the primary leukocytes responsible for priming T cells. To find and activate naïve T cells, DCs must migrate to lymph nodes, yet the cellular programs responsible for this key step remain unclear. DC migration to lymph nodes and the subsequent T-cell response are disrupted in a mouse we recently described lacking the NOD-like receptor NLRP10 (NLR family, pyrin domain containing 10); however, the mechanism by which this pattern recognition receptor governs DC migration remained unknown. Using a proteomic approach, we discovered that DCs from Nlrp10 knockout mice lack the guanine nucleotide exchange factor DOCK8 (dedicator of cytokinesis 8), which regulates cytoskeleton dynamics in multiple leukocyte populations; in humans, loss-of-function mutations in Dock8 result in severe immunodeficiency. Surprisingly, Nlrp10 knockout mice crossed to other backgrounds had normal DOCK8 expression. This suggested that the original Nlrp10 knockout strain harbored an unexpected mutation in Dock8, which was confirmed using whole-exome sequencing. Consistent with our original report, NLRP3 inflammasome activation remained unaltered in NLRP10-deficient DCs even after restoring DOCK8 function; however, these DCs recovered the ability to migrate. Isolated loss of DOCK8 via targeted deletion confirmed its absolute requirement for DC migration. Because mutations in Dock genes have been discovered in other mouse lines, we analyzed the diversity of Dock8 across different murine strains and found that C3H/HeJ mice also harbor a Dock8 mutation that partially impairs DC migration. We conclude that DOCK8 is an important regulator of DC migration during an immune response and is prone to mutations that disrupt its crucial function.
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  • 94
    Publication Date: 2015-09-08
    Description: Antibody modulation of T-cell coinhibitory (e.g., CTLA-4) or costimulatory (e.g., 4-1BB) receptors promotes clinical responses to a variety of cancers. Therapeutic cancer vaccination, in contrast, has produced limited clinical benefit and no curative therapies. The E6 and E7 oncoproteins of human papilloma virus (HPV) drive the majority of genital cancers, and many oropharyngeal tumors. We discovered 15–19 amino acid peptides from HPV-16 E6/E7 for which induction of T-cell immunity correlates with disease-free survival in patients treated for high-grade cervical neoplasia. We report here that intranasal vaccination with these peptides and the adjuvant alpha-galactosylceramide elicits systemic and mucosal T-cell responses leading to reduced HPV+ TC-1 tumor growth and prolonged survival in mice. We hypothesized that the inability of these T cells to fully reject established tumors resulted from suppression in the tumor microenvironment which could be ameliorated through checkpoint modulation. Combining this E6/E7 peptide vaccine with checkpoint blockade produced only modest benefit; however, coadministration with a 4-1BB agonist antibody promoted durable regression of established genital TC-1 tumors. Relative to other therapies tested, this combination of vaccine and α4-1BB promoted the highest CD8+ versus regulatory FoxP3+ T-cell ratios, elicited 2- to 5-fold higher infiltration by E7-specific CTL, and evoked higher densities of highly cytotoxic TcEO (T cytotoxic Eomesodermin) CD8 (〉70-fold) and ThEO (T helper Eomesodermin) CD4 (〉17-fold) T cells. These findings have immediate clinical relevance both in terms of the direct clinical utility of the vaccine studied and in illustrating the potential of 4-1BB antibody to convert therapeutic E6/E7 vaccines already in clinical trials into curative therapies.
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  • 95
    Publication Date: 2015-02-17
    Description: The virulence of Plasmodium falciparum, the causative agent of the deadliest form of human malaria, is attributed to its ability to evade human immunity through antigenic variation. These parasites alternate between expression of variable antigens, encoded by members of a multicopy gene family named var. Immune evasion through antigenic variation depends on tight regulation of var gene expression, ensuring that only a single var gene is expressed at a time while the rest of the family is maintained transcriptionally silent. Understanding how a single gene is chosen for activation is critical for understanding mutually exclusive expression but remains a mystery. Here, we show that antisense long noncoding RNAs (lncRNAs) initiating from var introns are associated with the single active var gene at the time in the cell cycle when the single var upstream promoter is active. We demonstrate that these antisense transcripts are incorporated into chromatin, and that expression of these antisense lncRNAs in trans triggers activation of a silent var gene in a sequence- and dose-dependent manner. On the other hand, interference with these lncRNAs using complement peptide nucleic acid molecules down-regulated the active var gene, erased the epigenetic memory, and induced expression switching. Altogether, our data provide evidence that these antisense lncRNAs play a key role in regulating var gene activation and mutually exclusive expression.
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  • 96
    Publication Date: 2015-12-14
    Description: Hyperpolarization-activated, cyclic nucleotide-gated cation (HCN) channels are critical regulators of neuronal excitability, but less is known about their possible roles in synaptic plasticity and memory circuits. Here, we characterized the HCN gene organization, channel properties, distribution, and involvement in associative and nonassociative forms of learning in Aplysia californica. Aplysia has only one HCN gene, which codes for a channel that has many similarities to the mammalian HCN channel. The cloned acHCN gene was expressed in Xenopus oocytes, which displayed a hyperpolarization-induced inward current that was enhanced by cGMP as well as cAMP. Similarly to its homologs in other animals, acHCN is permeable to K+ and Na+ ions, and is selectively blocked by Cs+ and ZD7288. We found that acHCN is predominantly expressed in inter- and motor neurons, including LFS siphon motor neurons, and therefore tested whether HCN channels are involved in simple forms of learning of the siphon-withdrawal reflex in a semiintact preparation. ZD7288 (100 μM) significantly reduced an associative form of learning (classical conditioning) but had no effect on two nonassociative forms of learning (intermediate-term sensitization and unpaired training) or baseline responses. The HCN current is enhanced by nitric oxide (NO), which may explain the postsynaptic role of NO during conditioning. HCN current in turn enhances the NMDA-like current in the motor neurons, suggesting that HCN channels contribute to conditioning through this pathway.
