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  • Synthetic Biology and Assembly Cloning  (70)
  • Atmosphere-ocean interaction  (51)
  • Oxford University Press  (70)
  • American Meteorological Society  (51)
  • MDPI Publishing
  • Nature Publishing Group
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  • Oxford University Press  (70)
  • American Meteorological Society  (51)
  • MDPI Publishing
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  • 1
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. 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 43 (2013): 1589–1610, doi:10.1175/JPO-D-12-0173.1.
    Description: This study investigates the exchange of momentum between the atmosphere and ocean using data collected from four oceanic field experiments. Direct covariance estimates of momentum fluxes were collected in all four experiments and wind profiles were collected during three of them. The objective of the investigation is to improve parameterizations of the surface roughness and drag coefficient used to estimate the surface stress from bulk formulas. Specifically, the Coupled Ocean–Atmosphere Response Experiment (COARE) 3.0 bulk flux algorithm is refined to create COARE 3.5. Oversea measurements of dimensionless shear are used to investigate the stability function under stable and convective conditions. The behavior of surface roughness is then investigated over a wider range of wind speeds (up to 25 m s−1) and wave conditions than have been available from previous oversea field studies. The wind speed dependence of the Charnock coefficient α in the COARE algorithm is modified to , where m = 0.017 m−1 s and b = −0.005. When combined with a parameterization for smooth flow, this formulation gives better agreement with the stress estimates from all of the field programs at all winds speeds with significant improvement for wind speeds over 13 m s−1. Wave age– and wave slope–dependent parameterizations of the surface roughness are also investigated, but the COARE 3.5 wind speed–dependent formulation matches the observations well without any wave information. The available data provide a simple reason for why wind speed–, wave age–, and wave slope–dependent formulations give similar results—the inverse wave age varies nearly linearly with wind speed in long-fetch conditions for wind speeds up to 25 m s−1.
    Description: This work was funded by the National Science Foundation Grant OCE04-24536 as part of the CLIVAR Mode Water Dynamics Experiment (CLIMODE) and the Office of Naval Research Grant N00014-05-1-0139 as part of the CBLAST-LOW program.
    Description: 2014-02-01
    Keywords: Wind shear ; Wind stress ; Atmosphere-ocean interaction ; Fluxes ; Momentum ; Algorithms
    Repository Name: Woods Hole Open Access Server
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  • 2
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2012. 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 25 (2012): 2622–2651, doi:10.1175/JCLI-D-11-00301.1.
    Description: This study presents an overview of the El Niño–Southern Oscillation (ENSO) phenomenon and Pacific decadal variability (PDV) simulated in a multicentury preindustrial control integration of the NCAR Community Climate System Model version 4 (CCSM4) at nominal 1° latitude–longitude resolution. Several aspects of ENSO are improved in CCSM4 compared to its predecessor CCSM3, including the lengthened period (3–6 yr), the larger range of amplitude and frequency of events, and the longer duration of La Niña compared to El Niño. However, the overall magnitude of ENSO in CCSM4 is overestimated by ~30%. The simulated ENSO exhibits characteristics consistent with the delayed/recharge oscillator paradigm, including correspondence between the lengthened period and increased latitudinal width of the anomalous equatorial zonal wind stress. Global seasonal atmospheric teleconnections with accompanying impacts on precipitation and temperature are generally well simulated, although the wintertime deepening of the Aleutian low erroneously persists into spring. The vertical structure of the upper-ocean temperature response to ENSO in the north and south Pacific displays a realistic seasonal evolution, with notable asymmetries between warm and cold events. The model shows evidence of atmospheric circulation precursors over the North Pacific associated with the “seasonal footprinting mechanism,” similar to observations. Simulated PDV exhibits a significant spectral peak around 15 yr, with generally realistic spatial pattern and magnitude. However, PDV linkages between the tropics and extratropics are weaker than observed.
    Description: M. Alexander, A. Capotondi, and J. Scott’s participation was supported by a grant from the NSF Climate and Large-scale Dynamics Program. Y.-O. Kwon gratefully acknowledges support from a WHOI Heyman fellowship and a grant from the NSF Climate and Largescale Dynamics Program. The CESM project is supported by the National Science Foundation and the Office of Science (BER) of the U.S. Department of Energy.
    Description: 2012-10-15
    Keywords: Atmosphere-ocean interaction ; El Nino ; ENSO ; La Nina ; Pacific decadal oscillation ; Climate models
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  • 3
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2012. 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 25 (2012): 3515–3531, doi:10.1175/JCLI-D-11-00028.1.
    Description: The study examined global variability of air–sea sensible heat flux (SHF) from 1980 to 2009 and the large-scale atmospheric and ocean circulations that gave rise to this variability. The contribution of high-latitude wintertime SHF was identified, and the relative importance of the effect of the sea–air temperature difference versus the effect of wind on decadal SHF variability was analyzed using an empirical orthogonal function (EOF) approach. The study showed that global SHF anomalies are strongly modulated by SHF at high latitudes (poleward of 45°) during winter seasons. Decadal variability of global wintertime SHF can be reasonably represented by the sum of two leading EOF modes, namely, the boreal wintertime SHF in the northern oceans and the austral wintertime SHF in the southern oceans. The study also showed that global wintertime SHF is modulated by the prominent modes of the large-scale atmospheric circulation at high latitudes. The increase of global SHF in the 1990s is attributable to the strengthening of the Southern Hemisphere annular mode index, while the decrease of global SHF after 2000 is due primarily to the downward trend of the Arctic Oscillation index. This study identified the important effects of wind direction and speed on SHF variability. Changes in winds modify the sea–air temperature gradient by advecting cold and dry air from continents and by imposing changes in wind-driven oceanic processes that affect sea surface temperature (SST). The pattern of air temperature anomalies dominates over the pattern of SST anomalies and dictates the pattern of decadal SHF variability.
    Description: The study is supported by the NOAA Office of Climate Observations (OCO) and the WHOI Arctic Climate Initiative. X. Song acknowledges the support from the China Scholarship Council, National Natural Science Foundation of China (NSFC) (40930844, 40976004, and 40921004) and the Ministry of Education’s 111 Project (B07036).
    Description: 2012-11-15
    Keywords: Atmosphere-ocean interaction
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  • 4
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2012. 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 25 (2012): 3549–3565, doi:10.1175/JCLI-D-11-00320.1.
    Description: The recently released NCEP Climate Forecast System Reanalysis (CFSR) is used to examine the response to ENSO in the northeast tropical Pacific Ocean (NETP) during 1979–2009. The normally cool Pacific sea surface temperatures (SSTs) associated with wind jets through the gaps in the Central American mountains at Tehuantepec, Papagayo, and Panama are substantially warmer (colder) than the surrounding ocean during El Niño (La Niña) events. Ocean dynamics generate the ENSO-related SST anomalies in the gap wind regions as the surface fluxes damp the SSTs anomalies, while the Ekman heat transport is generally in quadrature with the anomalies. The ENSO-driven warming is associated with large-scale deepening of the thermocline; with the cold thermocline water at greater depths during El Niño in the NETP, it is less likely to be vertically mixed to the surface, particularly in the gap wind regions where the thermocline is normally very close to the surface. The thermocline deepening is enhanced to the south of the Costa Rica Dome in the Papagayo region, which contributes to the local ENSO-driven SST anomalies. The NETP thermocline changes are due to coastal Kelvin waves that initiate westward-propagating Rossby waves, and possibly ocean eddies, rather than by local Ekman pumping. These findings were confirmed with regional ocean model experiments: only integrations that included interannually varying ocean boundary conditions were able to simulate the thermocline deepening and localized warming in the NETP during El Niño events; the simulation with variable surface fluxes, but boundary conditions that repeated the seasonal cycle, did not.
    Description: This research was supported by grants from the NOAA office of Global Programs and the NSF Climate and Global Dynamics Division.
    Description: 2012-11-15
    Keywords: North Pacific Ocean ; Atmosphere-ocean interaction ; ENSO ; Thermocline circulation ; Waves, oceanic ; Ocean models
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  • 5
    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 Climate 27 (2014): 2405–2416, doi:10.1175/JCLI-D-13-00359.1.
    Description: Several recent studies utilizing global climate models predict that the Pacific Equatorial Undercurrent (EUC) will strengthen over the twenty-first century. Here, historical changes in the tropical Pacific are investigated using the Simple Ocean Data Assimilation (SODA) reanalysis toward understanding the dynamics and mechanisms that may dictate such a change. Although SODA does not assimilate velocity observations, the seasonal-to-interannual variability of the EUC estimated by SODA corresponds well with moored observations over a ~20-yr common period. Long-term trends in SODA indicate that the EUC core velocity has increased by 16% century−1 and as much as 47% century−1 at fixed locations since the mid-1800s. Diagnosis of the zonal momentum budget in the equatorial Pacific reveals two distinct seasonal mechanisms that explain the EUC strengthening. The first is characterized by strengthening of the western Pacific trade winds and hence oceanic zonal pressure gradient during boreal spring. The second entails weakening of eastern Pacific trade winds during boreal summer, which weakens the surface current and reduces EUC deceleration through vertical friction. EUC strengthening has important ecological implications as upwelling affects the thermal and biogeochemical environment. Furthermore, given the potential large-scale influence of EUC strength and depth on the heat budget in the eastern Pacific, the seasonal strengthening of the EUC may help reconcile paradoxical observations of Walker circulation slowdown and zonal SST gradient strengthening. Such a process would represent a new dynamical “thermostat” on CO2-forced warming of the tropical Pacific Ocean, emphasizing the importance of ocean dynamics and seasonality in understanding climate change projections.
    Description: EJDis supported by NSFGrantsOCE-1031971 and OCE-1233282. KBK is supported by NSF Grant OCE-1233282.
    Description: 2014-09-15
    Keywords: Tropics ; Currents ; Ocean dynamics ; Atmosphere-ocean interaction ; Climate variability ; Reanalysis data
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  • 6
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. 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 26 (2013): 9839–9859, doi:10.1175/JCLI-D-12-00647.1.
    Description: Spatial and temporal covariability between the atmospheric transient eddy heat fluxes (i.e., υ′T′ and υ′q′) in the Northern Hemisphere winter (January–March) and the paths of the Gulf Stream (GS), Kuroshio Extension (KE), and Oyashio Extension (OE) are examined based on an atmospheric reanalyses and ocean observations for 1979–2009. For the climatological winter mean, the northward heat fluxes by the synoptic (2–8 days) transient eddies exhibit canonical storm tracks with their maxima collocated with the GS and KE/OE. The intraseasonal (8 days–3 months) counterpart, while having overall similar amplitude, shows a spatial pattern with more localized maxima near the major orography and blocking regions. Lateral heat flux divergence by transient eddies as the sum of the two frequency bands exhibits very close coupling with the exact locations of the ocean fronts. Linear regression is used to examine the lead–lag relationship between interannual changes in the northward heat fluxes by the transient eddies and the meridional changes in the paths of the GS, KE, and OE, respectively. One to three years prior to the northward shifts of each ocean front, the atmospheric storm tracks shift northward and intensify, which is consistent with wind-driven changes of the ocean. Following the northward shifts of the ocean fronts, the synoptic storm tracks weaken in all three cases. The zonally integrated northward heat transport by the synoptic transient eddies increases by ~5% of its maximum mean value prior to the northward shift of each ocean front and decreases to a similar amplitude afterward.
    Description: Support from the National Aeronautics and Space Administration (NASA) Physical Oceanography Program (NNX09AF35G to TJ and Y-OK) and the Department of Energy (DOE) Climate and Environmental Sciences Division (DE-SC0007052 to Y-OK) is gratefully acknowledged.
    Description: 2014-06-15
    Keywords: Atmosphere-ocean interaction ; Eddies ; Energy transport ; Storm tracks ; Heat budgets/fluxes
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  • 7
    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
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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 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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  • 9
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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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  • 10
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 47 (2017): 633-647, doi:10.1175/JPO-D-16-0089.1.
    Description: Interannual variability in the volumetric water mass distribution within the North Atlantic Subtropical Gyre is described in relation to variability in the Atlantic meridional overturning circulation. The relative roles of diabatic and adiabatic processes in the volume and heat budgets of the subtropical gyre are investigated by projecting data into temperature coordinates as volumes of water using an Argo-based climatology and an ocean state estimate (ECCO version 4). This highlights that variations in the subtropical gyre volume budget are predominantly set by transport divergence in the gyre. A strong correlation between the volume anomaly due to transport divergence and the variability of both thermocline depth and Ekman pumping over the gyre suggests that wind-driven heave drives transport anomalies at the gyre boundaries. This wind-driven heaving contributes significantly to variations in the heat content of the gyre, as do anomalies in the air–sea fluxes. The analysis presented suggests that wind forcing plays an important role in driving interannual variability in the Atlantic meridional overturning circulation and that this variability can be unraveled from spatially distributed hydrographic observations using the framework presented here.
    Description: DGE was supported by a Natural Environment Research Council studentship award at the University of Southampton. JMT’s contribution was supported by the U.S. National Science Foundation (Grant OCE-1332667). GF’s contribution was supported by the U.S. National Science Foundation through Grant OCE-0961713 and by the U.S. National Oceanic and Atmospheric Administration through Grant NA10OAR4310135. The contributions of JDZ and AJGN were supported by the NERC Grant ‘‘Climate scale analysis of air and water masses’’ (NE/ K012932/1). ACNG gratefully acknowledges support from the Leverhulme Trust, the Royal Society, and the Wolfson Foundation. LY was supported by NASA Ocean Vector Wind Science Team (OVWST) activities under Grant NNA10AO86G.
    Keywords: North Atlantic Ocean ; Atmosphere-ocean interaction ; Ekman pumping/transport ; Ocean circulation ; Water masses ; Inverse methods
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  • 11
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 31 (2018): 6245-6261, doi:10.1175/JCLI-D-17-0513.1.
    Description: Reconstructions of sea surface temperature (SST) based on instrumental observations suggest that the equatorial Pacific zonal SST gradient has increased over the twentieth century. While this increase is suggestive of the ocean dynamical thermostat mechanism of Clement et al., observations of a concurrent weakening of the zonal atmospheric (Walker) circulation are not. Here we show, using heat and momentum budget calculations on an ocean reanalysis dataset, that a seasonal weakening of the zonal atmospheric circulation is in fact consistent with cooling in the eastern equatorial Pacific (EEP) and thus an increase in the zonal SST gradient. This cooling is driven by a strengthening Equatorial Undercurrent (EUC) in response to decreased upper-ocean westward momentum associated with weakening equatorial zonal wind stress. This process can help to reconcile the seemingly contradictory twentieth-century trends in the tropical Pacific atmosphere and ocean. Moreover, it is shown that coupled general circulation models (CGCMs) do not correctly simulate this process; we identify a systematic bias in the relationship between changes in equatorial surface zonal wind stress in the EEP and EUC strength that may help to explain why observations and CGCMs have opposing trends in the zonal SST gradient over the twentieth century.
    Description: 2019-01-11
    Keywords: Tropics ; Atmosphere-ocean interaction ; Climate change ; Climate models ; Trends
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  • 12
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2010. 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 40 (2010): 2768–2777, doi:10.1175/2010JPO4461.1.
    Description: Although sustained observations yield a description of the mean equatorial current system from the western Pacific to the eastern terminus of the Tropical Atmosphere Ocean (TAO) array, a comprehensive observational dataset suitable for describing the structure and pathways of the Equatorial Undercurrent (EUC) east of 95°W does not exist and therefore climate models are unconstrained in a region that plays a critical role in ocean–atmosphere coupling. Furthermore, ocean models suggest that the interaction between the EUC and the Galápagos Islands (92°W) has a striking effect on the basic state and coupled variability of the tropical Pacific. To this end, the authors interpret historical measurements beginning with those made in conjunction with the discovery of the Pacific EUC in the 1950s, analyze velocity measurements from an equatorial TAO mooring at 85°W, and analyze a new dataset from archived shipboard ADCP measurements. Together, the observations yield a possible composite description of the EUC structure and pathways in the eastern equatorial Pacific that may be useful for model validation and guiding future observation.
    Description: Karnauskas acknowledges the WHOI Penzance Endowed Fund in Support of Assistant Scientists.
    Keywords: Atmosphere-ocean interaction ; Currents ; In situ observations ; Model evaluation/performance ; Pacific Ocean ; Tropics
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  • 13
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. 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 26 (2013): 9774–9790, doi:10.1175/JCLI-D-12-00862.1.
    Description: The influence of the Atlantic meridional overturning circulation (AMOC) variability on the atmospheric circulation is investigated in a control simulation of the NCAR Community Climate System Model, version 3 (CCSM3), where the AMOC evolves from an oscillatory regime into a red noise regime. In the latter, an AMOC intensification is followed during winter by a positive North Atlantic Oscillation (NAO). The atmospheric response is robust and controlled by AMOC-driven SST anomalies, which shift the heat release to the atmosphere northward near the Gulf Stream/North Atlantic Current. This alters the low-level atmospheric baroclinicity and shifts the maximum eddy growth northward, affecting the storm track and favoring a positive NAO. The AMOC influence is detected in the relation between seasonal upper-ocean heat content or SST anomalies and winter sea level pressure. In the oscillatory regime, no direct AMOC influence is detected in winter. However, an upper-ocean heat content anomaly resembling the AMOC footprint precedes a negative NAO. This opposite NAO polarity seems due to the southward shift of the Gulf Stream during AMOC intensification, displacing the maximum baroclinicity southward near the jet exit. As the mode has somewhat different patterns when using SST, the wintertime impact of the AMOC lacks robustness in this regime. However, none of the signals compares well with the observed influence of North Atlantic SST anomalies on the NAO because SST is dominated in CCSM3 by the meridional shifts of the Gulf Stream/North Atlantic Current that covary with the AMOC. Hence, although there is some potential climate predictability in CCSM3, it is not realistic.
