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  • Biochemistry and Biotechnology  (13,095)
  • Turbulence
  • Wiley-Blackwell  (13,121)
  • American Meteorological Society  (41)
  • MDPI  (4)
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  • 1
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    Ionospheric Turbulence and the Equatorial Plasma Density Irregularities: Scaling Features and RODI (2021)
    MDPI
    Details
    Publication Date: 2021-03-10
    Description: In the framework of space weather, the understanding of the physical mechanisms responsible for the generation of ionospheric irregularities is particularly relevant for their effects on global positioning and communication systems. Ionospheric equatorial plasma bubbles are one of the possible irregularities. In this work, using data from the ESA Swarm mission, we investigate the scaling features of electron density fluctuations characterizing equatorial plasma bubbles. Results strongly support a turbulence character of these structures and suggest the existence of a clear link between the observed scaling properties and the value of the Rate Of change of electron Density Index (RODI). This link is discussed, and RODI is proposed as a reliable proxy for the identification of plasma bubbles.
    Description: This research received financial support from European Space Agency (ESA contract N. 4000125663/18/I-NB-“EO Science for Society Permanently Open Call for Proposals EOEP-5 BLOCK4” (INTENS)) and from the Italian MIUR-PRIN grant 2017APKP7T on “Circumterrestrial Environment: Impact of Sun–Earth Interaction”.
    Description: Published
    Description: 759
    Description: 2A. Fisica dell'alta atmosfera
    Description: JCR Journal
    Keywords: Turbulence ; Electron density irregularities ; Equatorial topside ionosphere ; Swarm constellation ; 01.02. Ionosphere
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 2
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    Electric Field Multifractal Features in the High-Latitude Ionosphere: CSES-01 Observations (2021)
    MDPI
    Details
    Publication Date: 2021-05-31
    Description: In the polar ionosphere, the electric field is characterized by broadband and power law spectral densities at small/short spatio-temporal scales, which support a possible turbulent nature of the electric field fluctuations. Here, we investigate the multifractal character of the full three-dimensional electric field in the polar ionosphere as recorded on board the first Chinese Seismo- Electromagnetic Satellite (CSES-01). The results of our analysis prove a clear different degree of multifractality of the electric field fluctuations approaching either the polar cap trailing edge or the auroral region. The observed differences in the multifractal character are interpreted in terms of the different natures of the particle precipitation in the polar cap and in the auroral region. A possible link between the multifractal nature of electric field fluctuations, parallel to the geomagnetic field, and filamentation of field aligned currents (FACs) is established
    Description: Contract ASI “LIMADOU Scienza+” n 2020-31-HH.0 PNRA18 00289-A “Space weather in Polar Ionosphere: the Role of Turbulence”.
    Description: Published
    Description: 646
    Description: 2A. Fisica dell'alta atmosfera
    Description: JCR Journal
    Keywords: auroral ionosphere ; electric field ; Turbulence ; Fractals ; 01.02. Ionosphere
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
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    On Turbulent Features of E × B Plasma Motion in the Auroral Topside Ionosphere: Some Results from CSES-01 Satellite (2022)
    MDPI
    Details
    Publication Date: 2022-04-22
    Description: The recent Chinese Seismo-Electromagnetic Satellite (CSES-01) provides a good opportunity to investigate some features of plasma properties and its motion in the topside ionosphere. Using simultaneous measurements from the electric field detector and the magnetometers onboard CSES-01, we investigate some properties of the plasma ExB drift velocity for a case study during a crossing of the Southern auroral region in the topside ionosphere. In detail, we analyze the spectral and scaling features of the plasma drift velocity and provide evidence of the turbulent character of the ExB drift. Our results provide an evidence of the occurrence of 2D ExB intermittent convective turbulence for the plasma motion in the topside ionospheric F2 auroral region at scales from tens of meters to tens of kilometers. The intermittent character of the observed turbulence suggests that the macro-scale intermittent structure is isomorphic with a quasi-1D fractal structure, as happens, for example, in the case of a filamentary or thin-tube-like structure. Furthermore, in the analyzed range of scales we found that both magnetohydrodynamic and kinetic processes may affect the plasma dynamics at spatial scales below 2 km. The results are discussed and compared with previous results reported in the literature.
    Description: Published
    Description: 1936
    Description: 2A. Fisica dell'alta atmosfera
    Description: JCR Journal
    Keywords: Turbulence ; Auroral ionosphere ; ExB plasma motion ; 01.02. Ionosphere
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
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    The role of whitecapping in thickening the ocean surface boundary layer (2015)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015): 2006–2024, doi:10.1175/JPO-D-14-0234.1.
    Description: The effects of wind-driven whitecapping on the evolution of the ocean surface boundary layer are examined using an idealized one-dimensional Reynolds-averaged Navier–Stokes numerical model. Whitecapping is parameterized as a flux of turbulent kinetic energy through the sea surface and through an adjustment of the turbulent length scale. Simulations begin with a two-layer configuration and use a wind that ramps to a steady stress. This study finds that the boundary layer begins to thicken sooner in simulations with whitecapping than without because whitecapping introduces energy to the base of the boundary layer sooner than shear production does. Even in the presence of whitecapping, shear production becomes important for several hours, but then inertial oscillations cause shear production and whitecapping to alternate as the dominant energy sources for mixing. Details of these results are sensitive to initial and forcing conditions, particularly to the turbulent length scale imposed by breaking waves and the transfer velocity of energy from waves to turbulence. After 1–2 days of steady wind, the boundary layer in whitecapping simulations has thickened more than the boundary layer in simulations without whitecapping by about 10%–50%, depending on the forcing and initial conditions.