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  • 97
    Publication Date: 2015-06-22
    Description: Genetic factors are important determinants of the onset and progression of diabetes mellitus. Numerous susceptibility genes for type 2 diabetes, including potassium voltage-gated channel, KQT-like subfamily Q, member1 (KCNQ1), have been identified in humans by genome-wide analyses and other studies. Experiments with genetically modified mice have also implicated various genes in the pathogenesis of diabetes. However, the possible effects of the parent of origin for diabetes susceptibility alleles on disease onset have remained unclear. Here, we show that a mutation at the Kcnq1 locus reduces pancreatic β-cell mass in mice by epigenetic modulation only when it is inherited from the father. The noncoding RNA KCNQ1 overlapping transcript1 (Kcnq1ot1) is expressed from the Kcnq1 locus and regulates the expression of neighboring genes on the paternal allele. We found that disruption of Kcnq1 results in reduced Kcnq1ot1 expression as well as the increased expression of cyclin-dependent kinase inhibitor 1C (Cdkn1c), an imprinted gene that encodes a cell cycle inhibitor, only when the mutation is on the paternal allele. Furthermore, histone modification at the Cdkn1c promoter region in pancreatic islets was found to contribute to this phenomenon. Our observations suggest that the Kcnq1 genomic region directly regulates pancreatic β-cell mass and that genomic imprinting may be a determinant of the onset of diabetes mellitus.
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  • 98
    Publication Date: 2015-02-09
    Description: There is strong evidence that the core deficits of schizophrenia result from dysfunction of the dopamine (DA) system, but details of this dysfunction remain unclear. We previously reported a model of transgenic mice that selectively and reversibly overexpress DA D2 receptors (D2Rs) in the striatum (D2R-OE mice). D2R-OE mice display deficits in cognition and motivation that are strikingly similar to the deficits in cognition and motivation observed in patients with schizophrenia. Here, we show that in vivo, both the firing rate (tonic activity) and burst firing (phasic activity) of identified midbrain DA neurons are impaired in the ventral tegmental area (VTA), but not in the substantia nigra (SN), of D2R-OE mice. Normalizing striatal D2R activity by switching off the transgene in adulthood recovered the reduction in tonic activity of VTA DA neurons, which is concordant with the rescue in motivation that we previously reported in our model. On the other hand, the reduction in burst activity was not rescued, which may be reflected in the observed persistence of cognitive deficits in D2R-OE mice. We have identified a potential molecular mechanism for the altered activity of DA VTA neurons in D2R-OE mice: a reduction in the expression of distinct NMDA receptor subunits selectively in identified mesolimbic DA VTA, but not nigrostriatal DA SN, neurons. These results suggest that functional deficits relevant for schizophrenia symptoms may involve differential regulation of selective DA pathways.
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  • 99
    Publication Date: 2015-09-28
    Description: Intranasal (i.n.) infections preferentially generate Th17 cells. We explored the basis for this anatomic preference by tracking polyclonal CD4+ T cells specific for an MHC class II-bound peptide from the mucosal pathogen Streptococcus pyogenes. S. pyogenes MHC class II-bound peptide-specific CD4+ T cells were first activated in the cervical lymph nodes following i.n. inoculation and then differentiated into Th17 cells. S. pyogenes-induced Th17 formation depended on TGF-β1 from dendritic cells and IL-6 from a CD301b+ dendritic cell subset located in the cervical lymph nodes but not the spleen. Thus, the tendency of i.n. infection to induce Th17 cells is related to cytokine production by specialized dendritic cells that drain this site.
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  • 100
    Publication Date: 2015-09-14
    Description: Sickle cell disease (SCD) is an inherited disorder caused by a point mutation in the β-globin gene, leading to the production of abnormally shaped red blood cells. Sickle cells are prone to hemolysis and thereby release free heme into plasma, causing oxidative stress and inflammation that in turn result in damage to multiple organs. The transcription factor Nrf2 (nuclear factor erythroid 2-related factor 2) is a master regulator of the antioxidant cell-defense system. Here we show that constitutive Nrf2 activation by ablation of its negative regulator Keap1 (kelch-like ECH-associated protein 1) significantly improves symptoms in SCD model mice. SCD mice exhibit severe liver damage and lung inflammation associated with high expression levels of proinflammatory cytokines and adhesion molecules compared with normal mice. Importantly, these symptoms subsided after Nrf2 activation. Although hemolysis and stress erythropoiesis did not change substantially in the Nrf2-activated SCD mice, Nrf2 promoted the elimination of plasma heme released by sickle cells’ hemolysis and thereby reduced oxidative stress and inflammation, demonstrating that Nrf2 activation reduces organ damage and segregates inflammation from prevention of hemolysis in SCD mice. Furthermore, administration of the Nrf2 inducer CDDO-Im (2-cyano-3, 12 dioxooleana-1, 9 diene-28-imidazolide) also relieved inflammation and organ failure in SCD mice. These results support the contention that Nrf2 induction may be an important means to protect organs from the pathophysiology of sickle cell-induced damage.
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