    Description: Support from the NOAA Climate Program Office (Grant Number NA10OAR4310202) and the European Community 7th Framework Programme (FP7 2007-2013) under Grant Agreements GA212643 (THOR) and n.308299 (NACLIM) is gratefully acknowledged.
    Description: 2014-06-15
    Keywords: Atmosphere-ocean interaction ; North Atlantic Oscillation ; Thermohaline circulation ; Decadal variability
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  • 14
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. 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 26 (2013): 8476–8494, doi:10.1175/JCLI-D-12-00860.1.
    Description: Characteristics of atmospheric blocking in the Southern Hemisphere (SH) are explored in atmospheric general circulation model (AGCM) simulations with the Community Atmosphere Model, version 3, with a particular focus on the Australia–New Zealand sector. Preferred locations of blocking in SH observations and the associated seasonal cycle are well represented in the AGCM simulations, but the observed magnitude of blocking is underestimated throughout the year, particularly in late winter and spring. This is related to overly zonal flow due to an enhanced meridional pressure gradient in the model, which results in a decreased amplitude of the longwave trough/ridge pattern. A range of AGCM sensitivity experiments explores the effect on SH blocking of tropical heating, midlatitude sea surface temperatures, and land–sea temperature gradients created over the Australian continent during austral winter. The combined effects of tropical heating and extratropical temperature gradients are further explored in a configuration that is favorable for blocking in the Australia–New Zealand sector with warm SST anomalies to the north of Australia, cold to the southwest of Australia, warm to the southeast, and cool Australian land temperatures. The blocking-favorable configuration indicates a significant strengthening of the subtropical jet and a reduction in midlatitude flow, which results from changes in the thermal wind. While these overall changes in mean climate, predominantly forced by the tropical heating, enhance blocking activity, the magnitude of atmospheric blocking compared to observations is still underestimated. The blocking-unfavorable configuration with surface forcing anomalies of opposite sign results in a weakening subtropical jet, enhanced midlatitude flow, and significantly reduced blocking.
    Description: C.C.U. received support from the Australian Research Council through funding awarded to the Centre of Excellence for Climate System Science and the Penzance Endowed Fund at WHOI. P.C.M., M.J.P., and J.S.R. were funded by the CSIRO Climate Adaptation Flagship and the Managing Climate Variability R&D Program.
    Description: 2014-05-01
    Keywords: Australia ; Southern Hemisphere ; Atmosphere-ocean interaction ; Atmospheric circulation ; Blocking ; General circulation models
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  • 15
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2016. 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 46 (2016): 1705-1716, doi:10.1175/JPO-D-15-0221.1.
    Description: A rapid and broadband (1 h, 1 〈 f 〈 400 Hz) increase in pressure and vertical velocity on the deep ocean floor was observed on seven instruments comprising a 20-km array in the northeastern subtropical Pacific. The authors associate the jump with the passage of a cold front and focus on the 4- and 400-Hz spectra. At every station, the time of the jump is consistent with the front coming from the northwest. The apparent rate of progress, 10–20 km h−1 (2.8–5.6 m s−1), agrees with meteorological observations. The acoustic radiation below the front is modeled as arising from a moving half-plane of uncorrelated acoustic dipoles. The half-plane is preceded by a 10-km transition zone, over which the radiator strength increases linearly from zero. With this model, the time derivative of the jump at a station yields a second and independent estimate of the front’s speed, 8.5 km h−1 (2.4 m s−1). For the 4-Hz spectra, the source physics is taken to be Longuet-Higgins radiation. Its strength depends on the quantity , where Fζ is the wave amplitude power spectrum and I the overlap integral. Thus, the 1-h time constant observed in the bottom data implies a similar time constant for the growth of the wave field quantity behind the front. The spectra at 400 Hz have a similar time constant, but the jump occurs 25 min later. The implications of this difference for the source physics are uncertain.
    Description: The OBSANP cruise was funded by the Office of Naval Research under Grants N00014-10-1-0987, N00014-14-1-0324, N00014-10-1-0510, and N00014-10-1-0990.
    Keywords: Atm/Ocean Structure/ Phenomena ; Atmosphere-ocean interaction ; Cold fronts ; Marine boundary layer ; Sea state
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  • 16
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 48 (2018): 1533-1541, doi:10.1175/JPO-D-17-0267.1.
    Description: Our study analyzes measurements primarily from two Floating Instrument Platform (FLIP) field programs and from the Air–Sea Interaction Tower (ASIT) site to examine the relationship between the wind and sea surface stress for contrasting conditions. The direct relationship of the surface momentum flux to U2 is found to be better posed than the relationship between and U, where U is the wind speed and is the friction velocity. Our datasets indicate that the stress magnitude often decreases significantly with height near the surface due to thin marine boundary layers and/or enhanced stress divergence close to the sea surface. Our study attempts to correct the surface stress estimated from traditional observational levels by using multiple observational levels near the surface and extrapolating to the surface. The effect of stability on the surface stress appears to be generally smaller than errors due to the stress divergence. Definite conclusions require more extensive measurements close to the sea surface.
    Description: This work was supported by the U.S. Office of Naval Research through Award N00014-16-1-2600. We
    Description: 2019-01-10
    Keywords: Atmosphere-ocean interaction ; Marine boundary layer
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  • 17
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2010. 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 23 (2010): 3146–3154, doi:10.1175/2010JCLI3310.1.
    Description: The Atlantic meridional overturning circulation (AMOC) simulated in various ocean-only and coupled atmosphere–ocean numerical models often varies in time because of either forced or internal variability. The path of the Gulf Stream (GS) is one diagnostic variable that seems to be sensitive to the amplitude of the AMOC, yet previous modeling studies show a diametrically opposed relationship between the two variables. In this note this issue is revisited, bringing together ocean observations and comparisons with the GFDL Climate Model version 2.1 (CM2.1), both of which suggest a more southerly (northerly) GS path when the AMOC is relatively strong (weak). Also shown are some examples of possible diagnostics to compare various models and observations on the relationship between shifts in GS path and changes in AMOC strength in future studies.
    Description: We wish to acknowledge support (TJ) from WHOI’s Paul Fye Chair and NASA (NNXZX09AF35G) and to NOAA/OAR (RZ) for this work.
    Keywords: Sea surface temperature ; Meridional overturning circulation ; Gyres ; Coupled models ; Atmosphere-ocean interaction
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  • 18
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2012. 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 25 (2012): 6743–6755, doi:10.1175/JCLI-D-11-00549.1.
    Description: From 1969 to 1971 convection in the Labrador Sea shut down, thus interrupting the formation of the intermediate/dense water masses. The shutdown has been attributed to the surface freshening induced by the Great Salinity Anomaly (GSA), a freshwater anomaly in the subpolar North Atlantic. The abrupt resumption of convection in 1972, in contrast, is attributed to the extreme atmospheric forcing of that winter. Here oceanic and atmospheric data collected in the Labrador Sea at Ocean Weather Station Bravo and a one-dimensional mixed layer model are used to examine the causes of the shutdown and resumption of convection in detail. These results highlight the tight coupling of the ocean and atmosphere in convection regions and the need to resolve both components to correctly represent convective processes in the ocean. They are also relevant to present-day conditions given the increased ice melt in the Arctic Ocean and from the Greenland Ice Sheet. The analysis herein shows that the shutdown was initiated by the GSA-induced freshening as well as the mild 1968/69 winter. After the shutdown had begun, however, the continuing lateral freshwater flux as well as two positive feedbacks [both associated with the sea surface temperature (SST) decrease due to lack of convective mixing with warmer subsurface water] further inhibited convection. First, the SST decrease reduced the heat flux to the atmosphere by reducing the air–sea temperature gradient. Second, it further reduced the surface buoyancy loss by reducing the thermal expansion coefficient of the surface water. In 1972 convection resumed because of both the extreme atmospheric forcing and advection of saltier waters into the convection region.
    Description: This research was funded by a grant from the NWO/SRON User Support Programme Space Research. FS acknowledges support from OCE- 0850416 and NOAA NA08OAR4310569.
    Description: 2013-04-01
    Keywords: Atmosphere-ocean interaction ; Intermediate waters ; Oceanic variability
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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): 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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  • 20
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2016. 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 29 (2016): 6201-6221, doi:10.1175/JCLI-D-15-0694.1.
    Description: Anomalous conditions in the tropical oceans, such as those related to El Niño–Southern Oscillation and the Indian Ocean dipole, have been previously blamed for extended droughts and wet periods in Australia. Yet the extent to which Australian wet and dry spells can be driven by internal atmospheric variability remains unclear. Natural variability experiments are examined to determine whether prolonged extreme wet and dry periods can arise from internal atmospheric and land variability alone. Results reveal that this is indeed the case; however, these dry and wet events are found to be less severe than in simulations incorporating coupled oceanic variability. Overall, ocean feedback processes increase the magnitude of Australian rainfall variability by about 30% and give rise to more spatially coherent rainfall impacts. Over mainland Australia, ocean interactions lead to more frequent extreme events, particularly during the rainy season. Over Tasmania, in contrast, ocean–atmosphere coupling increases mean rainfall throughout the year. While ocean variability makes Australian rainfall anomalies more severe, droughts and wet spells of duration longer than three years are equally likely to occur in both atmospheric- and ocean-driven simulations. Moreover, they are essentially indistinguishable from what one expects from a Gaussian white noise distribution. Internal atmosphere–land-driven megadroughts and megapluvials that last as long as ocean-driven events are also identified in the simulations. This suggests that oceanic variability may be less important than previously assumed for the long-term persistence of Australian rainfall anomalies. This poses a challenge to accurate prediction of long-term dry and wet spells for Australia.
    Description: This study was supported by the Australian Research Council (ARC) under ARC-DP1094784, ARC-DP-150101331, ARC-FL100100214, and funding for C.C.U. from the National Science Foundation under AGS-1602455 and the ARC Centre of Excellence for Climate System Science.
    Description: 2017-02-19
    Keywords: Circulation/ Dynamics ; Atmosphere-ocean interaction ; Atm/Ocean Structure/ Phenomena ; Drought ; Precipitation ; Physical Meteorology and Climatology ; Climate variability ; Forecasting ; Climate prediction ; Variability
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  • 21
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 31 (2018): 4157-4174, doi:10.1175/JCLI-D-17-0654.1.
    Description: Decadal variabilities in Indian Ocean subsurface ocean heat content (OHC; 50–300 m) since the 1950s are examined using ocean reanalyses. This study elaborates on how Pacific variability modulates the Indian Ocean on decadal time scales through both oceanic and atmospheric pathways. High correlations between OHC and thermocline depth variations across the entire Indian Ocean Basin suggest that OHC variability is primarily driven by thermocline fluctuations. The spatial pattern of the leading mode of decadal Indian Ocean OHC variability closely matches the regression pattern of OHC on the interdecadal Pacific oscillation (IPO), emphasizing the role of the Pacific Ocean in determining Indian Ocean OHC decadal variability. Further analyses identify different mechanisms by which the Pacific influences the eastern and western Indian Ocean. IPO-related anomalies from the Pacific propagate mainly through oceanic pathways in the Maritime Continent to impact the eastern Indian Ocean. By contrast, in the western Indian Ocean, the IPO induces wind-driven Ekman pumping in the central Indian Ocean via the atmospheric bridge, which in turn modifies conditions in the southwestern Indian Ocean via westward-propagating Rossby waves. To confirm this, a linear Rossby wave model is forced with wind stresses and eastern boundary conditions based on reanalyses. This linear model skillfully reproduces observed sea surface height anomalies and highlights both the oceanic connection in the eastern Indian Ocean and the role of wind-driven Ekman pumping in the west. These findings are also reproduced by OGCM hindcast experiments forced by interannual atmospheric boundary conditions applied only over the Pacific and Indian Oceans, respectively.
    Description: This research was supported by a scholarship from the China Scholarship Council (CSC) to X. J., a research fellowship by the Alexander von Humboldt Foundation to C. C. U., an NSF OCE PO Grant (OCE- 1242989) to Y.-O. K., the ONR Young Investigator Award (N00014-15-1-2588) to H. S., and a research grant from the Ministry of Science and Technology of the People’s Republic of China to Tsinghua University (2017YFA0603902).
    Description: 2018-10-30
    Keywords: Atmosphere-ocean interaction
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  • 22
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 31 (2018): 2771-2796, doi:10.1175/JCLI-D-17-0061.1.
    Description: The Generalized Equilibrium Feedback Analysis (GEFA) is used to distinguish the influence of the Oyashio Extension (OE) and the Kuroshio Extension (KE) variability on the atmosphere from 1979 to 2014 from that of the main SST variability modes, using seasonal mean anomalies. Remote SST anomalies are associated with each single oceanic regressor, but the multivariate approach efficiently confines their SST footprints. In autumn [October–December (OND)], the OE meridional shifts are followed by a North Pacific Oscillation (NPO)-like signal. The OE influence is not investigated in winter [December–February (DJF)] because of multicollinearity, but a robust response with a strong signal over the Bering Sea is found in late winter/early spring [February–April (FMA)], a northeastward strengthening of the Aleutian low following a northward OE shift. A robust response to the KE variability is found in autumn, but not in winter and late winter when the KE SST footprint becomes increasingly small and noisy as regressors are added in GEFA. In autumn, a positive PDO is followed by a northward strengthening of the Aleutian low and a southward shift of the storm track in the central Pacific, reflecting the surface heat flux footprint in the central Pacific. In winter, the PDO shifts the maximum baroclinicity and storm track southward, the response strongly tilts westward with height in the North Pacific, and there is a negative NAO-like teleconnection. In late winter, the North Pacific NPO-like response to the PDO interferes negatively with the response to the OE and is only detected when the OE is represented in GEFA. A different PDO influence on the atmospheric circulation is found from 1958 to 1977.
    Description: This research has received funding from the European Union 7th Framework Program (FP7 2007-2013) under Grant Agreement 308299 (NACLIM) and from NSF Grants AGS CLD 1035423 and OCE PO 1242989.
    Keywords: Atmosphere-ocean interaction ; Boundary currents ; Pacific decadal oscillation ; Atmosphere-ocean interaction ; Empirical orthogonal functions ; Regression analysis
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  • 23
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2018. 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 31 (2018): 9881-9901, doi:10.1175/JCLI-D-17-0889.1.
    Description: The Atlantic meridional overturning circulation and associated poleward heat transport are balanced by northern heat loss to the atmosphere and corresponding water-mass transformation. The circulation of northward-flowing Atlantic Water at the surface and returning overflow water at depth is particularly manifested—and observed—at the Greenland–Scotland Ridge where the water masses are guided through narrow straits. There is, however, a rich variability in the exchange of water masses across the ridge on all time scales. Focusing on seasonal and interannual time scales, and particularly the gateways of the Denmark Strait and between the Faroe Islands and Shetland, we specifically assess to what extent the exchanges of water masses across the Greenland–Scotland Ridge relate to wind forcing. On seasonal time scales, the variance explained of the observed exchanges can largely be related to large-scale wind patterns, and a conceptual model shows how this wind forcing can manifest via a barotropic, cyclonic circulation. On interannual time scales, the wind stress impact is less direct as baroclinic mechanisms gain importance and observations indicate a shift in the overflows from being more barotropically to more baroclinically forced during the observation period. Overall, the observed Greenland–Scotland Ridge exchanges reflect a horizontal (cyclonic) circulation on seasonal time scales, while the interannual variability more represents an overturning circulation.
    Description: This research was supported by the Research Council of Norway project NORTH (Grant 229763). Additional support for M. A. Spall was provided by National Science Foundation Grant OCE- 1558742, for T. Eldevik and S. Østerhus by the European Union’s Horizon 2020 research and innovation program project Blue-Action (Grant 727852), and for S. Østerhus by the European Framework Programs under Grant Agreement 308299 (NACLIM).
    Keywords: Ocean circulation ; Thermocline circulation ; Atmosphere-ocean interaction ; North Atlantic Oscillation ; Statistical techniques ; Time series
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  • 24
    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): 1343–1363, doi:10.1175/JCLI-D-13-00148.1.
    Description: The climate of West Antarctica is strongly influenced by remote forcing from the tropical Pacific. For example, recent surface warming over West Antarctica reflects atmospheric circulation changes over the Amundsen Sea, driven by an atmospheric Rossby wave response to tropical sea surface temperature (SST) anomalies. Here, it is demonstrated that tropical Pacific SST anomalies also influence the source and transport of marine-derived aerosols to the West Antarctic Ice Sheet. Using records from four firn cores collected along the Amundsen coast of West Antarctica, the relationship between sea ice–modulated chemical species and large-scale atmospheric variability in the tropical Pacific from 1979 to 2010 is investigated. Significant correlations are found between marine biogenic aerosols and sea salts, and SST and sea level pressure in the tropical Pacific. In particular, La Niña–like conditions generate an atmospheric Rossby wave response that influences atmospheric circulation over Pine Island Bay. Seasonal regression of atmospheric fields on methanesulfonic acid (MSA) reveals a reduction in onshore wind velocities in summer at Pine Island Bay, consistent with enhanced katabatic flow, polynya opening, and coastal dimethyl sulfide production. Seasonal regression of atmospheric fields on chloride (Cl−) reveals an intensification in onshore wind velocities in winter, consistent with sea salt transport from offshore source regions. Both the source and transport of marine aerosols to West Antarctica are found to be modulated by similar atmospheric dynamics in response to remote forcing. Finally, the regional ice-core array suggests that there is both a temporally and a spatially varying response to remote tropical forcing.