    Description: We thank Skidmore College for financial and infrastructure support, and Skidmore and the National Science Foundation for funding travel to meetings where early versions of this work were presented. We also thank the National Science Foundation, Oregon State University, Jonathan Nash, and Joe Jurisa for funding and hosting a workshop on River Plume Mixing in October, 2013, where ideas and context for this paper were developed.
    Description: 2016-02-01
    Keywords: Circulation/ Dynamics ; Mixing ; Turbulence ; Wave breaking ; Wind stress ; Atm/Ocean Structure/ Phenomena ; Mixed layer
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Coral reef drag coefficients—surface gravity wave enhancement (2018)
    American Meteorological Society
    Details
    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): 1555-1566, doi:10.1175/JPO-D-17-0231.1.
    Description: A primary challenge in modeling flow over shallow coral reefs is accurately characterizing the bottom drag. Previous studies over continental shelves and sandy beaches suggest surface gravity waves should enhance the drag on the circulation over coral reefs. The influence of surface gravity waves on drag over four platform reefs in the Red Sea is examined using observations from 6-month deployments of current and pressure sensors burst sampling at 1Hz for 4–5min. Depth-average current fluctuations U0 within each burst are dominated by wave orbital velocities uw that account for 80%–90%of the burst variance and have a magnitude of order 10 cm s21, similar to the lower-frequency depth-average current Uavg. Previous studies have shown that the cross-reef bottom stress balances the pressure gradient over these reefs. A bottom stress estimate that neglects the waves (rCdaUavgjUavgj, where r is water density and Cda is a drag coefficient) balances the observed pressure gradient when uw is smaller than Uavg but underestimates the pressure gradient when uw is larger than Uavg (by a factor of 3–5 when uw 5 2Uavg), indicating the neglected waves enhance the bottom stress. In contrast, a bottom stress estimate that includes the waves [rCda(Uavg 1 U0)jUavg 1 U0j)] balances the observed pressure gradient independent of the relative size of uw and Uavg, indicating that this estimate accounts for the wave enhancement of the bottom stress. A parameterization proposed by Wright and Thompson provides a reasonable estimate of the total bottom stress (including the waves) given the burst-averaged current and the wave orbital velocity.
    Description: The Red Sea field program was supported by Awards USA 00002 and KSA 00011 made by KAUST. S. Lentz was supported for the analysis by NSF Award OCE-1558343.
    Description: 2019-01-13
    Keywords: Coastal flows ; Currents ; Dynamics ; Gravity waves ; Turbulence
    Repository Name: Woods Hole Open Access Server
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  • 6
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    Observations of turbulence in the ocean surface boundary layer : energetics and transport (2010)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2009. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 39 (2009): 1077–1096, doi:10.1175/2008JPO4044.1.
    Description: Observations of turbulent kinetic energy (TKE) dynamics in the ocean surface boundary layer are presented here and compared with results from previous observational, numerical, and analytic studies. As in previous studies, the dissipation rate of TKE is found to be higher in the wavy ocean surface boundary layer than it would be in a flow past a rigid boundary with similar stress and buoyancy forcing. Estimates of the terms in the turbulent kinetic energy equation indicate that, unlike in a flow past a rigid boundary, the dissipation rates cannot be balanced by local production terms, suggesting that the transport of TKE is important in the ocean surface boundary layer. A simple analytic model containing parameterizations of production, dissipation, and transport reproduces key features of the vertical profile of TKE, including enhancement near the surface. The effective turbulent diffusion coefficient for heat is larger than would be expected in a rigid-boundary boundary layer. This diffusion coefficient is predicted reasonably well by a model that contains the effects of shear production, buoyancy forcing, and transport of TKE (thought to be related to wave breaking). Neglect of buoyancy forcing or wave breaking in the parameterization results in poor predictions of turbulent diffusivity. Langmuir turbulence was detected concurrently with a fraction of the turbulence quantities reported here, but these times did not stand out as having significant differences from observations when Langmuir turbulence was not detected.
    Description: The Office of Naval Research funded this work as a part of CBLAST-Low.
    Keywords: Turbulence ; Boundary layer ; Sea/ocean surface ; Air-sea interaction ; Energy transport
    Repository Name: Woods Hole Open Access Server
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  • 7
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    Vertical structure of dissipation in the nearshore (2010)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2007. 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 37 (2007): 1764-1777, doi:10.1175/jpo3098.1.
    Description: The vertical structure of the dissipation of turbulence kinetic energy was observed in the nearshore region (3.2-m mean water depth) with a tripod of three acoustic Doppler current meters off a sandy ocean beach. Surface and bottom boundary layer dissipation scaling concepts overlap in this region. No depth-limited wave breaking occurred at the tripod, but wind-induced whitecapping wave breaking did occur. Dissipation is maximum near the surface and minimum at middepth, with a secondary maximum near the bed. The observed dissipation does not follow a surfzone scaling, nor does it follow a “log layer” surface or bottom boundary layer scaling. At the upper two current meters, dissipation follows a modified deep-water breaking-wave scaling. Vertical shear in the mean currents is negligible and shear production magnitude is much less than dissipation, implying that the vertical diffusion of turbulence is important. The increased near-bed secondary dissipation maximum results from a decrease in the turbulent length scale.
    Description: Funding was provided by NSF and ONR.
    Keywords: Turbulence ; Kinetic energy ; Ocean
    Repository Name: Woods Hole Open Access Server
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  • 8
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    Turbulence and diapycnal mixing in Drake Passage (2013)
    American Meteorological Society
    Details
    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 Physical Oceanography 42 (2012): 2143–2152, doi:10.1175/JPO-D-12-027.1.