    Description: This research was supported by an award from the Department of Energy Office of Science Graduate Fellowship Program (DOE SCGF) to ASC, a James E. and Barbara V. Moltz Research Fellowship to SBD, and grants from NSF-OPP (ANT- 0632031 and ANT-0631973), NSF-MRI (EAR- 1126217), and the NASA Cryosphere Program (NNX10AP09G), and a WHOI Andrew W. Mellon Foundation Award for Innovative Research.
    Description: 2014-08-01
    Keywords: Antarctica ; Sea ice ; Teleconnections ; Atmosphere-ocean interaction ; Climate records ; Interannual variability
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  • 25
    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 46 (2016): 439-459, doi:10.1175/JPO-D-15-0086.1.
    Description: The summertime California Current System (CCS) is characterized by energetic mesoscale eddies, whose sea surface temperature (SST) and surface current can significantly modify the wind stress and Ekman pumping. Relative importance of the eddy–wind interactions via SST and surface current in the CCS is examined using a high-resolution (7 km) regional coupled model with a novel coupling approach to isolate the small-scale air–sea coupling by SST and surface current. Results show that when the eddy-induced surface current is allowed to modify the wind stress, the spatially averaged surface eddy kinetic energy (EKE) is reduced by 42%, and this is primarily due to enhanced surface eddy drag and reduced wind energy transfer. In contrast, the eddy-induced SST–wind coupling has no significant impact on the EKE. Furthermore, eddy-induced SST and surface current modify the Ekman pumping via their crosswind SST gradient and surface vorticity gradient, respectively. The resultant magnitudes of the Ekman pumping velocity are comparable, but the implied feedback effects on the eddy statistics are different. The surface current-induced Ekman pumping mainly attenuates the amplitude of cyclonic and anticyclonic eddies, acting to reduce the eddy activity, while the SST-induced Ekman pumping primarily affects the propagation. Time mean–rectified change in SST is determined by the altered offshore temperature advection by the mean and eddy currents, but the magnitude of the mean SST change is greater with the eddy-induced current effect. The demonstrated remarkably strong dynamical response in the CCS system to the eddy-induced current–wind coupling indicates that eddy-induced current should play an important role in the regional coupled ocean–atmosphere system.
    Description: We thank NSF for support under GrantsOCE-0960770,OCE-1419235, andOCE-1419306. HS is grateful for the WHOI internal support from the Andrew W. Mellon Foundation Awards for Innovative Research and the additional support from the ONR We thank NSF for support under GrantsOCE-0960770,OCE-1419235, andOCE-1419306. HS is grateful for the WHOI internal support from the Andrew W. Mellon Foundation Awards for Innovative Research and the additional support from the ONR
    Description: 2016-05-30
    Keywords: Atm/Ocean Structure/ Phenomena ; Atmosphere-ocean interaction ; Ekman pumping ; Models and modeling ; Ocean models ; Regional models
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  • 26
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kwon, Y., Seo, H., Ummenhofer, C. C., & Joyce, T. M. Impact of multidecadal variability in Atlantic SST on winter atmospheric blocking. Journal of Climate, 33(3), (2020): 867-892, doi: 10.1175/JCLI-D-19-0324.1.
    Description: Recent studies have suggested that coherent multidecadal variability exists between North Atlantic atmospheric blocking frequency and the Atlantic multidecadal variability (AMV). However, the role of AMV in modulating blocking variability on multidecadal times scales is not fully understood. This study examines this issue primarily using the NOAA Twentieth Century Reanalysis for 1901–2010. The second mode of the empirical orthogonal function for winter (December–March) atmospheric blocking variability in the North Atlantic exhibits oppositely signed anomalies of blocking frequency over Greenland and the Azores. Furthermore, its principal component time series shows a dominant multidecadal variability lagging AMV by several years. Composite analyses show that this lag is due to the slow evolution of the AMV sea surface temperature (SST) anomalies, which is likely driven by the ocean circulation. Following the warm phase of AMV, the warm SST anomalies emerge in the western subpolar gyre over 3–7 years. The ocean–atmosphere interaction over these 3–7-yr periods is characterized by the damping of the warm SST anomalies by the surface heat flux anomalies, which in turn reduce the overall meridional gradient of the air temperature and thus weaken the meridional transient eddy heat flux in the lower troposphere. The anomalous transient eddy forcing then shifts the eddy-driven jet equatorward, resulting in enhanced Rossby wave breaking and blocking on the northern flank of the jet over Greenland. The opposite is true with the AMV cold phases but with much shorter lags, as the evolution of SST anomalies differs in the warm and cold phases.
    Description: We gratefully acknowledge support from the NSF Climate and Large-scale Dynamics Program (AGS-1355339) to Y-OK, HS, CCU, and TMJ, the NASA Physical Oceanography Program (NNX13AM59G) to Y-OK, HS, and TMJ, NOAA CPO Climate Variability and Predictability Program (NA13OAR4310139) and DOE CESD Regional and Global Model Analysis Program (DE-SC0019492) to Y-OK, and NSF Physical Oceanography Program (OCE-1419235) to HS. We are very grateful to the three anonymous reviewers and editor Dr. Mingfang Ting, for their thorough and insightful suggestions. The NOAA 20CR dataset was downloaded from the NOAA Earth System Research Laboratory Physical Science Division webpage (https://www.esrl.noaa.gov/psd/data/20thC_Rean/). Support for the 20CR Project version 2c dataset is provided by the U.S. Department of Energy, Office of Science Biological and Environmental Research (BER), and by the National Oceanic and Atmospheric Administration Climate Program Office. The HadISST dataset was downloaded from the U.K. Met Office Hadley Centre webpage (https://www.metoffice.gov.uk/hadobs/hadisst/). The ERA-20C dataset was downloaded from the ECMWF webpage (https://apps.ecmwf.int/datasets/data/era20c-daily/). The ERSST5 dataset was provided by the NOAA Earth System Research Laboratory Physical Science Division (https://www.esrl.noaa.gov/psd/data/gridded/data.noaa.ersst.v5.html).
    Keywords: North Atlantic Ocean ; Atmosphere-ocean interaction ; Blocking ; Climate variability ; Multidecadal variability ; North Atlantic Oscillation
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  • 27
    Publication Date: 2022-05-27
    Description: Author Posting. © American Meteorological Society, 2021. 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 102(10), (2021): E1936–E1951, https://doi.org/10.1175/BAMS-D-20-0113.1.
    Description: In the Bay of Bengal, the warm, dry boreal spring concludes with the onset of the summer monsoon and accompanying southwesterly winds, heavy rains, and variable air–sea fluxes. Here, we summarize the 2018 monsoon onset using observations collected through the multinational Monsoon Intraseasonal Oscillations in the Bay of Bengal (MISO-BoB) program between the United States, India, and Sri Lanka. MISO-BoB aims to improve understanding of monsoon intraseasonal variability, and the 2018 field effort captured the coupled air–sea response during a transition from active-to-break conditions in the central BoB. The active phase of the ∼20-day research cruise was characterized by warm sea surface temperature (SST 〉 30°C), cold atmospheric outflows with intermittent heavy rainfall, and increasing winds (from 2 to 15 m s−1). Accumulated rainfall exceeded 200 mm with 90% of precipitation occurring during the first week. The following break period was both dry and clear, with persistent 10–12 m s−1 wind and evaporation of 0.2 mm h−1. The evolving environmental state included a deepening ocean mixed layer (from ∼20 to 50 m), cooling SST (by ∼1°C), and warming/drying of the lower to midtroposphere. Local atmospheric development was consistent with phasing of the large-scale intraseasonal oscillation. The upper ocean stores significant heat in the BoB, enough to maintain SST above 29°C despite cooling by surface fluxes and ocean mixing. Comparison with reanalysis indicates biases in air–sea fluxes, which may be related to overly cool prescribed SST. Resolution of such biases offers a path toward improved forecasting of transition periods in the monsoon.
    Description: This work was supported through the U.S. Office of Naval Research’s Departmental Research Initiative: Monsoon Intraseasonal Oscillations in the Bay of Bengal, the Indian Ministry of Earth Science’s Ocean Mixing and Monsoons Program, and the Sri Lankan National Aquatic Resources Research and Development Agency. We thank the Captain and crew of the R/V Thompson for their help in data collection. Surface atmospheric fields included fluxes were quality controlled and processed by the Boundary Layer Observations and Processes Team within the NOAA Physical Sciences Laboratory. Forecast analysis was completed by India Meteorological Department. Drone image was taken by Shreyas Kamat with annotations by Gualtiero Spiro Jaeger. We also recognize the numerous researchers who supported cruise- and land-based measurements. This work represents Lamont-Doherty Earth Observatory contribution number 8503, and PMEL contribution number 5193.
    Description: 2022-04-01
    Keywords: Atmosphere-ocean interaction ; Monsoons ; In situ atmospheric observations ; In situ oceanic observations
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  • 28
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. 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 32(2), (2019): 549-573. doi: 10.1175/JCLI-D-18-0413.1.
    Description: Time series of surface meteorology and air–sea fluxes from the northern Bay of Bengal are analyzed, quantifying annual and seasonal means, variability, and the potential for surface fluxes to contribute significantly to variability in surface temperature and salinity. Strong signals were associated with solar insolation and its modulation by cloud cover, and, in the 5- to 50-day range, with intraseasonal oscillations (ISOs). The northeast (NE) monsoon (DJF) was typically cloud free, with strong latent heat loss and several moderate wind events, and had the only seasonal mean ocean heat loss. The spring intermonsoon (MAM) was cloud free and had light winds and the strongest ocean heating. Strong ISOs and Tropical Cyclone Komen were seen in the southwest (SW) monsoon (JJA), when 65% of the 2.2-m total rain fell, and oceanic mean heating was small. The fall intermonsoon (SON) initially had moderate convective systems and mean ocean heating, with a transition to drier winds and mean ocean heat loss in the last month. Observed surface freshwater flux applied to a layer of the observed thickness produced drops in salinity with timing and magnitude similar to the initial drops in salinity in the summer monsoon, but did not reproduce the salinity variability of the fall intermonsoon. Observed surface heat flux has the potential to cause the temperature trends of the different seasons, but uncertainty in how shortwave radiation is absorbed in the upper ocean limits quantifying the role of surface forcing in the evolution of mixed layer temperature.
    Description: The deployment of the Woods Hole Oceanographic Institution (WHOI) mooring and RW and JTF were supported by the U.S. Office of Naval Research, Grant N00014-13-1-0453. DS acknowledges support from the Ministry of Earth Sciences under India’s National Monsoon Mission. HS acknowledges support from the Office of Naval Research Grants N00014-13-1-0453 and N00014-17-12398. The deployment of the WHOI mooring was done by RV Sagar Nidhi and the recovery by RV Sagar Kanya; the help of the crew and science parties is gratefully acknowledged as is the ongoing support at NIOT in Chennai and by other colleagues in India of this mooring work. The work of the staff of the WHOI Upper Ocean Process Group in the design, building, deployment, and recovery of the mooring and in processing the data is gratefully acknowledged. The software for the wavelet analysis was provided by Torrence and Compo (1998). Feedback on the paper by Dr. Amit Tandon and two anonymous reviewers is gratefully acknowledged. This paper is dedicated to Dr. Frank Bradley.
    Description: 2019-06-28
    Keywords: Atmosphere-ocean interaction ; Monsoons ; Air-sea interaction ; Surface fluxes
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  • 29
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2013. 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 39 (2013): 450–469, doi:10.1175/JTECH-D-12-00078.1.
    Description: A surface mooring was deployed in the Gulf Stream for 15 months to investigate the role of air–sea interaction in mode water formation and other processes. The accuracies of the near-surface meteorological and oceanographic measurements are investigated. In addition, the impacts of these measurement errors on the estimation and study of the air–sea fluxes in the Gulf Stream are discussed. Pre- and postdeployment calibrations together with in situ comparison between shipboard and moored sensors supported the identification of biases due to sensor drifts, sensor electronics, and calibration errors. A postdeployment field study was used to further investigate the performance of the wind sensors. The use of redundant sensor sets not only supported the filling of data gaps but also allowed an examination of the contribution of random errors. Air–sea fluxes were also analyzed and computed from both Coupled Ocean–Atmosphere Response Experiment (COARE) bulk parameterization and using direct covariance measurements. The basic conclusion is that the surface buoy deployed in the Gulf Stream to support air–sea interaction research was successful, providing an improved 15-month record of surface meteorology, upper-ocean variability, and air–sea fluxes with known accuracies. At the same time, the coincident deployment of mean meteorological and turbulent flux sensors proved to be a successful strategy to certify the validity of the bulk formula fluxes over the midrange of wind speeds and to support further work to address the present shortcomings of the bulk formula methods at the low and high wind speeds.
    Description: The National Science Foundation (Grant OCE04-24536) funded this work, as part of the CLIVAR Mode Water Dynamics Experiment (CLIMODE). The Vetlesen Foundation is also acknowledged for the early support of S. Bigorre.
    Description: 2013-09-01
    Keywords: Atmosphere-ocean interaction ; Buoy observations
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  • 30
    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): 2842–2860, doi:10.1175/JCLI-D-13-00227.1.
    Description: Mooring measurements from the Kuroshio Extension System Study (June 2004–June 2006) and from the ongoing Kuroshio Extension Observatory (June 2004–present) are combined with float measurements of the Argo network to study the variability of the North Pacific Subtropical Mode Water (STMW) across the entire gyre, on time scales from days, to seasons, to a decade. The top of the STMW follows a seasonal cycle, although observations reveal that it primarily varies in discrete steps associated with episodic wind events. The variations of the STMW bottom depth are tightly related to the sea surface height (SSH), reflecting mesoscale eddies and large-scale variations of the Kuroshio Extension and recirculation gyre systems. Using the observed relationship between SSH and STMW, gridded SSH products and in situ estimates from floats are used to construct weekly maps of STMW thickness, providing nonbiased estimates of STMW total volume, annual formation and erosion volumes, and seasonal and interannual variability for the past decade. Year-to-year variations are detected, particularly a significant decrease of STMW volume in 2007–10 primarily attributable to a smaller volume formed. Variability of the heat content in the mode water region is dominated by the seasonal cycle and mesoscale eddies; there is only a weak link to STMW on interannual time scales, and no long-term trends in heat content and STMW thickness between 2002 and 2011 are detected. Weak lagged correlations among air–sea fluxes, oceanic heat content, and STMW thickness are found when averaged over the northwestern Pacific recirculation gyre region.
    Description: This work was sponsored by the National Science Foundation (Grants OCE-0220161, OCE-0825152, and OCE-0827125).
    Description: 2014-10-15
    Keywords: Atmosphere-ocean interaction ; Mesoscale processes ; Mesoscale systems ; Ocean dynamics ; Eddies ; Water masses
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  • 31
    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): 3298–3317, doi:JCLI-D-12-00700.1.
    Description: The subpolar North Atlantic is a center of variability of ocean properties, wind stress curl, and air–sea exchanges. Observations and hindcast simulations suggest that from the early 1970s to the mid-1990s the subpolar gyre became fresher while the gyre and meridional circulations intensified. This is opposite to the relationship of freshening causing a weakened circulation, most often reproduced by climate models. The authors hypothesize that both these configurations exist but dominate on different time scales: a fresher subpolar gyre when the circulation is more intense, at interannual frequencies (configuration A), and a saltier subpolar gyre when the circulation is more intense, at longer periods (configuration B). Rather than going into the detail of the mechanisms sustaining each configuration, the authors’ objective is to identify which configuration dominates and to test whether this depends on frequency, in preindustrial control runs of five climate models from phase 5 of the Coupled Model Intercomparison Project (CMIP5). To this end, the authors have developed a novel intercomparison method that enables analysis of freshwater budget and circulation changes in a physical perspective that overcomes model specificities. Lag correlations and a cross-spectral analysis between freshwater content changes and circulation indices validate the authors’ hypothesis, as configuration A is only visible at interannual frequencies while configuration B is mostly visible at decadal and longer periods, suggesting that the driving role of salinity on the circulation depends on frequency. Overall, this analysis underscores the large differences among state-of-the-art climate models in their representations of the North Atlantic freshwater budget.
    Description: JD and RC were funded by NSF through Project 0751896. JD was also funded by IFREMER through project RICCO.
    Description: 2014-11-01
    Keywords: Atmosphere-ocean interaction ; Freshwater ; Climate models ; Model comparison ; Climate variability ; North Atlantic Oscillation
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  • 32
    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 Physical Oceanography 44 (2014): 2569–2587, doi:10.1175/JPO-D-14-0026.1.
    Description: This paper describes the occurrence of diurnal restratification events found in the southeast trade wind regime off northern Chile. This is a region where persistent marine stratus clouds are found and where there is a less than complete understanding of the dynamics that govern the maintenance of the sea surface temperature. A surface mooring deployed in the region provides surface meteorological, air–sea flux, and upper-ocean temperature, salinity, and velocity data. In the presence of steady southeast trade winds and strong evaporation, a warm, salty surface mixed layer is found in the upper ocean. During the year, these trade winds, at times, drop dramatically and surface heating leads to the formation of shallow, warm diurnal mixed layers over one to several days. At the end of such a low wind period, mean sea surface temperature is warmer. Though magnitudes of the individual diurnal warming events are consistent with local forcing, as judged by running a one-dimensional model, the net warming at the end of a low wind event is more difficult to predict. This is found to stem from differences between the observed and predicted near-inertial shear and the depths over which the warmed water is distributed. As a result, the evolution of SST has a dependency on these diurnal restratification events and on near-surface processes that govern the depth over which the heat gained during such events is distributed.
    Description: RAW was supported by the NOAA Climate Program Office. SM and AT were supported by NASA Grant NNX12AD47G,ONR Grant N000140910196, and NSF-OCE 0928138 RAW.