    Description: Direct measurements of turbulence levels in the Drake Passage region of the Southern Ocean show a marked enhancement over the Phoenix Ridge. At this site, the Antarctic Circumpolar Current (ACC) is constricted in its flow between the southern tip of South America and the northern tip of the Antarctic Peninsula. Observed turbulent kinetic energy dissipation rates are enhanced in the regions corresponding to the ACC frontal zones where strong flow reaches the bottom. In these areas, turbulent dissipation levels reach 10−8 W kg−1 at abyssal and middepths. The mixing enhancement in the frontal regions is sufficient to elevate the diapycnal turbulent diffusivity acting in the deep water above the axis of the ridge to 1 × 10−4 m2 s−1. This level is an order of magnitude larger than the mixing levels observed upstream in the ACC above smoother bathymetry. Outside of the frontal regions, dissipation rates are O(10−10) W kg−1, comparable to the background levels of turbulence found throughout most mid- and low-latitude regions of the global ocean.
    Description: This work was supported by the U.S. National Science Foundation and by the Natural Environment Research Council of the United Kingdom.
    Description: 2013-06-01
    Keywords: Southern Ocean ; Turbulence ; Diapycnal mixing
    Repository Name: Woods Hole Open Access Server
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  • 9
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    Turbulence from breaking surface waves at a river mouth (2018)
    American Meteorological Society
    Details
    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): 435-453, doi:10.1175/JPO-D-17-0122.1.
    Description: Observations of surface waves, currents, and turbulence at the Columbia River mouth are used to investigate the source and vertical structure of turbulence in the surface boundary layer. Turbulent velocity data collected on board freely drifting Surface Wave Instrument Float with Tracking (SWIFT) buoys are corrected for platform motions to estimate turbulent kinetic energy (TKE) and TKE dissipation rates. Both of these quantities are correlated with wave steepness, which has previously been shown to determine wave breaking within the same dataset. Estimates of the turbulent length scale increase linearly with distance from the free surface, and roughness lengths estimated from velocity statistics scale with significant wave height. The vertical decay of turbulence is consistent with a balance between vertical diffusion and dissipation. Below a critical depth, a power-law scaling commonly applied in the literature works well to fit the data. Above this depth, an exponential scaling fits the data well. These results, which are in a surface-following reference frame, are reconciled with results from the literature in a fixed reference frame. A mapping between free-surface and mean-surface reference coordinates suggests 30% of the TKE is dissipated above the mean sea surface.
    Description: Funding for this project was provided by the Office of Naval Research as part of the RIVET-II DRI, and for the DARLA group.
    Keywords: Ocean ; Estuaries ; Gravity waves ; Turbulence ; Wave breaking ; In situ oceanic observations
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  • 10
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    The importance of tidal and lateral asymmetries in stratification to residual circulation in partially mixed estuaries (2010)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2007. 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 37 (2007): 1496-1511, doi:10.1175/jpo3071.1.
    Description: Measurements collected in the York River estuary, Virginia, demonstrate the important impact that tidal and lateral asymmetries in turbulent mixing have on the tidally averaged residual circulation. A reduction in turbulent mixing during the ebb phase of the tide caused by tidal straining of the axial density gradient results in increased vertical velocity shear throughout the water column during the ebb tide. In the absence of significant lateral differences in turbulent mixing, the enhanced ebb-directed transport caused by tidal straining is balanced by a reduction in the net seaward-directed barotropic pressure gradient, resulting in laterally uniform two-layer residual flow. However, the channel–shoal morphology of many drowned river valley estuaries often leads to lateral gradients in turbulent mixing. Tidal straining may then lead to tidal asymmetries in turbulent mixing near the deeper channel while the neighboring shoals remain relatively well mixed. As a result, the largest lateral asymmetries in turbulent mixing occur at the end of the ebb tide when the channel is significantly more stratified than the shoals. The reduced friction at the end of ebb delays the onset of the flood tide, increasing the duration of ebb in the channel. Conversely, over the shoal regions where stratification is more inhibited by tidal mixing, there is greater friction and the transition from ebb to flood occurs more rapidly. The resulting residual circulation is seaward over the channel and landward over the shoal. The shoal–channel segregation of this barotropically induced estuarine residual flow is opposite to that typically associated with baroclinic estuarine circulation over channel–shoal bathymetry.
    Description: Support for this research was provided by the National Science Foundation Division of Ocean Sciences Grant OCE- 9984941.
    Keywords: Tides ; Ocean circulation ; Estuaries ; Turbulence
    Repository Name: Woods Hole Open Access Server
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  • 11
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    The turbulent oscillator : a mechanism of low-frequency variability of the wind-driven ocean gyres (2010)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2007. 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. 37 (2007): 2363-2386, doi:10.1175/jpo3118.1.
    Description: Intrinsic low-frequency variability is studied in the idealized, quasigeostrophic, midlatitude, wind-driven ocean gyres operating at large Reynolds number. A robust decadal variability mode driven by the transient mesoscale eddies is found and analyzed. The variability is a turbulent phenomenon, which is driven by the competition between the eddy rectification process and the potential vorticity anomalies induced by changes of the intergyre transport
    Description: Funding for Pavel Berloff was provided by NSF Grants OCE-0091836 and OCE- 0344094, by the U.K. Royal Society Fellowship, and by the Newton Trust Award, A. M. Hogg was supported by an Australian Research Council Postdoctoral Fellowship (DP0449851) during this work, and William K. Dewar was supported by NSF Grants OCE-0424227 and OCE-0550139.