    Description: 2015-03-01
    Keywords: Atm/Ocean Structure/ Phenomena ; Atmosphere-ocean interaction ; Boundary layer ; Diurnal effects ; Mixed layer
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  • 33
    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): 3596–3618, doi:10.1175/JCLI-D-13-00070.1.
    Description: Estimates of the recent mean and time varying water mass transformation rates associated with North Atlantic surface-forced overturning are presented. The estimates are derived from heat and freshwater surface fluxes and sea surface temperature fields from six atmospheric reanalyses—the Japanese 25-yr Reanalysis (JRA), the NCEP–NCAR reanalysis (NCEP1), the NCEP–U.S. Department of Energy (DOE) reanalysis (NCEP2), the European Centre for Medium-Range Weather Forecasts (ECMWF) Interim Re-Analysis (ERA-I), the Climate Forecast System Reanalysis (CFSR), and the Modern-Era Reanalysis for Research and Applications (MERRA)—together with sea surface salinity fields from two globally gridded datasets (World Ocean Atlas and Met Office EN3 datasets). The resulting 12 estimates of the 1979–2007 mean surface-forced streamfunction all depict a subpolar cell, with maxima north of 45°N, near σ = 27.5 kg m−3, and a subtropical cell between 20° and 40°N, near σ = 26.1 kg m−3. The mean magnitude of the subpolar cell varies between 12 and 18 Sv (1 Sv ≡ 106 m3 s−1), consistent with estimates of the overturning circulation from subsurface observations. Analysis of the thermal and haline components of the surface density fluxes indicates that large differences in the inferred low-latitude circulation are largely a result of the biases in reanalysis net heat flux fields, which range in the global mean from −13 to 19 W m−2. The different estimates of temporal variability in the subpolar cell are well correlated with each other. This suggests that the uncertainty associated with the choice of reanalysis product does not critically limit the ability of the method to infer the variability in the subpolar overturning. In contrast, the different estimates of subtropical variability are poorly correlated with each other, and only a subset of them captures a significant fraction of the variability in independently estimated North Atlantic Subtropical Mode Water volume.
    Description: JPG is funded by UK Natural Environment Research Council New Investigator Grant NE/I001654/1. Y-OK was supported by the U.S. National Science Foundation under Grant OCE-0424492. RJB is supported by a fellowship from the UK National Centre for Earth Observation.
    Description: 2014-11-15
    Keywords: Atmosphere-ocean interaction ; Meridional overturning circulation ; Ocean circulation
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  • 34
    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 144 (2016): 877-896, doi:10.1175/MWR-D-15-0275.1.
    Description: This paper describes a new model (method) called Satellite-derived North Atlantic Profiles (SNAP) that seeks to provide a high-resolution, near-real-time ocean thermal field to aid tropical cyclone (TC) forecasting. Using about 139 000 observed temperature profiles, a spatially dependent regression model is developed for the North Atlantic Ocean during hurricane season. A new step introduced in this work is that the daily mixed layer depth is derived from the output of a one-dimensional Price–Weller–Pinkel ocean mixed layer model with time-dependent surface forcing. The accuracy of SNAP is assessed by comparison to 19 076 independent Argo profiles from the hurricane seasons of 2011 and 2013. The rms differences of the SNAP-estimated isotherm depths are found to be 10–25 m for upper thermocline isotherms (29°–19°C), 35–55 m for middle isotherms (18°–7°C), and 60–100 m for lower isotherms (6°–4°C). The primary error sources include uncertainty of sea surface height anomaly (SSHA), high-frequency fluctuations of isotherm depths, salinity effects, and the barotropic component of SSHA. These account for roughly 29%, 25%, 19%, and 10% of the estimation error, respectively. The rms differences of TC-related ocean parameters, upper-ocean heat content, and averaged temperature of the upper 100 m, are ~10 kJ cm−2 and ~0.8°C, respectively, over the North Atlantic basin. These errors are typical also of the open ocean underlying the majority of TC tracks. Errors are somewhat larger over regions of greatest mesoscale variability (i.e., the Gulf Stream and the Loop Current within the Gulf of Mexico).
    Description: IFP is supported by Grants NSC 101-2628-M-002-001-MY4 and MOST 103-2111-M-002 -002 -MY3. JFP and SRJ were supported by the U.S. Office of Naval Research under the project “Impact of Typhoons on the North Pacific, ITOP.”
    Description: 2016-06-08
    Keywords: Atm/Ocean Structure/ Phenomena ; Atmosphere-ocean interaction ; Oceanic mixed layer ; Tropical cyclones ; Observational techniques and algorithms ; Satellite observations
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  • 35
    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): 2861–2885, doi:10.1175/JCLI-D-13-00437.1.
    Description: The representation of the El Niño–Southern Oscillation (ENSO) under historical forcing and future projections is analyzed in 34 models from the Coupled Model Intercomparison Project phase 5 (CMIP5). Most models realistically simulate the observed intensity and location of maximum sea surface temperature (SST) anomalies during ENSO events. However, there exist systematic biases in the westward extent of ENSO-related SST anomalies, driven by unrealistic westward displacement and enhancement of the equatorial wind stress in the western Pacific. Almost all CMIP5 models capture the observed asymmetry in magnitude between the warm and cold events (i.e., El Niños are stronger than La Niñas) and between the two types of El Niños: that is, cold tongue (CT) El Niños are stronger than warm pool (WP) El Niños. However, most models fail to reproduce the asymmetry between the two types of La Niñas, with CT stronger than WP events, which is opposite to observations. Most models capture the observed peak in ENSO amplitude around December; however, the seasonal evolution of ENSO has a large range of behavior across the models. The CMIP5 models generally reproduce the duration of CT El Niños but have biases in the evolution of the other types of events. The evolution of WP El Niños suggests that the decay of this event occurs through heat content discharge in the models rather than the advection of SST via anomalous zonal currents, as seems to occur in observations. No consistent changes are seen across the models in the location and magnitude of maximum SST anomalies, frequency, or temporal evolution of these events in a warmer world.
    Description: 2014-10-15
    Keywords: Atmosphere-ocean interaction ; Climate change ; Climate variability ; ENSO ; Climate models ; Model evaluation/performance
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  • 36
    Publication Date: 2022-06-10
    Description: Author Posting. © American Meteorological Society , 2021. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Zippel, S. F., Farrar, J. T., Zappa, C. J., Miller, U., St Laurent, L., Ijichi, T., Weller, R. A., McRaven, L., Nylund, S., & Le Bel, D. Moored turbulence measurements using pulse-coherent doppler sonar. Journal of Atmospheric and Oceanic Technology, 38(9), (2021): 1621–1639, https://doi.org/10.1175/JTECH-D-21-0005.1.
    Description: Upper-ocean turbulence is central to the exchanges of heat, momentum, and gases across the air–sea interface and therefore plays a large role in weather and climate. Current understanding of upper-ocean mixing is lacking, often leading models to misrepresent mixed layer depths and sea surface temperature. In part, progress has been limited by the difficulty of measuring turbulence from fixed moorings that can simultaneously measure surface fluxes and upper-ocean stratification over long time periods. Here we introduce a direct wavenumber method for measuring turbulent kinetic energy (TKE) dissipation rates ϵ from long-enduring moorings using pulse-coherent ADCPs. We discuss optimal programming of the ADCPs, a robust mechanical design for use on a mooring to maximize data return, and data processing techniques including phase-ambiguity unwrapping, spectral analysis, and a correction for instrument response. The method was used in the Salinity Processes Upper-Ocean Regional Study (SPURS) to collect two year-long datasets. We find that the mooring-derived TKE dissipation rates compare favorably to estimates made nearby from a microstructure shear probe mounted to a glider during its two separate 2-week missions for O(10−8) ≤ ϵ ≤ O(10−5) m2 s−3. Periods of disagreement between turbulence estimates from the two platforms coincide with differences in vertical temperature profiles, which may indicate that barrier layers can substantially modulate upper-ocean turbulence over horizontal scales of 1–10 km. We also find that dissipation estimates from two different moorings at 12.5 and at 7 m are in agreement with the surface buoyancy flux during periods of strong nighttime convection, consistent with classic boundary layer theory.
    Description: This work was funded by NASA as part of the Salinity Processes in the Upper Ocean Regional Study (SPURS), supporting field work for SPURS-1 (NASA Grant NNX11AE84G), for SPURS-2 (NASA Grant NNX15AG20G), and for analysis (NASA Grant 80NSSC18K1494). Funding for early iterations of this project associated with the VOCALS project and Stratus 9 mooring was provided by NSF (Awards 0745508 and 0745442). Additional funding was provided by ONR Grant N000141812431 and NSF Award 1756839. The Stratus Ocean Reference Station is funded by the Global Ocean Monitoring and Observing Program of the National Oceanic and Atmospheric Administration (CPO FundRef Number 100007298), through the Cooperative Institute for the North Atlantic Region (CINAR) under Cooperative Agreement NA14OAR4320158. Microstructure measurements made from the glider were supported by NSF (Award 1129646).
    Keywords: Ocean ; Turbulence ; Atmosphere-ocean interaction ; Boundary layer ; Oceanic mixed layer ; In situ oceanic observations
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  • 37
    Publication Date: 2022-06-17
    Description: Author Posting. © American Meteorological Society, 2021. 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 34(22), (2021): 9093–9113, https://doi.org/10.1175/JCLI-D-21-0142.1.
    Description: This study examines the role of the relative wind (RW) effect (wind relative to ocean current) in the regional ocean circulation and extratropical storm track in the south Indian Ocean. Comparison of two high-resolution regional coupled model simulations with and without the RW effect reveals that the most conspicuous ocean circulation response is the significant weakening of the overly energetic anticyclonic standing eddy off Port Elizabeth, South Africa, a biased feature ascribed to upstream retroflection of the Agulhas Current (AC). This opens a pathway through which the AC transports the warm and salty water mass from the subtropics, yielding marked increases in sea surface temperature (SST), upward turbulent heat flux (THF), and meridional SST gradient in the Agulhas retroflection region. These thermodynamic and dynamic changes are accompanied by the robust strengthening of the local low-tropospheric baroclinicity and the baroclinic wave activity in the atmosphere. Examination of the composite life cycle of synoptic-scale storms subjected to the high-THF events indicates a robust strengthening of the extratropical storms far downstream. Energetics calculations for the atmosphere suggest that the baroclinic energy conversion from the basic flow is the chief source of increased eddy available potential energy, which is subsequently converted to eddy kinetic energy, providing for the growth of transient baroclinic waves. Overall, the results suggest that the mechanical and thermal air–sea interactions are inherently and inextricably linked together to substantially influence the extratropical storm tracks in the south Indian Ocean.
    Description: Seo acknowledges the support from the NSF (OCE-2022846), NOAA (NA19OAR4310376), ONR (N00014-17-12398), and the Andrew W. Mellon Foundation Endowed Fund for Innovative Research at Woods Hole Oceanographic Institution (WHOI). Song is supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (NRF-2019R1C1C1003663). O’Neill was supported by the NASA Grants 80NSSC19K1117 and 80NSSC19K1011.
    Keywords: Atmosphere-ocean interaction ; Extratropical cyclones ; Wind stress ; Boundary currents ; Storm tracks
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  • 38
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2020. 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 33(10), (2020): 4109-4120, doi:10.1175/JCLI-D-19-0294.1.
    Description: This study suggests that the Gulf Stream influence on the wintertime North Atlantic troposphere is most pronounced when the eddy-driven jet (EDJ) is farthest south and better collocated with the Gulf Stream. Using the reanalysis dataset NCEP-CFSR for December–February 1979–2009, the daily EDJ latitude is separated into three regimes (northern, central, and southern). It is found that the average trajectory of atmospheric fronts covaries with EDJ latitude. In the southern EDJ regime (~19% of the time), the frequency of near-surface atmospheric fronts that pass across the Gulf Stream is maximized. Analysis suggests that this leads to significant strengthening in near-surface atmospheric frontal convergence resulting from strong air–sea sensible heat flux gradients (due to strong temperature gradients in the atmosphere and ocean). In recent studies, it was shown that the pronounced band of time-mean near-surface wind convergence across the Gulf Stream is set by atmospheric fronts. Here, it is shown that an even smaller subset of atmospheric fronts—those associated with a southern EDJ—primarily sets the time mean, due to enhanced Gulf Stream air–sea interaction. Furthermore, statistically significant anomalies in vertical velocity extending well above the boundary layer are identified in association with changes in EDJ latitude. These anomalies are particularly strong for a southern EDJ and are spatially consistent with increases in near-surface atmospheric frontal convergence over the Gulf Stream. These results imply that much of the Gulf Stream influence on the time-mean atmosphere is modulated on synoptic time scales, and enhanced when the EDJ is farthest south.
    Description: For part of this study, R. P. was funded by the Weston Howland Jr. postdoctoral scholarship at Woods Hole Oceanographic Institution. We gratefully acknowledge the support to Y.-O. K. from the NOAA CPO Climate Variability and Predictability program (NA13OAR4310139), the DOE Regional and Global Model Analysis program (DE-SC0014433 and DE-SC0019492), and the NSF AGS Climate and Large-scale Dynamics program and OCE Physical Oceanography program (AGS-1355339). We thank NCAR for allowing access to the NCEP-CFSR dataset, accessible at https://rda.ucar.edu. We thank the editor Hisashi Nakamura and the three reviewers whose comments have helped greatly improve the manuscript.
    Description: 2020-10-13
    Keywords: Atmosphere-ocean interaction ; Atmosphere-ocean interaction
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  • 39
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2020. 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 33(19), (2020): 8415-8437, doi:10.1175/JCLI-D-19-0954.1.
    Description: Four state-of-the-art satellite-based estimates of ocean surface latent heat fluxes (LHFs) extending over three decades are analyzed, focusing on the interannual variability and trends of near-global averages and regional patterns. Detailed intercomparisons are made with other datasets including 1) reduced observation reanalyses (RedObs) whose exclusion of satellite data renders them an important independent diagnostic tool; 2) a moisture budget residual LHF estimate using reanalysis moisture transport, atmospheric storage, and satellite precipitation; 3) the ECMWF Reanalysis 5 (ERA5); 4) Remote Sensing Systems (RSS) single-sensor passive microwave and scatterometer wind speed retrievals; and 5) several sea surface temperature (SST) datasets. Large disparities remain in near-global satellite LHF trends and their regional expression over the 1990–2010 period, during which time the interdecadal Pacific oscillation changed sign. The budget residual diagnostics support the smaller RedObs LHF trends. The satellites, ERA5, and RedObs are reasonably consistent in identifying contributions by the 10-m wind speed variations to the LHF trend patterns. However, contributions by the near-surface vertical humidity gradient from satellites and ERA5 trend upward in time with respect to the RedObs ensemble and show less agreement in trend patterns. Problems with wind speed retrievals from Special Sensor Microwave Imager/Sounder satellite sensors, excessive upward trends in trends in Optimal Interpolation Sea Surface Temperature (OISST AVHRR-Only) data used in most satellite LHF estimates, and uncertainties associated with poor satellite coverage before the mid-1990s are noted. Possibly erroneous trends are also identified in ERA5 LHF associated with the onset of scatterometer wind data assimilation in the early 1990s.
    Description: FRR, JBR, and MGB acknowledge support for this investigation through the NASA Energy and Water Cycle Study (NEWS), Dr. Jared Entin, Program Manager. MS acknowledges the financial support by the EUMETSAT member states through CM SAF. The NOAA-CIRES-DOE Twentieth Century Reanalysis Project version 3 used resources of the National Energy Research Scientific Computing Center managed by Lawrence Berkeley National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract DE-AC02-05CH11231 and used resources of NOAA’s remotely deployed high-performance computing systems. Support for the Twentieth Century Reanalysis Project version 3 dataset is provided by the U.S. DOE, Office of Science Biological and Environmental Research (BER), by the NOAA Climate Program Office, and by the NOAA Physical Sciences Laboratory. RSS products are supported by funding from the NASA Earth Science Division. H. Tomita acknowledges support from JSPS Grants JP18H03726, JP18H03737, and JP19H05696 and JAXA Announcement EO-2. We gratefully acknowledge provision and institutional support for the following SST datasets: ESA CCI (http://data.ceda.ac.uk/neodc/esacci/sst/data/CDR_v2/); NOAA Optimum Interpolation 1/4 Degree Daily Sea Surface Temperature (OISST) Analysis, version 2, (https:/doi.org/10.7289/V5SQ8XB5); NOAA ERSST v5 (https:/doi.org/10.7289/V5T72FNM) and access to COBE-SST2 provided by the NOAA/OAR/ESRL PSD (boyin.huang@noaa.gov); 20CRv3 data are available at the NERSC Science Tape Gateway via portal.nersc.gov.
    Description: 2021-03-01
    Keywords: Atmosphere-ocean interaction ; Hydrologic cycle ; Microwave observations ; Satellite observations ; Reanalysis data ; Decadal variability
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  • 40
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2020. 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 33(6), (2020): 2389-2406, doi:10.1175/JCLI-D-19-0112.1.
    Description: This study investigates the modulation of North Pacific Oscillation (NPO) variability upon initiation of the East Asian winter monsoon (EAWM). The data show that the initiation of EAWM in the Philippine Sea strongly connects to the southern lobe variability of the NPO in January followed by a basin-scale oceanic Victoria mode pattern. No apparent connection was found for the northern lobe of the NPO when the ENSO signals are removed. The strengthening of the EAWM in November interacts with the Kuroshio front and generates a low-level heating source in the Philippine Sea. Significant Rossby wave sources are then formed in the lower to midtroposphere. Wave ray tracing analyses confirm the atmospheric teleconnection established by the Rossby wave propagation in the mid- to upper troposphere. Analyses of the origin of wave trajectories from the Philippine Sea show a clear eastward propagating pathway that affects the southern lobe of the NPO from the southern lobe of the western Pacific pattern at 500 hPa and above on the time scale of 20 days. No ray trajectories from the lower troposphere can propagate eastward to influence the central-eastern subtropical Pacific. The wave propagation process is further supported by the coupled model experiments.
    Description: We thank three anonymous reviewers for their constructive comments that have helped to improve the clarity of the presentation. This study was supported by the MOST Grants 107-2611-M-002-013-MY4 and 108-2111-M-002-006 -MY3, Taiwan.
    Description: 2020-08-21
    Keywords: Atmosphere-ocean interaction ; ENSO ; Climate variability ; Interannual variability
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  • 41
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2018. 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 31 (2018): 8627-8643, doi:10.1175/JCLI-D-18-0010.1.
    Description: Drought has severe consequences for humans and their environment, yet we have a limited understanding of the drivers of drought across the full range of time scales on which it occurs. Here, the atmosphere and ocean conditions that drive this continuum of drought variability in southwestern North America (SWNA) are studied using the latest observationally based products, paleoclimate reconstructions, and state-of-the-art Earth system model simulations of the last millennium. A novel application of the self-organizing maps (SOM) methodology allows for a visualization of the continuum of climate states coinciding with thousands of droughts of varying lengths in last millennium simulations from the Community Earth System Model (CESM), the Goddard Institute for Space Studies Model E2-R (GISS E2-R), and eight other members from phase 5 of the Coupled Model Intercomparison Project (CMIP5). It is found that most droughts are associated with a cool Pacific decadal oscillation (PDO) pattern, but persistent droughts can coincide with a variety of ocean–atmosphere states, including time periods showing a warm PDO or weak ocean–atmosphere anomalies. Many CMIP5 models simulate similar SWNA teleconnection patterns, but the SOM analysis demonstrates that models simulate different continuums of ocean–atmosphere states coinciding with droughts of different lengths, suggesting fundamental differences in their drought dynamics. These findings have important implications for our understanding and simulation of the drivers of persistent drought, and for their potential predictability.
    Description: The National Science Foundation EaSM2 Grant (AGS1243125) supported this work.
    Keywords: Atmosphere-ocean interaction ; Drought ; Paleoclimate ; Ensembles ; General circulation models ; Climate variability
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  • 42
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 30 (2017): 4965-4981, doi:10.1175/JCLI-D-16-0228.1.
    Description: To improve the understanding of storm tracks and western boundary current (WBC) interactions, surface storm tracks in 12 CMIP5 models are examined against ERA-Interim. All models capture an equatorward displacement toward the WBCs in the locations of the surface storm tracks’ maxima relative to those at 850 hPa. An estimated storm-track metric is developed to analyze the location of the surface storm track. It shows that the equatorward shift is influenced by both the lower-tropospheric instability and the baroclinicity. Basin-scale spatial correlations between models and ERA-Interim for the storm tracks, near-surface stability, SST gradient, and baroclinicity are calculated to test the ability of the GCMs’ match reanalysis. An intermodel comparison of the spatial correlations suggests that differences (relative to ERA-Interim) in the position of the storm track aloft have the strongest influence on differences in the surface storm-track position. However, in the North Atlantic, biases in the surface storm track north of the Gulf Stream are related to biases in the SST. An analysis of the strength of the storm tracks shows that most models generate a weaker storm track at the surface than 850 hPa, consistent with observations, although some outliers are found. A linear relationship exists among the models between storm-track amplitudes at 500 and 850 hPa, but not between 850 hPa and the surface. In total, the work reveals a dual role in forcing the surface storm track from aloft and from the ocean surface in CMIP5 models, with the atmosphere having the larger relative influence.
    Description: JFB was partially supported by the NOAA Climate Program Office’s Modeling, Analysis, Predictions, and Projections program (Grant NA15OAR4310094). Y-OK was supported by NSF Division of Atmospheric and Geospace Science Climate and Large-scale Dynamics Program (AGS-1355339), NASA Physical Oceanography Program (NNX13AM59G), and DOE Office of Biological and Environmental Research Regional and Global Climate Modeling Program (DE-SC0014433). RJS was supported by DOE Office of Biological and Environmental Research (DE-SC0006743) and NSF Directorate for Geosciences Division of Ocean Sciences (1419584),
    Description: 2017-10-03
    Keywords: Atmosphere-ocean interaction ; Storm tracks
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  • 43
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 47 (2017): 1921-1939, doi:10.1175/JPO-D-16-0146.1.
    Description: The role of surface gravity waves in structuring the air–sea momentum flux is examined in the middle reaches of Chesapeake Bay. Observed wave spectra showed that wave direction in Chesapeake Bay is strongly correlated with basin geometry. Waves preferentially developed in the direction of maximum fetch, suggesting that dominant wave frequencies may be commonly and persistently misaligned with local wind forcing. Direct observations from an ultrasonic anemometer and vertical array of ADVs show that the magnitude and direction of stress changed across the air–sea interface, suggesting that a stress divergence occurred at or near the water surface. Using a numerical wave model in combination with direct flux measurements, the air–sea momentum flux was partitioned between the surface wave field and the mean flow. Results indicate that the surface wave field can store or release a significant fraction of the total momentum flux depending on the direction of the wind. When wind blew across dominant fetch axes, the generation of short gravity waves stored as much as 40% of the total wind stress. Accounting for the storage of momentum in the surface wave field closed the air–sea momentum budget. Agreement between the direction of Lagrangian shear and the direction of the stress vector in the mixed surface layer suggests that the observed directional difference was due to the combined effect of breaking waves producing downward sweeps of momentum in the direction of wave propagation and the straining of that vorticity field in a manner similar to Langmuir turbulence.
    Description: This work was supported by National Science Foundation Grants OCE-1061609 and OCE-1339032.
    Description: 2018-01-13
    Keywords: Atmosphere-ocean interaction ; Coastal flows ; Mixing ; Momentum ; Wind stress ; Wind waves
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  • 44
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. 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 32(8), (2019): 2185-2205. doi:10.1175/JCLI-D-18-0538.1.
    Description: Much attention has been paid to the climatic impacts of changes in the Kuroshio Extension, instead of the Kuroshio in the East China Sea (ECS). This study, however, reveals the prominent influences of the lateral shift of the Kuroshio at interannual time scale in late spring [April–June (AMJ)] on the sea surface temperature (SST) and precipitation in summer around the ECS, based on high-resolution satellite observations and ERA-Interim. A persistent offshore displacement of the Kuroshio during AMJ can result in cold SST anomalies in the northern ECS and the Japan/East Sea until late summer, which correspondingly causes anomalous cooling of the lower troposphere. Consequently, the anomalous cold SST in the northern ECS acts as a key driver to robustly enhance the precipitation from the Yangtze River delta to Kyushu in early summer (May–August) and over the central ECS in late summer (July–September). In view of the moisture budget analysis, two different physical processes modulated by the lateral shift of the Kuroshio are identified to account for the distinct responses of precipitation in early and late summer, respectively. First, the anomalous cold SST in the northern ECS induced by the Kuroshio offshore shift is likely conducive to the earlier arrival of the mei-yu–baiu front at 30°–32°N and its subsequent slower northward movement, which may prolong the local rainy season, leading to the increased rain belt in early summer. Second, the persistent cold SST anomalies in late summer strengthen the near-surface baroclinicity and the associated strong atmospheric fronts embedded in the extratropical cyclones over the central ECS, which in turn enhances the local rainfall.
    Description: We appreciate three anonymous reviewers for their thoughtful and constructive comments. This work is supported by the National Key Research and Development Program of China (2016YFA0601804), the National Natural Science Foundation of China (NSFC) Projects (91858102, 41490643, 41490640, 41506009, U1606402) and the OUC–WHOI joint research program (21366).
    Description: 2019-10-01
    Keywords: Continental shelf/slope ; Atmosphere-ocean interaction ; Boundary currents ; Precipitation ; Interannual variability
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  • 45
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. 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 49(4), (2019): 1035-1053, doi:10.1175/JPO-D-18-0136.1.
    Description: Ocean stratification and the vertical extent of the mixed layer influence the rate at which the ocean and atmosphere exchange properties. This process has direct impacts for anthropogenic heat and carbon uptake in the Southern Ocean. Submesoscale instabilities that evolve over space (1–10 km) and time (from hours to days) scales directly influence mixed layer variability and are ubiquitous in the Southern Ocean. Mixed layer eddies contribute to mixed layer restratification, while down-front winds, enhanced by strong synoptic storms, can erode stratification by a cross-frontal Ekman buoyancy flux. This study investigates the role of these submesoscale processes on the subseasonal and interannual variability of the mixed layer stratification using four years of high-resolution glider data in the Southern Ocean. An increase of stratification from winter to summer occurs due to a seasonal warming of the mixed layer. However, we observe transient decreases in stratification lasting from days to weeks, which can arrest the seasonal restratification by up to two months after surface heat flux becomes positive. This leads to interannual differences in the timing of seasonal restratification by up to 36 days. Parameterizing the Ekman buoyancy flux in a one-dimensional mixed layer model reduces the magnitude of stratification compared to when the model is run using heat and freshwater fluxes alone. Importantly, the reduced stratification occurs during the spring restratification period, thereby holding important implications for mixed layer dynamics in climate models as well as physical–biological coupling in the Southern Ocean.
    Description: MdP acknowledges numerous research visits to the Department of Marine Science, University of Gothenburg, and a visit to Woods Hole Oceanographic Institution, which greatly enhanced this work. We thank SANAP and the captain and crew of the S.A. Agulhas II for their assistance in the deployment and retrieval of the gliders. We acknowledge the work of SAMERC-STS for housing, managing, and piloting the gliders. SS was supported by NRF-SANAP Grant SNA14071475720 and a Wallenberg Academy Fellowship (WAF 2015.0186). Lastly, SS thanks the numerous technical assistance, advice, and IOP hosting provided by Geoff Shilling and Craig Lee of the Applied Physics Laboratory, University of Washington.
    Description: 2020-04-11
    Keywords: Atmosphere-ocean interaction ; Fronts ; Oceanic mixed layer ; In situ oceanic observations ; Interannual variability ; Seasonal cycle
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  • 46
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 30 (2017): 9679-9702, doi:10.1175/JCLI-D-16-0707.1.
    Description: The North Atlantic atmospheric circulation response to the meridional shifts of the Gulf Stream (GS) path is examined using a large ensemble of high-resolution hemispheric-scale Weather Research and Forecasting Model simulations. The model is forced with a broad range of wintertime sea surface temperature (SST) anomalies derived from a lag regression on a GS index. The primary result of the model experiments, supported in part by an independent analysis of a reanalysis dataset, is that the large-scale quasi-steady North Atlantic circulation response is remarkably nonlinear about the sign and amplitude of the SST anomaly chosen over a wide range of GS shift scenarios. The nonlinear response prevails over the weak linear response and resembles the negative North Atlantic Oscillation (NAO), the leading intrinsic mode of variability in the model and the observations. Further analysis of the associated dynamics reveals that the nonlinear responses are accompanied by the shift of the North Atlantic eddy-driven jet, which is reinforced, with nearly equal importance, by the high-frequency transient eddy feedback and the low-frequency wave-breaking events. Additional sensitivity simulations confirm that the nonlinearity of the circulation response is a robust feature found over the broad parameter space encompassing not only the varied SST but also the absence/presence of tropical influence, the varying lateral boundary conditions, and the initialization scheme. The result highlights the fundamental importance of the intrinsically nonlinear transient eddy dynamics and the eddy–mean flow interactions in generating the nonlinear downstream response to the meridional shifts in the Gulf Stream.
    Description: The authors are grateful for the support from NASA (NNX13AM59G) and the NSF (AGS-1355339, OCE-1419235).
    Description: 2018-05-07
    Keywords: North Atlantic Ocean ; Blocking ; North Atlantic Oscillation ; Atmosphere-ocean interaction ; Regional models ; Climate variability
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  • 47
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2020. 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 33(17), (2020): 7697-7714, https://doi.org/10.1175/JCLI-D-20-0115.1.
    Description: The decadal to multidecadal mixed layer variability is investigated in a region south of the Kuroshio Extension (130°E–180°, 25°–35°N), an area where the North Pacific subtropical mode water forms, during 1948–2012. By analyzing the mixed layer heat budget with different observational and reanalysis data, here we show that the decadal to multidecadal variability of the mixed layer temperature and mixed layer depth is covaried with the Atlantic multidecadal oscillation (AMO), instead of the Pacific decadal oscillation (PDO). The mixed layer temperature has strong decadal to multidecadal variability, being warm before 1970 and after 1990 (AMO positive phase) and cold during 1970–90 (AMO negative phase), and so does the mixed layer depth. The dominant process for the mixed layer temperature decadal to multidecadal variability is the Ekman advection, which is controlled by the zonal wind changes related to the AMO. The net heat flux into the ocean surface Qnet acts as a damping term and it is mainly from the effect of latent heat flux and partially from sensible heat flux. While the wind as well as mixed layer temperature decadal changes related to the PDO are weak in the western Pacific Ocean. Our finding proposes the possible influence of the AMO on the northwestern Pacific Ocean mixed layer variability, and could be a potential predictor for the decadal to multidecadal climate variability in the western Pacific Ocean.
    Description: Xiaopei Lin is supported by the China’s national key research and development projects (2016YFA0601803) and the National Natural Science Foundation of China (41925025 and U1606402). Baolan Wu is supported by the China Scholarship Council (201806330010). Lisan Yu thanks NOAA for support for her study on climate change and variability.
    Keywords: Atmosphere-ocean interaction ; Boundary currents ; Hadley circulation ; Ocean dynamics ; Teleconnections
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  • 48
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2012. 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 25 (2012): 7781–7801, doi:10.1175/JCLI-D-11-00442.1.
    Description: Air–sea fluxes from the Community Climate System Model version 4 (CCSM4) are compared with the Coordinated Ocean-Ice Reference Experiment (CORE) dataset to assess present-day mean biases, variability errors, and late twentieth-century trend differences. CCSM4 is improved over the previous version, CCSM3, in both air–sea heat and freshwater fluxes in some regions; however, a large increase in net shortwave radiation into the ocean may contribute to an enhanced hydrological cycle. The authors provide a new baseline for assessment of flux variance at annual and interannual frequency bands in future model versions and contribute a new metric for assessing the coupling between the atmospheric and oceanic planetary boundary layer (PBL) schemes of any climate model. Maps of the ratio of CCSM4 variance to CORE reveal that variance on annual time scales has larger error than on interannual time scales and that different processes cause errors in mean, annual, and interannual frequency bands. Air temperature and specific humidity in the CCSM4 atmospheric boundary layer (ABL) follow the sea surface conditions much more closely than is found in CORE. Sensible and latent heat fluxes are less of a negative feedback to sea surface temperature warming in the CCSM4 than in the CORE data with the model’s PBL allowing for more heating of the ocean’s surface.
    Description: The CESM project is supported by the National Science Foundation and the Office of Science (BER) of the U.S. Department of Energy. S. Stevensonwas supported byNASAGrantNNX09A020H and B. Fox-Kemper by Grants NSF 0934737 and NASA NNX09AF38G.
    Description: 2013-05-15
    Keywords: Atmosphere-ocean interaction ; Boundary layer ; Sea surface temperature ; Climate models ; Coupled models ; Model evaluation/performance
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  • 49
    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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  • 50
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2020. 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 33(15), (2020): 6707-6730, https://doi.org/10.1175/JCLI-D-19-0579.1.
    Description: The long-term trend of sea surface salinity (SSS) reveals an intensification of the global hydrological cycle due to human-induced climate change. This study demonstrates that SSS variability can also be used as a measure of terrestrial precipitation on interseasonal to interannual time scales, and to locate the source of moisture. Seasonal composites during El Niño–Southern Oscillation/Indian Ocean dipole (ENSO/IOD) events are used to understand the variations of moisture transport and precipitation over Australia, and their association with SSS variability. As ENSO/IOD events evolve, patterns of positive or negative SSS anomaly emerge in the Indo-Pacific warm pool region and are accompanied by atmospheric moisture transport anomalies toward Australia. During co-occurring La Niña and negative IOD events, salty anomalies around the Maritime Continent (north of Australia) indicate freshwater export and are associated with a significant moisture transport that converges over Australia to create anomalous wet conditions. In contrast, during co-occurring El Niño and positive IOD events, a moisture transport divergence anomaly over Australia results in anomalous dry conditions. The relationship between SSS and atmospheric moisture transport also holds for pure ENSO/IOD events but varies in magnitude and spatial pattern. The significant pattern correlation between the moisture flux divergence and SSS anomaly during the ENSO/IOD events highlights the associated ocean–atmosphere coupling. A case study of the extreme hydroclimatic events of Australia (e.g., the 2010/11 Brisbane flood) demonstrates that the changes in SSS occur before the peak of ENSO/IOD events. This raises the prospect that tracking of SSS variability could aid the prediction of Australian rainfall.
    Description: This research is funded through the Earth System and Climate Change Hub of the Australian government’s National Environmental Science Programme. The assistance of computing resources from the National Computational Infrastructure supported by the Australian Government is acknowledged. CCU acknowledges support from the U.S. National Science Foundation under Grant OCE-1663704. MF was supported by the by Centre for Southern Hemisphere Oceans Research (CSHOR), which is a joint initiative between the Qingdao National Laboratory for Marine Science and Technology (QNLM), CSIRO, University of New South Wales and University of Tasmania. The authors wish to acknowledge PyFerret (https://ferret.pmel.noaa.gov/Ferret/) and the Cimate Data Operators (https://code.mpimet.mpg.de/projects/cdo/) for the data analysis and graphical representations in this paper.