    Keywords: Turbulence ; Gyres ; Transport ; Potential vorticity ; Mesoscale processes
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  • 12
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    The influence of stratification and nonlocal turbulent production on estuarine turbulence : an assessment of turbulence closure with field observations (2011)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2011. 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 41 (2011): 166-185, doi:10.1175/2010JPO4470.1.
    Description: Field observations of turbulent kinetic energy (TKE), dissipation rate ε, and turbulent length scale demonstrate the impact of both density stratification and nonlocal turbulent production on turbulent momentum flux. The data were collected in a highly stratified salt wedge estuary using the Mobile Array for Sensing Turbulence (MAST). Estimates of the dominant length scale of turbulent motions obtained from the vertical velocity spectra provide field confirmation of the theoretical limitation imposed by either the distance to the boundary or the Ozmidov scale, whichever is smaller. Under boundary-limited conditions, anisotropy generally increases with increasing shear and decreased distance to the boundary. Under Ozmidov-limited conditions, anisotropy increases rapidly when the gradient Richardson number exceeds 0.25. Both boundary-limited and Ozmidov-limited conditions demonstrate significant deviations from a local production–dissipation balance that are largely consistent with simple scaling relationships for the vertical divergence in TKE flux. Both the impact of stratification and deviation from equilibrium turbulence observed in the data are largely consistent with commonly used turbulence closure models that employ “nonequilibrium” stability functions. The data compare most favorably with the nonequilibrium version of the L. H. Kantha and C. A. Clayson stability functions. Not only is this approach more consistent with the observed critical gradient Richardson number of 0.25, but it also accounts for the large deviations from equilibrium turbulence in a manner consistent with the observations.
    Description: The funding for this research was obtained from ONR Grant N00014-06-1-0292 and NSF Grants and OCE-08-25226 and OCE-08-24871.
    Keywords: Turbulence ; Estuaries ; Kinetic energy
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  • 13
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    The role of advection, straining, and mixing on the tidal variability of estuarine stratification (2012)
    American Meteorological Society
    Details
    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 Physical Oceanography 42 (2012): 855–868, doi:10.1175/JPO-D-10-05010.1.
    Description: Data from the Hudson River estuary demonstrate that the tidal variations in vertical salinity stratification are not consistent with the patterns associated with along-channel tidal straining. These observations result from three additional processes not accounted for in the traditional tidal straining model: 1) along-channel and 2) lateral advection of horizontal gradients in the vertical salinity gradient and 3) tidal asymmetries in the strength of vertical mixing. As a result, cross-sectionally averaged values of the vertical salinity gradient are shown to increase during the flood tide and decrease during the ebb. Only over a limited portion of the cross section does the observed stratification increase during the ebb and decrease during the flood. These observations highlight the three-dimensional nature of estuarine flows and demonstrate that lateral circulation provides an alternate mechanism that allows for the exchange of materials between surface and bottom waters, even when direct turbulent mixing through the pycnocline is prohibited by strong stratification.
    Description: The funding for this research was obtained from NSF Grant OCE-08-25226.
    Description: 2012-11-01
    Keywords: Mixing ; Ocean circulation ; Shear structure/flows ; Transport ; Turbulence
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  • 14
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    Internal waves and turbulence in the Antarctic Circumpolar Current (2013)
    American Meteorological Society
    Details
    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): 259–282, doi:10.1175/JPO-D-11-0194.1.
    Description: This study reports on observations of turbulent dissipation and internal wave-scale flow properties in a standing meander of the Antarctic Circumpolar Current (ACC) north of the Kerguelen Plateau. The authors characterize the intensity and spatial distribution of the observed turbulent dissipation and the derived turbulent mixing, and consider underpinning mechanisms in the context of the internal wave field and the processes governing the waves’ generation and evolution. The turbulent dissipation rate and the derived diapycnal diffusivity are highly variable with systematic depth dependence. The dissipation rate is generally enhanced in the upper 1000–1500 m of the water column, and both the dissipation rate and diapycnal diffusivity are enhanced in some places near the seafloor, commonly in regions of rough topography and in the vicinity of strong bottom flows associated with the ACC jets. Turbulent dissipation is high in regions where internal wave energy is high, consistent with the idea that interior dissipation is related to a breaking internal wave field. Elevated turbulence occurs in association with downward-propagating near-inertial waves within 1–2 km of the surface, as well as with upward-propagating, relatively high-frequency waves within 1–2 km of the seafloor. While an interpretation of these near-bottom waves as lee waves generated by ACC jets flowing over small-scale topographic roughness is supported by the qualitative match between the spatial patterns in predicted lee wave radiation and observed near-bottom dissipation, the observed dissipation is found to be only a small percentage of the energy flux predicted by theory. The mismatch suggests an alternative fate to local dissipation for a significant fraction of the radiated energy.
    Description: SW acknowledges the support of the Grantham Institute for Climate Change, Imperial College London. ACNG acknowledges the support of a NERC Advanced Research Fellowship (Grant NE/C517633/1). KLP acknowledges support from Woods Hole Oceanographic Institution bridge support funds.
    Description: 2013-08-01
    Keywords: Diapycnal mixing ; Internal waves ; Turbulence
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  • 15
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    Wind-wave effects on estuarine turbulence : a comparison of observations and second-moment closure predictions (2018)
    American Meteorological Society
    Details
    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): 905-923, doi:10.1175/JPO-D-17-0133.1.