    Keywords: Atmosphere-ocean interaction ; El Nino ; Extreme events ; La Nina ; Precipitation ; Salinity
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  • 51
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2020. 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 33(9), (2020): 3863-3882, doi:10.1175/JCLI-D-19-0687.1.
    Description: The direct response of the cold-season atmospheric circulation to the Arctic sea ice loss is estimated from observed sea ice concentration (SIC) and an atmospheric reanalysis, assuming that the atmospheric response to the long-term sea ice loss is the same as that to interannual pan-Arctic SIC fluctuations with identical spatial patterns. No large-scale relationship with previous interannual SIC fluctuations is found in October and November, but a negative North Atlantic Oscillation (NAO)/Arctic Oscillation follows the pan-Arctic SIC fluctuations from December to March. The signal is field significant in the stratosphere in December, and in the troposphere and tropopause thereafter. However, multiple regressions indicate that the stratospheric December signal is largely due to concomitant Siberian snow-cover anomalies. On the other hand, the tropospheric January–March NAO signals can be unambiguously attributed to SIC variability, with an Iceland high approaching 45 m at 500 hPa, a 2°C surface air warming in northeastern Canada, and a modulation of blocking activity in the North Atlantic sector. In March, a 1°C northern Europe cooling is also attributed to SIC. An SIC impact on the warm Arctic–cold Eurasia pattern is only found in February in relation to January SIC. Extrapolating the most robust results suggests that, in the absence of other forcings, the SIC loss between 1979 and 2016 would have induced a 2°–3°C decade−1 winter warming in northeastern North America and a 40–60 m decade−1 increase in the height of the Iceland high, if linearity and perpetual winter conditions could be assumed.
    Description: This research was supported by the Blue-Action project (European Union’s Horizon 2020 research and innovation program, Grant 727852) and by the National Science Foundation (OPP 1736738).
    Description: 2020-10-06
    Keywords: Atmosphere-ocean interaction ; Climate change ; Climate variability ; Ice loss/growth
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  • 52
    Publication Date: 2016-07-28
    Description: Genetic engineering projects often require control over when a protein is degraded. To this end, we use a fusion between a degron and an inactivating peptide that can be added to the N-terminus of a protein. When the corresponding protease is expressed, it cleaves the peptide and the protein is degraded. Three protease:cleavage site pairs from Potyvirus are shown to be orthogonal and active in exposing degrons, releasing inhibitory domains and cleaving polyproteins. This toolbox is applied to the design of genetic circuits as a means to control regulator activity and degradation. First, we demonstrate that a gate can be constructed by constitutively expressing an inactivated repressor and having an input promoter drive the expression of the protease. It is also shown that the proteolytic release of an inhibitory domain can improve the dynamic range of a transcriptional gate (200-fold repression). Next, we design polyproteins containing multiple repressors and show that their cleavage can be used to control multiple outputs. Finally, we demonstrate that the dynamic range of an output can be improved (8-fold to 190-fold) with the addition of a protease-cleaved degron. Thus, controllable proteolysis offers a powerful tool for modulating and expanding the function of synthetic gene circuits.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 53
    Publication Date: 2013-09-26
    Description: In reverse genetics, a gene’s function is elucidated through targeted modifications in the coding region or associated DNA cis -regulatory elements. To this purpose, recently developed customizable transcription activator-like effector nucleases (TALENs) have proven an invaluable tool, allowing introduction of double-strand breaks at predetermined sites in the genome. Here we describe a practical and efficient method for the targeted genome engineering in Drosophila . We demonstrate TALEN-mediated targeted gene integration and efficient identification of mutant flies using a traceable marker phenotype. Furthermore, we developed an easy TALEN assembly (easyT) method relying on simultaneous reactions of DNA Bae I digestion and ligation, enabling construction of complete TALENs from a monomer unit library in a single day. Taken together, our strategy with easyT and TALEN-plasmid microinjection simplifies mutant generation and enables isolation of desired mutant fly lines in the F 1 generation.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 54
    Publication Date: 2013-06-08
    Description: Transcription activator-like effector nucleases (TALENs) are a powerful new approach for targeted gene disruption in various animal models, but little is known about their activities in Mus musculus, the widely used mammalian model organism. Here, we report that direct injection of in vitro transcribed messenger RNA of TALEN pairs into mouse zygotes induced somatic mutations, which were stably passed to the next generation through germ-line transmission. With one TALEN pair constructed for each of 10 target genes, mutant F0 mice for each gene were obtained with the mutation rate ranged from 13 to 67% and an average of ~40% of total healthy newborns with no significant differences between C57BL/6 and FVB/N genetic background. One TALEN pair with single mismatch to their intended target sequence in each side failed to yield any mutation. Furthermore, highly efficient germ-line transmission was obtained, as all the F0 founders tested transmitted the mutations to F1 mice. In addition, we also observed that one bi-allele mutant founder of Lepr gene, encoding Leptin receptor, had similar diabetic phenotype as db/db mouse. Together, our results suggest that TALENs are an effective genetic tool for rapid gene disruption with high efficiency and heritability in mouse with distinct genetic background.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 55
    Publication Date: 2013-06-08
    Description: We describe a new cell-free protein synthesis (CFPS) method for site-specific incorporation of non-natural amino acids (nnAAs) into proteins in which the orthogonal tRNA (o-tRNA) and the modified protein (i.e. the protein containing the nnAA) are produced simultaneously. Using this method, 0.9–1.7 mg/ml of modified soluble super-folder green fluorescent protein (sfGFP) containing either p -azido- l -phenylalanine (pAzF) or p -propargyloxy- l -phenylalanine (pPaF) accumulated in the CFPS solutions; these yields correspond to 50–88% suppression efficiency. The o-tRNA can be transcribed either from a linearized plasmid or from a crude PCR product. Comparison of two different o-tRNAs suggests that the new platform is not limited by Ef-Tu recognition of the acylated o-tRNA at sufficiently high o-tRNA template concentrations. Analysis of nnAA incorporation across 12 different sites in sfGFP suggests that modified protein yields and suppression efficiencies (i.e. the position effect) do not correlate with any of the reported trends. Sites that were ineffectively suppressed with the original o-tRNA were better suppressed with an optimized o-tRNA (o-tRNA opt ) that was evolved to be better recognized by Ef-Tu. This new platform can also be used to screen scissile ribozymes for improved catalysis.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 56
    Publication Date: 2015-05-03
    Description: Transformation-associated recombination (TAR) protocol allowing the selective isolation of full-length genes complete with their distal enhancer regions and entire genomic loci with sizes up to 250 kb from complex genomes in yeast S. cerevisiae has been developed more than a decade ago. However, its wide spread usage has been impeded by a low efficiency (0.5–2%) of chromosomal region capture during yeast transformants which in turn requires a time-consuming screen of hundreds of colonies. Here, we demonstrate that pre-treatment of genomic DNA with CRISPR-Cas9 nucleases to generate double-strand breaks near the targeted genomic region results in a dramatic increase in the fraction of gene-positive colonies (up to 32%). As only a dozen or less yeast transformants need to be screened to obtain a clone with the desired chromosomal region, extensive experience with yeast is no longer required. A TAR-CRISPR protocol may help to create a bank of human genes, each represented by a genomic copy containing its native regulatory elements, that would lead to a significant advance in functional, structural and comparative genomics, in diagnostics, gene replacement, generation of animal models for human diseases and has a potential for gene therapy.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 57
    Publication Date: 2015-04-21
    Description: RNA research and therapy relies primarily on synthetic RNAs. We employed recombinant RNA technology toward large-scale production of pre-miRNA agents in bacteria, but found the majority of target RNAs were not or negligibly expressed. We thus developed a novel strategy to achieve consistent high-yield biosynthesis of chimeric RNAs carrying various small RNAs (e.g. miRNAs, siRNAs and RNA aptamers), which was based upon an optimal noncoding RNA scaffold (OnRS) derived from tRNA fusion pre-miR-34a (tRNA/mir-34a). Multi-milligrams of chimeric RNAs (e.g. OnRS/miR-124, OnRS/GFP-siRNA, OnRS/Neg (scrambled RNA) and OnRS/MGA (malachite green aptamer)) were readily obtained from 1 l bacterial culture. Deep sequencing analyses revealed that mature miR-124 and target GFP-siRNA were selectively released from chimeric RNAs in human cells. Consequently, OnRS/miR-124 was active in suppressing miR-124 target gene expression and controlling cellular processes, and OnRS/GFP-siRNA was effective in knocking down GFP mRNA levels and fluorescent intensity in ES-2/GFP cells and GFP -transgenic mice. Furthermore, the OnRS/MGA sensor offered a specific strong fluorescence upon binding MG, which was utilized as label-free substrate to accurately determine serum RNase activities in pancreatic cancer patients. These results demonstrate that OnRS-based bioengineering is a common, robust and versatile strategy to assemble various types of small RNAs for broad applications.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 58
    Publication Date: 2016-01-09
    Description: Proteins adhere to DNA at locations and with strengths that depend on the protein conformation, the underlying DNA sequence and the ionic content of the solution. A facile technique to probe the positions and strengths of protein-DNA binding would aid in understanding these important interactions. Here, we describe a ‘DNA pulley’ for position-resolved nano-mechanical measurements of protein-DNA interactions. A molecule of DNA is tethered by one end to a glass surface, and by the other end to a magnetic bead. The DNA is stretched horizontally by a magnet, and a nanoscale knife made of silicon nitride is manipulated to contact, bend and scan along the DNA. The mechanical profile of the DNA at the contact with the knife is probed via nanometer-precision optical tracking of the magnetic bead. This system enables detection of protein bumps on the DNA and localization of their binding sites. We study theoretically the technical requirements to detect mechanical heterogeneities in the DNA itself.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 59
    Publication Date: 2016-01-09
    Description: Synthetic biology seeks to envision living cells as a matter of engineering. However, increasing evidence suggests that the genetic load imposed by the incorporation of synthetic devices in a living organism introduces a sort of unpredictability in the design process. As a result, individual part characterization is not enough to predict the behavior of designed circuits and thus, a costly trial-error process is eventually required. In this work, we provide a new theoretical framework for the predictive treatment of the genetic load. We mathematically and experimentally demonstrate that dependences among genes follow a quantitatively predictable behavior. Our theory predicts the observed reduction of the expression of a given synthetic gene when an extra genetic load is introduced in the circuit. The theory also explains that such dependence qualitatively differs when the extra load is added either by transcriptional or translational modifications. We finally show that the limitation of the cellular resources for gene expression leads to a mathematical formulation that converges to an expression analogous to the Ohm's law for electric circuits. Similitudes and divergences with this law are outlined. Our work provides a suitable framework with predictive character for the design process of complex genetic devices in synthetic biology.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 60
    Publication Date: 2016-08-20
    Description: Light-regulated modules offer unprecedented new ways to control cellular behavior in precise spatial and temporal resolution. The availability of such tools may dramatically accelerate the progression of synthetic biology applications. Nonetheless, current optogenetic toolbox of prokaryotes has potential issues such as lack of rapid and switchable control, less portable, low dynamic expression and limited parts. To address these shortcomings, we have engineered a novel bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly using the blue light dependent DNA-binding protein EL222. We demonstrated that by modulating the dosage of light pulses or intensity we could control the level of gene expression precisely. We show that both light-inducible and repressible system can function in parallel with high spatial precision in a single cell and can be switched stably between ON- and OFF-states by repetitive pulses of blue light. In addition, the light-inducible and repressible expression kinetics were quantitatively analysed using a mathematical model. We further apply the system, for the first time, to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal. Overall, our modular approach layers a transformative platform for next-generation light-controllable synthetic biology systems in prokaryotes.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 61
    Publication Date: 2016-08-20
    Description: Current DNA assembly methods for preparing highly purified linear subassemblies require complex and time-consuming in vitro manipulations that hinder their ability to construct megabase-sized DNAs (e.g. synthetic genomes). We have developed a new method designated ‘CasHRA ( Cas 9-facilitated H omologous R ecombination A ssembly)’ that directly uses large circular DNAs in a one-step in vivo assembly process. The large circular DNAs are co-introduced into Saccharomyces cerevisiae by protoplast fusion, and they are cleaved by RNA-guided Cas9 nuclease to release the linear DNA segments for subsequent assembly by the endogenous homologous recombination system. The CasHRA method allows efficient assembly of multiple large DNA segments in vivo ; thus, this approach should be useful in the last stage of genome construction. As a proof of concept, we combined CasHRA with an upstream assembly method (Gibson procedure of genome assembly) and successfully constructed a 1.03 Mb MGE-syn1.0 ( M inimal G enome of Escherichia coli ) that contained 449 essential genes and 267 important growth genes. We expect that CasHRA will be widely used in megabase-sized genome constructions.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 62
    Publication Date: 2015-10-15
    Description: Natural regulatory networks contain many interacting components that allow for fine-tuning of switching and memory properties. Building simple bistable switches, synthetic biologists have learned the design principles of complex natural regulatory networks. However, most switches constructed so far are so simple (e.g. comprising two regulators) that they are functional only within a limited parameter range. Here, we report the construction of robust, tunable bistable switches in Escherichia coli using three heterologous protein regulators (ExsADC) that are sequestered into an inactive complex through a partner swapping mechanism. On the basis of mathematical modeling, we accurately predict and experimentally verify that the hysteretic region can be fine-tuned by controlling the interactions of the ExsADC regulatory cascade using the third member ExsC as a tuning knob. Additionally, we confirm that a dual-positive feedback switch can markedly increase the hysteretic region, compared to its single-positive feedback counterpart. The dual-positive feedback switch displays bistability over a 10 6 -fold range of inducer concentrations, to our knowledge, the largest range reported so far. This work demonstrates the successful interlocking of sequestration-based ultrasensitivity and positive feedback, a design principle that can be applied to the construction of robust, tunable, and predictable genetic programs to achieve increasingly sophisticated biological behaviors.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 63
    Publication Date: 2016-06-03
    Description: We have investigated transcriptional interference between convergent genes in E. coli and demonstrate substantial interference for inter-promoter distances of as far as 3 kb. Interference can be elicited by both strong 70 dependent and T7 promoters. In the presented design, a strong promoter driving gene expression of a ‘forward’ gene interferes with the expression of a ‘reverse’ gene by a weak promoter. This arrangement allows inversely correlated gene expression without requiring further regulatory components. Thus, modulation of the activity of the strong promoter alters expression of both the forward and the reverse gene. We used this design to develop a dual selection system for conditional operator site binding, allowing positive selection both for binding and for non-binding to DNA. This study demonstrates the utility of this novel system using the Lac repressor as a model protein for conditional DNA binding, and spectinomycin and chloramphenicol resistance genes as positive selection markers in liquid culture. Randomized LacI libraries were created and subjected to subsequent dual selection, but mispairing IPTG and selection cues in respect to the wild-type LacI response, allowing the isolation of a LacI variant with a reversed IPTG response within three rounds of library generation and dual selection.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 64
    Publication Date: 2015-04-21
    Description: We describe solid-phase cloning (SPC) for high-throughput assembly of expression plasmids. Our method allows PCR products to be put directly into a liquid handler for capture and purification using paramagnetic streptavidin beads and conversion into constructs by subsequent cloning reactions. We present a robust automated protocol for restriction enzyme based SPC and its performance for the cloning of 〉60 000 unique human gene fragments into expression vectors. In addition, we report on SPC-based single-strand assembly for applications where exact control of the sequence between fragments is needed or where multiple inserts are to be assembled. In this approach, the solid support allows for head-to-tail assembly of DNA fragments based on hybridization and polymerase fill-in. The usefulness of head-to-tail SPC was demonstrated by assembly of 〉150 constructs with up to four DNA parts at an average success rate above 80%. We report on several applications for SPC and we suggest it to be particularly suitable for high-throughput efforts using laboratory workstations.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 65
    Publication Date: 2012-09-27
    Description: Genome-scale engineering of living organisms requires precise and economical methods to efficiently modify many loci within chromosomes. One such example is the directed integration of chemically synthesized single-stranded deoxyribonucleic acid (oligonucleotides) into the chromosome of Escherichia coli during replication. Herein, we present a general co-selection strategy in multiplex genome engineering that yields highly modified cells. We demonstrate that disparate sites throughout the genome can be easily modified simultaneously by leveraging selectable markers within 500 kb of the target sites. We apply this technique to the modification of 80 sites in the E. coli genome.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 66
    Publication Date: 2016-03-01
    Description: Microfluidics may revolutionize our ability to write synthetic DNA by addressing several fundamental limitations associated with generating novel genetic constructs. Here we report the first de novo synthesis and cell-free cloning of custom DNA libraries in sub-microliter reaction droplets using programmable digital microfluidics. Specifically, we developed Programmable Order Polymerization (POP), Microfluidic Combinatorial Assembly of DNA (M-CAD) and Microfluidic In-vitro Cloning (MIC) and applied them to de novo synthesis, combinatorial assembly and cell-free cloning of genes, respectively. Proof-of-concept for these methods was demonstrated by programming an autonomous microfluidic system to construct and clone libraries of yeast ribosome binding sites and bacterial Azurine, which were then retrieved in individual droplets and validated. The ability to rapidly and robustly generate designer DNA molecules in an autonomous manner should have wide application in biological research and development.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 67
    Publication Date: 2016-03-01
    Description: Recent developments in synthetic biology have positioned lactic acid bacteria (LAB) as a major class of cellular chassis for applications. To achieve the full potential of LAB, one fundamental prerequisite is the capacity for rapid engineering of complex gene networks, such as natural biosynthetic pathways and multicomponent synthetic circuits, into which cellular functions are encoded. Here, we present a synthetic biology platform for rapid construction and optimization of large-scale gene networks in LAB. The platform involves a copy-controlled shuttle for hosting target networks and two associated strategies that enable efficient genetic editing and phenotypic validation. By using a nisin biosynthesis pathway and its variants as examples, we demonstrated multiplex, continuous editing of small DNA parts, such as ribosome-binding sites, as well as efficient manipulation of large building blocks such as genes and operons. To showcase the platform, we applied it to expand the phenotypic diversity of the nisin pathway by quickly generating a library of 63 pathway variants. We further demonstrated its utility by altering the regulatory topology of the nisin pathway for constitutive bacteriocin biosynthesis. This work demonstrates the feasibility of rapid and advanced engineering of gene networks in LAB, fostering their applications in biomedicine and other areas.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 68
    Publication Date: 2015-12-02
    Description: Optimizing bio-production involves strain and process improvements performed as discrete steps. However, environment impacts genotype and a strain that is optimal under one set of conditions may not be under different conditions. We present a methodology to simultaneously vary genetic and process factors, so that both can be guided by design of experiments (DOE). Advances in DNA assembly and gene insulation facilitate this approach by accelerating multi-gene pathway construction and the statistical interpretation of screening data. This is applied to a 6-aminocaproic acid (6-ACA) pathway in Escherichia coli consisting of six heterologous enzymes. A 32-member fraction factorial library is designed that simultaneously perturbs expression and media composition. This is compared to a 64-member full factorial library just varying expression (0.64 Mb of DNA assembly). Statistical analysis of the screening data from these libraries leads to different predictions as to whether the expression of enzymes needs to increase or decrease. Therefore, if genotype and media were varied separately this would lead to a suboptimal combination. This is applied to the design of a strain and media composition that increases 6-ACA from 9 to 48 mg/l in a single optimization step. This work introduces a generalizable platform to co-optimize genetic and non-genetic factors.
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  • 69
    Publication Date: 2012-06-06
    Description: A chemistry-based artificial restriction DNA cutter (ARCUT) was recently prepared from Ce(IV)/EDTA complex and a pair of pseudo-complementary peptide nucleic acids. This cutter has freely tunable scission-site and site specificity. In this article, homologous recombination (HR) in human cells was promoted by cutting a substrate DNA with ARCUT, and the efficiency of this bioprocess was optimized by various chemical and biological approaches. Of two kinds of terminal structure formed by ARCUT, 3'-overhang termini provided by 1.7-fold higher efficiency than 5'-overhang termini. A longer homology length (e.g. 698 bp) was about 2-fold more favorable than shorter one (e.g. 100 bp). When the cell cycle was synchronized to G2/M phase with nocodazole, the HR was promoted by about 2-fold. Repression of the NHEJ-relevant proteins Ku70 and Ku80 by siRNA increased the efficiency by 2- to 3-fold. It was indicated that appropriate combination of all these chemical and biological approaches should be very effective to promote ARCUT-mediated HR in human cells.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 70
    Publication Date: 2012-04-24
    Description: We describe a novel cloning method termed SLiCE (Seamless L i gation Cloning Extract) that utilizes easy to generate bacterial cell extracts to assemble multiple DNA fragments into recombinant DNA molecules in a single in vitro recombination reaction. SLiCE overcomes the sequence limitations of traditional cloning methods, facilitates seamless cloning by recombining short end homologies (≥15 bp) with or without flanking heterologous sequences and provides an effective strategy for directional subcloning of DNA fragments from Bacteria Artificial Chromosomes (BACs) or other sources. SLiCE is highly cost effective as a number of standard laboratory bacterial strains can serve as sources for SLiCE extract. In addition, the cloning efficiencies and capabilities of these strains can be greatly improved by simple genetic modifications. As an example, we modified the DH10B Escherichia coli strain to express an optimized prophage Red recombination system. This strain, termed PPY, facilitates SLiCE with very high efficiencies and demonstrates the versatility of the method.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 71
    Publication Date: 2012-04-24
    Description: Targeted gene addition to mammalian genomes is central to biotechnology, basic research and gene therapy. For example, gene targeting to the ROSA26 locus by homologous recombination in embryonic stem cells is commonly used for mouse transgenesis to achieve ubiquitous and persistent transgene expression. However, conventional methods are not readily adaptable to gene targeting in other cell types. The emerging zinc finger nuclease (ZFN) technology facilitates gene targeting in diverse species and cell types, but an optimal strategy for engineering highly active ZFNs is still unclear. We used a modular assembly approach to build ZFNs that target the ROSA26 locus. ZFN activity was dependent on the number of modules in each zinc finger array. The ZFNs were active in a variety of cell types in a time- and dose-dependent manner. The ZFNs directed gene addition to the ROSA26 locus, which enhanced the level of sustained gene expression, the uniformity of gene expression within clonal cell populations and the reproducibility of gene expression between clones. These ZFNs are a promising resource for cell engineering, mouse transgenesis and pre-clinical gene therapy studies. Furthermore, this characterization of the modular assembly method provides general insights into the implementation of the ZFN technology.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 72
    Publication Date: 2012-05-13
    Description: A simple approach for creating libraries of circularly permuted proteins is described that is called PERMutation Using Transposase Engineering (PERMUTE). In PERMUTE, the transposase MuA is used to randomly insert a minitransposon that can function as a protein expression vector into a plasmid that contains the open reading frame (ORF) being permuted. A library of vectors that express different permuted variants of the ORF-encoded protein is created by: (i) using bacteria to select for target vectors that acquire an integrated minitransposon; (ii) excising the ensemble of ORFs that contain an integrated minitransposon from the selected vectors; and (iii) circularizing the ensemble of ORFs containing integrated minitransposons using intramolecular ligation. Construction of a Thermotoga neapolitana adenylate kinase (AK) library using PERMUTE revealed that this approach produces vectors that express circularly permuted proteins with distinct sequence diversity from existing methods. In addition, selection of this library for variants that complement the growth of Escherichia coli with a temperature-sensitive AK identified functional proteins with novel architectures, suggesting that PERMUTE will be useful for the directed evolution of proteins with new functions.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 73
    Publication Date: 2012-02-28
    Description: Synthetic scaffolds that permit spatial and temporal organization of enzymes in living cells are a promising post-translational strategy for controlling the flow of information in both metabolic and signaling pathways. Here, we describe the use of plasmid DNA as a stable, robust and configurable scaffold for arranging biosynthetic enzymes in the cytoplasm of Escherichia coli . This involved conversion of individual enzymes into custom DNA-binding proteins by genetic fusion to zinc-finger domains that specifically bind unique DNA sequences. When expressed in cells that carried a rationally designed DNA scaffold comprising corresponding zinc finger binding sites, the titers of diverse metabolic products, including resveratrol, 1,2-propanediol and mevalonate were increased as a function of the scaffold architecture. These results highlight the utility of DNA scaffolds for assembling biosynthetic enzymes into functional metabolic structures. Beyond metabolism, we anticipate that DNA scaffolds may be useful in sequestering different types of enzymes for specifying the output of biological signaling pathways or for coordinating other assembly-line processes such as protein folding, degradation and post-translational modifications.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 74
    Publication Date: 2014-03-13
    Description: To reveal the full potential of human pluripotent stem cells, new methods for rapid, site-specific genomic engineering are needed. Here, we describe a system for precise genetic modification of human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). We identified a novel human locus, H11 , located in a safe, intergenic, transcriptionally active region of chromosome 22, as the recipient site, to provide robust, ubiquitous expression of inserted genes. Recipient cell lines were established by site-specific placement of a ‘landing pad’ cassette carrying attP sites for phiC31 and Bxb1 integrases at the H11 locus by spontaneous or TALEN-assisted homologous recombination. Dual integrase cassette exchange (DICE) mediated by phiC31 and Bxb1 integrases was used to insert genes of interest flanked by phiC31 and Bxb1 attB sites at the H11 locus, replacing the landing pad. This system provided complete control over content, direction and copy number of inserted genes, with a specificity of 100%. A series of genes, including mCherry and various combinations of the neural transcription factors LMX1a, FOXA2 and OTX2, were inserted in recipient cell lines derived from H9 ESC, as well as iPSC lines derived from a Parkinson’s disease patient and a normal sibling control. The DICE system offers rapid, efficient and precise gene insertion in ESC and iPSC and is particularly well suited for repeated modifications of the same locus.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 75
    Publication Date: 2014-03-13
    Description: Recombineering, which is the use of homologous recombination for DNA engineering in Escherichia coli , usually uses antibiotic selection to identify the intended recombinant. When combined in a second step with counterselection using a small molecule toxin, seamless products can be obtained. Here, we report the advantages of a genetic strategy using CcdB as the counterselectable agent. Expression of CcdB is toxic to E. coli in the absence of the CcdA antidote so counterselection is initiated by the removal of CcdA expression. CcdB counterselection is robust and does not require titrations or experiment-to-experiment optimization. Because counterselection strategies necessarily differ according to the copy number of the target, we describe two variations. For multi-copy targets, we use two E. coli hosts so that counterselection is exerted by the transformation step that is needed to separate the recombined and unrecombined plasmids. For single copy targets, we put the ccdA gene onto the temperature-sensitive pSC101 Red expression plasmid so that counterselection is exerted by the standard temperature shift to remove the expression plasmid. To reduce unwanted intramolecular recombination, we also combined CcdB counterselection with Redα omission. These options improve the use of counterselection in recombineering with BACs, plasmids and the E. coli chromosome.
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  • 76
    Publication Date: 2013-12-07
    Description: The two-step process of selection and counter-selection is a standard way to enable genetic modification and engineering of bacterial genomes using homologous recombination methods. The tetA and sacB genes are contained in a DNA cassette and confer a novel dual counter-selection system. Expression of tetA confers bacterial resistance to tetracycline (Tc R ) and also causes sensitivity to the lipophillic chelator fusaric acid; sacB causes sensitivity to sucrose. These two genes are introduced as a joint DNA cassette into Escherichia coli by selection for Tc R . A medium containing both fusaric acid and sucrose has been developed, in which, coexpression of tetA-sacB is orders of magnitude more sensitive as a counter-selection agent than either gene alone. In conjunction with the homologous recombination methods of recombineering and P1 transduction, this powerful system has been used to select changes in the bacterial genome that cannot be directly detected by other counter-selection systems.
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  • 77
    Publication Date: 2014-02-28
    Description: DNA ‘assembly’ from ‘building blocks’ remains a cornerstone in synthetic biology, whether it be for gene synthesis (~1 kb), pathway engineering (~10 kb) or synthetic genomes (〉100 kb). Despite numerous advances in the techniques used for DNA assembly, verification of the assembly is still a necessity, which becomes cost-prohibitive and a logistical challenge with increasing scale. Here we describe for the first time a comprehensive, high-throughput solution for structural DNA assembly verification by restriction digest using exhaustive in silico enzyme screening, rolling circle amplification of plasmid DNA, capillary electrophoresis and automated digest pattern recognition. This low-cost and robust methodology has been successfully used to screen over 31 000 clones of DNA constructs at 〈$1 per sample.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 78
    Publication Date: 2014-02-28
    Description: Synthetic biology requires effective methods to assemble DNA parts into devices and to modify these devices once made. Here we demonstrate a convenient rapid procedure for DNA fragment assembly using site-specific recombination by C31 integrase. Using six orthogonal attP / attB recombination site pairs with different overlap sequences, we can assemble up to five DNA fragments in a defined order and insert them into a plasmid vector in a single recombination reaction. C31 integrase-mediated assembly is highly efficient, allowing production of large libraries suitable for combinatorial gene assembly strategies. The resultant assemblies contain arrays of DNA cassettes separated by recombination sites, which can be used to manipulate the assembly by further recombination. We illustrate the utility of these procedures to (i) assemble functional metabolic pathways containing three, four or five genes; (ii) optimize productivity of two model metabolic pathways by combinatorial assembly with randomization of gene order or ribosome binding site strength; and (iii) modify an assembled metabolic pathway by gene replacement or addition.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 79
    Publication Date: 2014-04-03
    Description: A conditional gene expression system that is fast-acting, is tunable and achieves single-gene specificity was recently developed for yeast. A gene placed directly downstream of a modified GAL1 promoter containing six Zif268 binding sequences (with single nucleotide spacing) was shown to be selectively inducible in the presence of β-estradiol, so long as cells express the artificial transcription factor, Z 3 EV (a fusion of the Zif268 DNA binding domain, the ligand binding domain of the human estrogen receptor and viral protein 16). We show the strength of Z 3 EV-responsive promoters can be modified using straightforward design principles. By moving Zif268 binding sites toward the transcription start site, expression output can be nearly doubled. Despite the reported requirement of estrogen receptor dimerization for hormone-dependent activation, a single binding site suffices for target gene activation. Target gene expression levels correlate with promoter binding site copy number and we engineer a set of inducible promoter chassis with different input–output characteristics. Finally, the coupling between inducer identity and gene activation is flexible: the ligand specificity of Z 3 EV can be re-programmed to respond to a non-hormone small molecule with only five amino acid substitutions in the human estrogen receptor domain, which may prove useful for industrial applications.