    Description: Observations of turbulent kinetic energy, dissipation, and turbulent stress were collected in the middle reaches of Chesapeake Bay and were used to assess second-moment closure predictions of turbulence generated beneath breaking waves. Dissipation scaling indicates that the turbulent flow structure observed during a 10-day wind event was dominated by a three-layer response that consisted of 1) a wave transport layer, 2) a surface log layer, and 3) a tidal, bottom boundary layer limited by stable stratification. Below the wave transport layer, turbulent mixing was limited by stable stratification. Within the wave transport layer, where dissipation was balanced by a divergence in the vertical turbulent kinetic energy flux, the eddy viscosity was significantly underestimated by second-moment turbulence closure models, suggesting that breaking waves homogenized the mixed surface layer to a greater extent than the simple model of TKE diffusing away from a source at the surface. While the turbulent transport of TKE occurred largely downgradient, the intermittent downward sweeps of momentum generated by breaking waves occurred largely independent of the mean shear. The underprediction of stress in the wave transport layer by second-moment closures was likely due to the inability of the eddy viscosity model to capture the nonlocal turbulent transport of the momentum flux beneath breaking waves. Finally, the authors hypothesize that large-scale coherent turbulent eddies played a significant role in transporting momentum generated near the surface to depth.
    Description: This work was supported by National Science Foundation Grants OCE-1061609 and OCE-1339032.
    Description: 2018-10-19
    Keywords: Mixing ; Turbulence ; Waves, oceanic ; Boundary layer
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  • 16
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    Observed variations in turbulent mixing efficiency in the deep ocean (2018)
    American Meteorological Society
    Details
    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): 1815-1830, doi:10.1175/JPO-D-17-0275.1.
    Description: Recent progress in direct numerical simulations (DNSs) of stratified turbulent flows has led to increasing attention to the validity of the constancy of the dissipation flux coefficient Γ in the Osborn’s eddy diffusivity model. Motivated by lack of observational estimates of Γ, particularly under weakly stratified deep-ocean conditions, this study estimates Γ using deep microstructure profiles collected in various regions of the North Pacific and Southern Oceans. It is shown that Γ is not constant but varies significantly with the Ozmidov/Thorpe scale ratio ROT in a fashion similar to that obtained by previous DNS studies. Efficient mixing events with Γ ~ O(1) and ROT ~ O(0.1) tend to be frequently observed in the deep ocean (i.e., weak stratification), while moderate mixing events with Γ ~ O(0.1) and ROT ~ O(1) tend to be observed in the upper ocean (i.e., strong stratification). The observed negative relationship between Γ and ROT is consistent with a simple scaling that can be derived from classical turbulence theories. In contrast, the observed results exhibit no definite relationships between Γ and the buoyancy Reynolds number Reb, although Reb has long been thought to be another key parameter that controls Γ.
    Description: This study was supported by MEXT KAKENHI Grant JP15H05824 and JSPS KAKENHI Grant JP15H02131.
    Description: 2019-02-15
    Keywords: Abyssal circulation ; Mixing ; Subgrid-scale processes ; Turbulence ; In situ oceanic observations
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    Dynamics of three-dimensional turbulent wall plumes and implications for estimates of submarine glacier melting (2018)
    American Meteorological Society
    Details
    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):1941-1950, doi:10.1175/JPO-D-17-0194.1.
    Description: Subglacial discharges have been observed to generate buoyant plumes along the ice face of Greenland tidewater glaciers. These plumes have been traditionally modeled using classical plume theory, and their characteristic parameters (e.g., velocity) are employed in the widely used three-equation melt parameterization. However, the applicability of plume theory for three-dimensional turbulent wall plumes is questionable because of the complex near-wall plume dynamics. In this study, corrections to the classical plume theory are introduced to account for the presence of a wall. In particular, the drag and entrainment coefficients are quantified for a three-dimensional turbulent wall plume using data from direct numerical simulations. The drag coefficient is found to be an order of magnitude larger than that for a boundary layer flow over a flat plate at a similar Reynolds number. This result suggests a significant increase in the melting estimates by the current parameterization. However, the volume flux in a wall plume is found to be one-half that of a conical plume that has 2 times the buoyancy flux. This finding suggests that the total entrainment (per unit area) of ambient water is the same and that the plume scalar characteristics (i.e., temperature and salinity) can be predicted reasonably well using classical plume theory.
    Description: This work was supported by the Linné FLOW Centre at KTH and the Academy of Finland Center of Excellence Programme Grant 307331 (author Ezhova) and by VR Swedish Research Council GrantVR2014-5001 (author Brandt). Support to author Cenedese was given by NSF Project OCE-1434041.
    Description: 2019-02-27
    Keywords: Buoyancy ; Entrainment ; Turbulence
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    The modification of bottom boundary layer turbulence and mixing by internal waves shoaling on a barrier reef (2012)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2011. 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 41 (2011): 2223–2241, doi:10.1175/2011JPO4344.1.
    Description: Results are presented from an observational study of stratified, turbulent flow in the bottom boundary layer on the outer southeast Florida shelf. Measurements of momentum and heat fluxes were made using an array of acoustic Doppler velocimeters and fast-response temperature sensors in the bottom 3 m over a rough reef slope. Direct estimates of flux Richardson number Rf confirm previous laboratory, numerical, and observational work, which find mixing efficiency not to be a constant but rather to vary with Frt, Reb, and Rig. These results depart from previous observations in that the highest levels of mixing efficiency occur for Frt 〈 1, suggesting that efficient mixing can also happen in regions of buoyancy-controlled turbulence. Generally, the authors find that turbulence in the reef bottom boundary layer is highly variable in time and modified by near-bed flow, shear, and stratification driven by shoaling internal waves.