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  • 80
    Publication Date: 2012-03-29
    Description: We demonstrate a system for cloning and modifying the chloroplast genome from the green alga, Chlamydomonas reinhardtii . Through extensive use of sequence stabilization strategies, the ex vivo genome is assembled in yeast from a collection of overlapping fragments. The assembled genome is then moved into bacteria for large-scale preparations and transformed into C. reinhardtii cells. This system also allows for the generation of simultaneous, systematic and complex genetic modifications at multiple loci in vivo. We use this system to substitute genes encoding core subunits of the photosynthetic apparatus with orthologs from a related alga, Scenedesmus obliquus . Once transformed into algae, the substituted genome recombines with the endogenous genome, resulting in a hybrid plastome comprising modifications in disparate loci. The in vivo function of the genomes described herein demonstrates that simultaneous engineering of multiple sites within the chloroplast genome is now possible. This work represents the first steps toward a novel approach for creating genetic diversity in any or all regions of a chloroplast genome.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 81
    Publication Date: 2012-02-17
    Description: The increasing interest in genetic manipulation of bacterial host metabolic pathways for protein or small molecule production has led to a need to add new genes to a chromosome quickly and easily without leaving behind a selectable marker. The present report describes a vector and four-day procedure that enable site-specific chromosomal insertion of cloned genes in a context insulated from external transcription, usable once in a construction series. The use of rhamnose-inducible transcription from rhaBp allows regulation of the inserted genes independently of the commonly used IPTG and arabinose strategies. Using lacZ as a reporter, we first show that expression from the rhamnose promoter is tightly regulatable, exhibiting very low leakage of background expression compared with background, and moderate rhamnose-induced expression compared with IPTG-induced expression from lacp . Second, the expression of a DNA methyltransferase was used to show that rhamnose regulation yielded on-off expression of this enzyme, such that a resident high-copy plasmid was either fully sensitive or fully resistant to isoschizomer restriction enzyme cleavage. In both cases, growth medium manipulation allows intermediate levels of expression. The vehicle can also be adapted as an ORF-cloning vector.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 82
    Publication Date: 2012-02-17
    Description: The development of economical and high-throughput gene synthesis technology has been hampered by the high occurrence of errors in the synthesized products, which requires expensive labor and time to correct. Here, we describe an error correction reaction (ECR), which employs Surveyor, a mismatch-specific DNA endonuclease, to remove errors from synthetic genes. In ECR reactions, errors are revealed as mismatches by re-annealing of the synthetic gene products. Mismatches are recognized and excised by a combination of mismatch-specific endonuclease and 3'-〉5' exonuclease activities in the reaction mixture. Finally, overlap extension polymerase chain reaction (OE-PCR) re-assembles the resulting fragments into intact genes. The process can be iterated for increased fidelity. With two iterations, we were able to reduce errors in synthetic genes by 〉16-fold, yielding a final error rate of ~1 in 8700 bp.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 83
    Publication Date: 2014-09-27
    Description: The precise control of gene expression is essential in basic biological research as well as in biotechnological applications. Most regulated systems available in yeast enable only the overexpression of the target gene, excluding the possibility of intermediate or weak expression. Moreover, these systems are frequently toxic or depend on growth conditions. We constructed a heterologous transcription factor that overcomes these limitations. Our system is a fusion of the bacterial LexA DNA-binding protein, the human estrogen receptor (ER) and an activation domain (AD). The activity of this chimera, called LexA-ER-AD, is tightly regulated by the hormone β-estradiol. The selection of the AD proved to be crucial to avoid toxic effects and to define the range of activity that can be precisely tuned with β-estradiol. As our system is based on a heterologous DNA-binding domain, induction in different metabolic contexts is possible. Additionally, by controlling the number of LexA-binding sites in the target promoter, one can scale the expression levels up or down. Overall, our LexA-ER-AD system is a valuable tool to precisely control gene expression in different experimental contexts without toxic side effects.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 84
    Publication Date: 2014-09-27
    Description: Inspired by the developments of synthetic biology and the need for improved genetic tools to exploit cyanobacteria for the production of renewable bioproducts, we developed a versatile platform for the construction of broad-host-range vector systems. This platform includes the following features: (i) an efficient assembly strategy in which modules released from 3 to 4 donor plasmids or produced by polymerase chain reaction are assembled by isothermal assembly guided by short GC-rich overlap sequences. (ii) A growing library of molecular devices categorized in three major groups: (a) replication and chromosomal integration; (b) antibiotic resistance; (c) functional modules. These modules can be assembled in different combinations to construct a variety of autonomously replicating plasmids and suicide plasmids for gene knockout and knockin. (iii) A web service, the CYANO-VECTOR assembly portal, which was built to organize the various modules, facilitate the in silico construction of plasmids, and encourage the use of this system. This work also resulted in the construction of an improved broad-host-range replicon derived from RSF1010, which replicates in several phylogenetically distinct strains including a new experimental model strain Synechocystis sp. WHSyn, and the characterization of nine antibiotic cassettes, four reporter genes, four promoters, and a ribozyme-based insulator in several diverse cyanobacterial strains.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 85
    Publication Date: 2014-11-28
    Description: Mammalian synthetic biology may provide novel therapeutic strategies, help decipher new paths for drug discovery and facilitate synthesis of valuable molecules. Yet, our capacity to genetically program cells is currently hampered by the lack of efficient approaches to streamline the design, construction and screening of synthetic gene networks. To address this problem, here we present a framework for modular and combinatorial assembly of functional (multi)gene expression vectors and their efficient and specific targeted integration into a well-defined chromosomal context in mammalian cells. We demonstrate the potential of this framework by assembling and integrating different functional mammalian regulatory networks including the largest gene circuit built and chromosomally integrated to date (6 transcription units, 27kb) encoding an inducible memory device. Using a library of 18 different circuits as a proof of concept, we also demonstrate that our method enables one-pot/single-flask chromosomal integration and screening of circuit libraries. This rapid and powerful prototyping platform is well suited for comparative studies of genetic regulatory elements, genes and multi-gene circuits as well as facile development of libraries of isogenic engineered cell lines.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 86
    Publication Date: 2012-10-10
    Description: A major challenge in metabolic engineering and synthetic biology is to balance the flux of an engineered heterologous metabolic pathway to achieve high yield and productivity in a target organism. Here, we report a simple, efficient and programmable approach named ‘customized optimization of metabolic pathways by combinatorial transcriptional engineering (COMPACTER)’ for rapid tuning of gene expression in a heterologous pathway under distinct metabolic backgrounds. Specifically, a library of mutant pathways is created by de novo assembly of promoter mutants of varying strengths for each pathway gene in a target organism followed by high-throughput screening/selection. To demonstrate this approach, a single round of COMPACTER was used to generate both a xylose utilizing pathway with near-highest efficiency and a cellobiose utilizing pathway with highest efficiency that were ever reported in literature for both laboratory and industrial yeast strains. Interestingly, these engineered xylose and cellobiose utilizing pathways were all host-specific. Therefore, COMPACTER represents a powerful approach to tailor-make metabolic pathways for different strain backgrounds, which is difficult if not impossible to achieve by existing pathway engineering methods.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 87
    Publication Date: 2012-10-10
    Description: We developed a highly scalable ‘shotgun’ DNA synthesis technology by utilizing microchip oligonucleotides, shotgun assembly and next-generation sequencing technology. A pool of microchip oligonucleotides targeting a penicillin biosynthetic gene cluster were assembled into numerous random fragments, and tagged with 20 bp degenerate barcode primer pairs. An optimal set of error-free fragments were identified by high-throughput DNA sequencing, selectively amplified using the barcode sequences, and successfully assembled into the target gene cluster.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 88
    Publication Date: 2013-09-06
    Description: We developed a framework for quick and reliable construction of complex gene circuits for genetically engineering mammalian cells. Our hierarchical framework is based on a novel nucleotide addressing system for defining the position of each part in an overall circuit. With this framework, we demonstrate construction of synthetic gene circuits of up to 64 kb in size comprising 11 transcription units and 33 basic parts. We show robust gene expression control of multiple transcription units by small molecule inducers in human cells with transient transfection and stable chromosomal integration of these circuits. This framework enables development of complex gene circuits for engineering mammalian cells with unprecedented speed, reliability and scalability and should have broad applicability in a variety of areas including mammalian cell fermentation, cell fate reprogramming and cell-based assays.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 89
    Publication Date: 2014-04-15
    Description: RGB marking and DNA barcoding are two cutting-edge technologies in the field of clonal cell marking. To combine the virtues of both approaches, we equipped LeGO vectors encoding red, green or blue fluorescent proteins with complex DNA barcodes carrying color-specific signatures. For these vectors, we generated highly complex plasmid libraries that were used for the production of barcoded lentiviral vector particles. In proof-of-principle experiments, we used barcoded vectors for RGB marking of cell lines and primary murine hepatocytes. We applied single-cell polymerase chain reaction to decipher barcode signatures of individual RGB-marked cells expressing defined color hues. This enabled us to prove clonal identity of cells with one and the same RGB color. Also, we made use of barcoded vectors to investigate clonal development of leukemia induced by ectopic oncogene expression in murine hematopoietic cells. In conclusion, by combining RGB marking and DNA barcoding, we have established a novel technique for the unambiguous genetic marking of individual cells in the context of normal regeneration as well as malignant outgrowth. Moreover, the introduction of color-specific signatures in barcodes will facilitate studies on the impact of different variables (e.g. vector type, transgenes, culture conditions) in the context of competitive repopulation studies.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 90
    Publication Date: 2014-04-15
    Description: Insertional oncogene activation and aberrant splicing have proved to be major setbacks for retroviral stem cell gene therapy. Integrase-deficient human immunodeficiency virus-1-derived vectors provide a potentially safer approach, but their circular genomes are rapidly lost during cell division. Here we describe a novel lentiviral vector (LV) that incorporates human ß-interferon scaffold/matrix-associated region sequences to provide an origin of replication for long-term mitotic maintenance of the episomal LTR circles. The resulting ‘anchoring’ non-integrating lentiviral vector (aniLV) achieved initial transduction rates comparable with integrating vector followed by progressive establishment of long-term episomal expression in a subset of cells. Analysis of aniLV-transduced single cell-derived clones maintained without selective pressure for 〉100 rounds of cell division showed sustained transgene expression from episomes and provided molecular evidence for long-term episome maintenance. To evaluate aniLV performance in primary cells, we transduced lineage-depleted murine hematopoietic progenitor cells, observing GFP expression in clonogenic progenitor colonies and peripheral blood leukocyte chimerism following transplantation into conditioned hosts. In aggregate, our studies suggest that scaffold/matrix-associated region elements can serve as molecular anchors for non-integrating lentivector episomes, providing sustained gene expression through successive rounds of cell division and progenitor differentiation in vitro and in vivo .
    Keywords: Synthetic Biology and Assembly Cloning
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  • 91
    Publication Date: 2014-11-12
    Description: Assembly of DNA ‘parts’ to create larger constructs is an essential enabling technique for bioengineering and synthetic biology. Here we describe a simple method, PaperClip, which allows flexible assembly of multiple DNA parts from currently existing libraries cloned in any vector. No restriction enzymes, mutagenesis of internal restriction sites, or reamplification to add end homology are required. Order of assembly is directed by double stranded oligonucleotides—‘Clips’. Clips are formed by ligation of pairs of oligonucleotides corresponding to the ends of each part. PaperClip assembly can be performed by polymerase chain reaction or by cell extract-mediated recombination. Once multi-use Clips have been prepared, assembly of at least six DNA parts in any order can be accomplished with high efficiency within several hours.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 92
    Publication Date: 2014-08-15
    Description: Synthetic biology has significantly advanced the design of mammalian trigger-inducible transgene-control devices that are able to programme complex cellular behaviour. Fruit-based benzoate derivatives licensed as food additives, such as flavours (e.g. vanillate) and preservatives (e.g. benzoate), are a particularly attractive class of trigger compounds for orthogonal mammalian transgene control devices because of their innocuousness, physiological compatibility and simple oral administration. Capitalizing on the genetic componentry of the soil bacterium Comamonas testosteroni , which has evolved to catabolize a variety of aromatic compounds, we have designed different mammalian gene expression systems that could be induced and repressed by the food additives benzoate and vanillate. When implanting designer cells engineered for gene switch-driven expression of the human placental secreted alkaline phosphatase (SEAP) into mice, blood SEAP levels of treated animals directly correlated with a benzoate-enriched drinking programme. Additionally, the benzoate-/vanillate-responsive device was compatible with other transgene control systems and could be assembled into higher-order control networks providing expression dynamics reminiscent of a lap-timing stopwatch. Designer gene switches using licensed food additives as trigger compounds to achieve antagonistic dual-input expression profiles and provide novel control topologies and regulation dynamics may advance future gene- and cell-based therapies.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 93
    Publication Date: 2016-03-19
    Description: While the cost of DNA sequencing has dropped by five orders of magnitude in the past decade, DNA synthesis remains expensive for many applications. Although DNA microarrays have decreased the cost of oligonucleotide synthesis, the use of array-synthesized oligos in practice is limited by short synthesis lengths, high synthesis error rates, low yield and the challenges of assembling long constructs from complex pools. Toward addressing these issues, we developed a protocol for multiplex pairwise assembly of oligos from array-synthesized oligonucleotide pools. To evaluate the method, we attempted to assemble up to 2271 targets ranging in length from 192–252 bases using pairs of array-synthesized oligos. Within sets of complexity ranging from 131–250 targets, we observed error-free assemblies for 90.5% of all targets. When all 2271 targets were assembled in one reaction, we observed error-free constructs for 70.6%. While the assembly method intrinsically increased accuracy to a small degree, we further increased accuracy by using a high throughput ‘Dial-Out PCR’ protocol, which combines Illumina sequencing with an in-house set of unique PCR tags to selectively amplify perfect assemblies from complex synthetic pools. This approach has broad applicability to DNA assembly and high-throughput functional screens.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 94
    Publication Date: 2012-12-14
    Description: Multivalent molecular interactions can be exploited to dramatically enhance the performance of an affinity reagent. The enhancement in affinity and specificity achieved with a multivalent construct depends critically on the effectiveness of the scaffold that joins the ligands, as this determines their positions and orientations with respect to the target molecule. Currently, no generalizable design rules exist for construction of an optimal multivalent ligand for targets with known structures, and the design challenge remains an insurmountable obstacle for the large number of proteins whose structures are not known. As an alternative to such design-based strategies, we report here a directed evolution-based method for generating optimal bivalent aptamers. To demonstrate this approach, we fused two thrombin aptamers with a randomized DNA sequence and used a microfluidic in vitro selection strategy to isolate scaffolds with exceptionally high affinities. Within five rounds of selection, we generated a bivalent aptamer that binds thrombin with an apparent dissociation constant (K d ) 〈10 pM, representing a ~200-fold improvement in binding affinity over the monomeric aptamers and a ~15-fold improvement over the best designed bivalent construct. The process described here can be used to produce high-affinity multivalent aptamers and could potentially be adapted to other classes of biomolecules.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 95
    Publication Date: 2013-07-16
    Description: Synthetic biology has significantly advanced the design of synthetic control devices, gene circuits and networks that can reprogram mammalian cells in a trigger-inducible manner. Prokaryotic helix-turn-helix motifs have become the standard resource to design synthetic mammalian transcription factors that tune chimeric promoters in a small molecule-responsive manner. We have identified a family of Actinomycetes transcriptional repressor proteins showing a tandem TetR-family signature and have used a synthetic biology-inspired approach to reveal the potential control dynamics of these bi-partite regulators. Daisy-chain assembly of well-characterized prokaryotic repressor proteins such as TetR, ScbR, TtgR or VanR and fusion to either the Herpes simplex transactivation domain VP16 or the Krueppel-associated box domain (KRAB) of the human kox-1 gene resulted in synthetic bi- and even tri-partite mammalian transcription factors that could reversibly program their individual chimeric or hybrid promoters for trigger-adjustable transgene expression using tetracycline (TET), -butyrolactones, phloretin and vanillic acid. Detailed characterization of the bi-partite ScbR-TetR-VP16 (ST-TA) transcription factor revealed independent control of TET- and -butyrolactone-responsive promoters at high and double-pole double-throw (DPDT) relay switch qualities at low intracellular concentrations. Similar to electromagnetically operated mechanical DPDT relay switches that control two electric circuits by a fully isolated low-power signal, TET programs ST-TA to progressively switch from TetR-specific promoter-driven expression of transgene one to ScbR-specific promoter-driven transcription of transgene two while ST-TA flips back to exclusive transgene 1 expression in the absence of the trigger antibiotic. We suggest that natural repressors and activators with tandem TetR-family signatures may also provide independent as well as DPDT-mediated control of two sets of transgenes in bacteria, and that their synthetic transcription-factor analogs may enable the design of compact therapeutic gene circuits for gene and cell-based therapies.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 96
    Publication Date: 2016-09-03
    Description: Libraries of well-characterised components regulating gene expression levels are essential to many synthetic biology applications. While widely available for the Gram-negative model bacterium Escherichia coli , such libraries are lacking for the Gram-positive model Bacillus subtilis , a key organism for basic research and biotechnological applications. Here, we engineered a genetic toolbox comprising libraries of promoters, Ribosome Binding Sites (RBS), and protein degradation tags to precisely tune gene expression in B. subtilis . We first designed a modular Expression Operating Unit (EOU) facilitating parts assembly and modifications and providing a standard genetic context for gene circuits implementation. We then selected native, constitutive promoters of B. subtilis and efficient RBS sequences from which we engineered three promoters and three RBS sequence libraries exhibiting ~14 000-fold dynamic range in gene expression levels. We also designed a collection of SsrA proteolysis tags of variable strength. Finally, by using fluorescence fluctuation methods coupled with two-photon microscopy, we quantified the absolute concentration of GFP in a subset of strains from the library. Our complete promoters and RBS sequences library comprising over 135 constructs enables tuning of GFP concentration over five orders of magnitude, from 0.05 to 700 μM. This toolbox of regulatory components will support many research and engineering applications in B. subtilis .
    Keywords: Synthetic Biology and Assembly Cloning
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  • 97
    Publication Date: 2012-08-08
    Description: Cy3B is an extremely bright and stable fluorescent dye, which is only available for coupling to nucleic acids post-synthetically. This severely limits its use in the fields of genomics, biology and nanotechnology. We have optimized the synthesis of Cy3B, and for the first time produced a diverse range of Cy3B monomers for use in solid-phase oligonucleotide synthesis. This molecular toolkit includes phosphoramidite monomers with Cy3B linked to deoxyribose, to the 5-position of thymine, and to a hexynyl linker, in addition to an oligonucleotide synthesis resin in which Cy3B is linked to deoxyribose. These monomers have been used to incorporate single and multiple Cy3B units into oligonucleotides internally and at both termini. Cy3B Taqman probes, Scorpions and HyBeacons have been synthesized and used successfully in mutation detection, and a dual Cy3B Molecular Beacon was synthesized and found to be superior to the corresponding Cy3B/DABCYL Beacon. Attachment of Cy3, Cy3B and Cy5 to the 5-position of thymidine by an ethynyl linker enabled the synthesis of an oligonucleotide FRET system. The rigid linker between the dye and nucleobase minimizes dye–dye and dye–DNA interactions and reduces fluorescence quenching. These reagents open up new future applications of Cy3B, including more sensitive single-molecule and cell-imaging studies.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 98
    Publication Date: 2013-01-20
    Description: Synthetic RNA control devices that use ribozymes as gene-regulatory components have been applied to controlling cellular behaviors in response to environmental signals. Quantitative measurement of the in vitro cleavage rate constants associated with ribozyme-based devices is essential for advancing the molecular design and optimization of this class of gene-regulatory devices. One of the key challenges encountered in ribozyme characterization is the efficient generation of full-length RNA from in vitro transcription reactions, where conditions generally lead to significant ribozyme cleavage. Current methods for generating full-length ribozyme-encoding RNA rely on a trans-blocking strategy, which requires a laborious gel separation and extraction step. Here, we develop a simple two-step gel-free process including cis-blocking and trans-activation steps to support scalable generation of functional full-length ribozyme-encoding RNA. We demonstrate our strategy on various types of natural ribozymes and synthetic ribozyme devices, and the cleavage rate constants obtained for the RNA generated from our strategy are comparable with those generated through traditional methods. We further develop a rapid, label-free ribozyme cleavage assay based on surface plasmon resonance, which allows continuous, real-time monitoring of ribozyme cleavage. The surface plasmon resonance-based characterization assay will complement the versatile cis-blocking and trans-activation strategy to broadly advance our ability to characterize and engineer ribozyme-based devices.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 99
    Publication Date: 2012-11-04
    Description: Recent advances have demonstrated the use of RNA-based control devices to program sophisticated cellular functions; however, the efficiency with which these devices can be quantitatively tailored has limited their broader implementation in cellular networks. Here, we developed a high-efficiency, high-throughput and quantitative two-color fluorescence-activated cell sorting-based screening strategy to support the rapid generation of ribozyme-based control devices with user-specified regulatory activities. The high-efficiency of this screening strategy enabled the isolation of a single functional sequence from a library of over 10 6 variants within two sorting cycles. We demonstrated the versatility of our approach by screening large libraries generated from randomizing individual components within the ribozyme device platform to efficiently isolate new device sequences that exhibit increased in vitro cleavage rates up to 10.5-fold and increased in vivo activation ratios up to 2-fold. We also identified a titratable window within which in vitro cleavage rates and in vivo gene-regulatory activities are correlated, supporting the importance of optimizing RNA device activity directly in the cellular environment. Our two-color fluorescence-activated cell sorting-based screen provides a generalizable strategy for quantitatively tailoring genetic control elements for broader integration within biological networks.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 100
    Publication Date: 2013-08-28
    Description: The ability to artificially control transcription is essential both to the study of gene function and to the construction of synthetic gene networks with desired properties. Cas9 is an RNA-guided double-stranded DNA nuclease that participates in the CRISPR-Cas immune defense against prokaryotic viruses. We describe the use of a Cas9 nuclease mutant that retains DNA-binding activity and can be engineered as a programmable transcription repressor by preventing the binding of the RNA polymerase (RNAP) to promoter sequences or as a transcription terminator by blocking the running RNAP. In addition, a fusion between the omega subunit of the RNAP and a Cas9 nuclease mutant directed to bind upstream promoter regions can achieve programmable transcription activation. The simple and efficient modulation of gene expression achieved by this technology is a useful asset for the study of gene networks and for the development of synthetic biology and biotechnological applications.
    Keywords: Synthetic Biology and Assembly Cloning
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