    Description: Funding was provided by grants from the National Oceanic and Atmospheric Administration’s National Undersea Research Program, National Science Foundation Grants OCE-0622967 and OCE- 0824972 to SGM, and the Singapore Stanford Program. Kristen Davis was supported by a National Defense Science and Engineering Graduate Fellowship and an ARCS Foundation Fellowship.
    Keywords: Boundary layer ; Turbulence ; Bottom currents ; Mixing ; Internal waves
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    Spontaneous generation of near-inertial waves by the Kuroshio Front (2015)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015): 2381–2406, doi:10.1175/JPO-D-14-0086.1.
    Description: While near-inertial waves are known to be generated by atmospheric storms, recent observations in the Kuroshio Front find intense near-inertial internal-wave shear along sloping isopycnals, even during calm weather. Recent literature suggests that spontaneous generation of near-inertial waves by frontal instabilities could represent a major sink for the subinertial quasigeostrophic circulation. An unforced three-dimensional 1-km-resolution model, initialized with the observed cross-Kuroshio structure, is used to explore this mechanism. After several weeks, the model exhibits growth of 10–100-km-scale frontal meanders, accompanied by O(10) mW m−2 spontaneous generation of near-inertial waves associated with readjustment of submesoscale fronts forced out of balance by mesoscale confluent flows. These waves have properties resembling those in the observations. However, they are reabsorbed into the model Kuroshio Front with no more than 15% dissipating or radiating away. Thus, spontaneous generation of near-inertial waves represents a redistribution of quasigeostrophic energy rather than a significant sink.
    Description: “The Study of Kuroshio Ecosystem Dynamics for Sustainable Fisheries (SKED)” supported by MEXT, MIT-Hayashi Seed Fund, ONR (Awards N000140910196 and N000141210101), NSF (Award OCE 0928617, 0928138) for support.
    Description: 2016-03-01
    Keywords: Circulation/ Dynamics ; Frontogenesis/frontolysis ; Fronts ; Internal waves ; Turbulence ; Upwelling/downwelling ; Atm/Ocean Structure/ Phenomena ; Jets
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    Biases in Thorpe-scale estimates of turbulence dissipation. Part I : Assessments from large-scale overturns in oceanographic data (2015)
    American Meteorological Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015): 2497–2521, doi:10.1175/JPO-D-14-0128.1.
    Description: Oceanic density overturns are commonly used to parameterize the dissipation rate of turbulent kinetic energy. This method assumes a linear scaling between the Thorpe length scale LT and the Ozmidov length scale LO. Historic evidence supporting LT ~ LO has been shown for relatively weak shear-driven turbulence of the thermocline; however, little support for the method exists in regions of turbulence driven by the convective collapse of topographically influenced overturns that are large by open-ocean standards. This study presents a direct comparison of LT and LO, using vertical profiles of temperature and microstructure shear collected in the Luzon Strait—a site characterized by topographically influenced overturns up to O(100) m in scale. The comparison is also done for open-ocean sites in the Brazil basin and North Atlantic where overturns are generally smaller and due to different processes. A key result is that LT/LO increases with overturn size in a fashion similar to that observed in numerical studies of Kelvin–Helmholtz (K–H) instabilities for all sites but is most clear in data from the Luzon Strait. Resultant bias in parameterized dissipation is mitigated by ensemble averaging; however, a positive bias appears when instantaneous observations are depth and time integrated. For a series of profiles taken during a spring tidal period in the Luzon Strait, the integrated value is nearly an order of magnitude larger than that based on the microstructure observations. Physical arguments supporting LT ~ LO are revisited, and conceptual regimes explaining the relationship between LT/LO and a nondimensional overturn size are proposed. In a companion paper, Scotti obtains similar conclusions from energetics arguments and simulations.
    Description: B.D.M. and S.K.V. gratefully acknowledge the support of the Office of Naval Research under Grants N00014-12-1-0279, N00014-12-1-0282, and N00014-12-1-0938 (Program Manager: Dr. Terri Paluszkiewicz). S.K.V. also acknowledges support of the National Science Foundation under Grant OCE-1151838. L.S.L. acknowledges support for BBTRE by the National Science Foundation by Contract OCE94-15589 and NATRE and IWISE by the Office of Naval Research by Contracts N00014-92-1323 and N00014-10-10315. J.N.M. was supported through Grant 1256620 from the National Science Foundation and the Office of Naval Research (IWISE Project).
    Description: 2016-04-01
    Keywords: Circulation/ Dynamics ; Diapycnal mixing ; Small scale processes ; Turbulence ; Atm/Ocean Structure/ Phenomena ; Mixing ; Observational techniques and algorithms ; Profilers, oceanic ; Models and modeling ; Parameterization
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    Characterization and modulation of Langmuir circulation in Chesapeake Bay (2015)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015): 2621–2639, doi:10.1175/JPO-D-14-0239.1.
    Description: Measurements made as part of a large-scale experiment to examine wind-driven circulation and mixing in Chesapeake Bay demonstrate that circulations consistent with Langmuir circulation play an important role in surface boundary layer dynamics. Under conditions when the turbulent Langmuir number Lat is low (〈0.5), the surface mixed layer is characterized by 1) elevated vertical turbulent kinetic energy; 2) decreased anisotropy; 3) negative vertical velocity skewness indicative of strong/narrow downwelling and weak/broad upwelling; and 4) strong negative correlations between low-frequency vertical velocity and the velocity in the direction of wave propagation. These characteristics appear to be primarily the result of the vortex force associated with the surface wave field, but convection driven by a destabilizing heat flux is observed and appears to contribute significantly to the observed negative vertical velocity skewness. Conditions that favor convection usually also have strong Langmuir forcing, and these two processes probably both contribute to the surface mixed layer turbulence. Conditions in which traditional stress-driven turbulence is important are limited in this dataset. Unlike other shallow coastal systems where full water column Langmuir circulation has been observed, the salinity stratification in Chesapeake Bay is nearly always strong enough to prevent full-depth circulation from developing.
    Description: The funding for this research was provided by the National Science Foundation Grants OCE-1339032 and OCE-1338518.
    Description: 2016-04-01
    Keywords: Circulation/ Dynamics ; Convection ; Instability ; Mixing ; Turbulence ; Wave breaking ; Wind stress
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    Impact of a localized source of subglacial discharge on the heat flux and submarine melting of a tidewater glacier : a laboratory study (2016)
    American Meteorological Society
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    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): 3155-3163, doi:10.1175/JPO-D-16-0123.1.
    Description: Idealized laboratory experiments have been conducted in a two-layer stratified fluid to investigate the leading-order dynamics that control submarine melting and meltwater export near a vertical ice–ocean interface as a function of subglacial discharge. In summer, the discharge of surface runoff at the base of a glacier (subglacial discharge) generates strong buoyant plumes that rise along the glacier front entraining ambient water along the way. The entrainment enhances the heat transport toward the glacier front and hence the submarine melt rate increases with the subglacial discharge rate. In the laboratory, the effect of subglacial discharge is simulated by introducing freshwater at freezing temperature from a point source at the base of an ice block representing the glacier. The circulation pattern observed both with and without subglacial discharge resembles those observed in previous observational and numerical studies. Buoyant plumes rise vertically until they find either their neutrally buoyant level or the free surface. Hence, the meltwater can deposit within the interior of the water column and not entirely at the free surface, as confirmed by field observations. The heat budget in the tank, calculated following a new framework, gives estimates of submarine melt rate that increase with the subglacial discharge and are in agreement with the directly measured submarine melting. This laboratory study provides the first direct measurements of submarine melt rates for different subglacial discharges, and the results are consistent with the predictions of previous theoretical and numerical studies.
    Description: Support to C. C. was given by the NSF project OCE- 1130008 and OCE-1434041. M. G. received support from the ‘‘Gori’’ Fellowship.
    Description: 2017-04-07
    Keywords: Glaciers ; Buoyancy ; Density currents ; Turbulence ; Laboratory/physical models
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    Rapid mixed layer depening by the combination of Langmuir and shear instabilities : a case study (2010)
    American Meteorological Society
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    Publication Date: 2022-05-26
    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): 2381-2400, doi:10.1175/2010JPO4403.1.
    Description: Langmuir circulation (LC) is a turbulent upper-ocean process driven by wind and surface waves that contributes significantly to the transport of momentum, heat, and mass in the oceanic surface layer. The authors have previously performed a direct comparison of large-eddy simulations and observations of the upper-ocean response to a wind event with rapid mixed layer deepening. The evolution of simulated crosswind velocity variance and spatial scales, as well as mixed layer deepening, was only consistent with observations if LC effects are included in the model. Based on an analysis of these validated simulations, in this study the fundamental differences in mixing between purely shear-driven turbulence and turbulence with LC are identified. In the former case, turbulent kinetic energy (TKE) production due to shear instabilities is largest near the surface, gradually decreasing to zero near the base of the mixed layer. This stands in contrast to the LC case in which at middepth range TKE production can be dominated by Stokes drift shear. Furthermore, the Eulerian mean vertical shear peaks near the base of the mixed layer so that TKE production by mean shear flow is elevated there. LC transports horizontal momentum efficiently downward leading to an along-wind velocity jet below LC downwelling regions at the base of the mixed layer. Locally enhanced vertical shear instabilities as a result of this jet efficiently erode the thermocline. In turn, enhanced breaking internal waves inject cold deep water into the mixed layer, where LC currents transport temperature perturbation advectively. Thus, LC and locally generated shear instabilities work intimately together to facilitate strongly the mixed layer deepening process.
    Description: This research was supported by the Office of Naval Research through Grants N00014-09-M-0112 (TK) and N00014-06-1-0178 (AP, JT). Author TK also received support from a Woods Hole Oceanographic Institution Cooperative Institute for Climate and Ocean Research Postdoctoral Scholarship.
    Keywords: Mixed layer ; Shear structure/flows ; Wind effects ; Turbulence ; Thermocline ; Internal waves ; Advection
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    Residual sediment fluxes in weakly-to-periodically stratified estuaries and tidal inlets (2013)
    American Meteorological Society
    Details
    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 Physical Oceanography 43 (2013): 1841–1861, doi:10.1175/JPO-D-12-0231.1.
    Description: In this idealized numerical modeling study, the composition of residual sediment fluxes in energetic (e.g., weakly or periodically stratified) tidal estuaries is investigated by means of one-dimensional water column models, with some focus on the sediment availability. Scaling of the underlying dynamic equations shows dependence of the results on the Simpson number (relative strength of horizontal density gradient) and the Rouse number (relative settling velocity) as well as impacts of the Unsteadiness number (relative tidal frequency). Here, the parameter space given by the Simpson and Rouse numbers is mainly investigated. A simple analytical model based on the assumption of stationarity shows that for small Simpson and Rouse numbers sediment flux is down estuary and vice versa for large Simpson and Rouse numbers. A fully dynamic water column model coupled to a second-moment turbulence closure model allows to decompose the sediment flux profiles into contributions from the transport flux (product of subtidal velocity and sediment concentration profiles) and the fluctuation flux profiles (tidal covariance between current velocity and sediment concentration). Three different types of bottom sediment pools are distinguished to vary the sediment availability, by defining a time scale for complete sediment erosion. For short erosion times scales, the transport sediment flux may dominate, but for larger erosion time scales the fluctuation sediment flux largely dominates the tidal sediment flux. When quarter-diurnal components are added to the tidal forcing, up-estuary sediment fluxes are strongly increased for stronger and shorter flood tides and vice versa. The theoretical results are compared to field observations in a tidally energetic inlet.
    Description: Project funding was provided by the German Research Foundation (DFG) in the framework of the Project ECOWS (Role of Estuarine Circulation for Transport of Suspended Particulate Matter in the Wadden Sea, BU 1199/11) and by the German Federal Ministry of Research and Education in the framework of the Project PACE [The future of the Wadden Sea sediment fluxes: still keeping pace with sea level rise? (FKZ 03F0634A)].
    Description: 2014-03-01
    Keywords: Channel flows ; Coastal flows ; Mixing ; Transport ; Turbulence ; Single column models
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    Suppression of internal wave breaking in the Antarctic Circumpolar Current near topography (2014)
    American Meteorological Society
    Details
    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): 1466–1492, doi:10.1175/JPO-D-12-0154.1.
    Description: Simultaneous full-depth microstructure measurements of turbulence and finestructure measurements of velocity and density are analyzed to investigate the relationship between turbulence and the internal wave field in the Antarctic Circumpolar Current. These data reveal a systematic near-bottom overprediction of the turbulent kinetic energy dissipation rate by finescale parameterization methods in select locations. Sites of near-bottom overprediction are typically characterized by large near-bottom flow speeds and elevated topographic roughness. Further, lower-than-average shear-to-strain ratios indicative of a less near-inertial wave field, rotary spectra suggesting a predominance of upward internal wave energy propagation, and enhanced narrowband variance at vertical wavelengths on the order of 100 m are found at these locations. Finally, finescale overprediction is typically associated with elevated Froude numbers based on the near-bottom shear of the background flow, and a background flow with a systematic backing tendency. Agreement of microstructure- and finestructure-based estimates within the expected uncertainty of the parameterization away from these special sites, the reproducibility of the overprediction signal across various parameterization implementations, and an absence of indications of atypical instrument noise at sites of parameterization overprediction, all suggest that physics not encapsulated by the parameterization play a role in the fate of bottom-generated waves at these locations. Several plausible underpinning mechanisms based on the limited available evidence are discussed that offer guidance for future studies.
    Description: The SOFine project is funded by the United Kingdom’s Natural Environmental Research Council (NERC) (Grant NE/G001510/1). SW acknowledges the support of anARCDiscovery Early CareerResearchAward (Grant DE120102927), as well as the Grantham Institute for Climate Change, Imperial College London, and the ARC Centre of Excellence for Climate System Science (Grant CE110001028). ACNG acknowledges the support of a NERC Advanced Research Fellowship (Grant NE/C517633/1).KLP acknowledges support fromWoods Hole Oceanographic Institution bridge support funds.
    Description: 2014-11-01
    Keywords: Circulation/ Dynamics ; Diapycnal mixing ; Internal waves ; Small scale processes ; Turbulence ; Observational techniques and algorithms ; In situ oceanic observations ; Profilers, oceanic
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    Direct estimate of lateral eddy diffusivity upstream of Drake Passage (2014)
    American Meteorological Society
    Details
    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): 2593–2616, doi:10.1175/JPO-D-13-0120.1.
    Description: The first direct estimate of the rate at which geostrophic turbulence mixes tracers across the Antarctic Circumpolar Current is presented. The estimate is computed from the spreading of a tracer released upstream of Drake Passage as part of the Diapycnal and Isopycnal Mixing Experiment in the Southern Ocean (DIMES). The meridional eddy diffusivity, a measure of the rate at which the area of the tracer spreads along an isopycnal across the Antarctic Circumpolar Current, is 710 ± 260 m2 s−1 at 1500-m depth. The estimate is based on an extrapolation of the tracer-based diffusivity using output from numerical tracers released in a one-twentieth of a degree model simulation of the circulation and turbulence in the Drake Passage region. The model is shown to reproduce the observed spreading rate of the DIMES tracer and suggests that the meridional eddy diffusivity is weak in the upper kilometer of the water column with values below 500 m2 s−1 and peaks at the steering level, near 2 km, where the eddy phase speed is equal to the mean flow speed. These vertical variations are not captured by ocean models presently used for climate studies, but they significantly affect the ventilation of different water masses.
    Description: NSF support through Awards OCE-1233832, OCE-1232962, and OCE-1048926 is gratefully acknowledged.
    Description: 2015-04-01
    Keywords: Geographic location/entity ; Southern Ocean ; Circulation/ Dynamics ; Diffusion ; Eddies ; Ocean circulation ; Turbulence ; Physical Meteorology and Climatology ; Isopycnal mixing
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    Enhanced diapycnal diffusivity in intrusive regions of the Drake Passage (2016)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    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): 1309-1321, doi:10.1175/JPO-D-15-0068.1.
    Description: Direct measurements of oceanic turbulent parameters were taken upstream of and across Drake Passage, in the region of the Subantarctic and Polar Fronts. Values of turbulent kinetic energy dissipation rate ε estimated by microstructure are up to two orders of magnitude lower than previously published estimates in the upper 1000 m. Turbulence levels in Drake Passage are systematically higher than values upstream, regardless of season. The dissipation of thermal variance χ is enhanced at middepth throughout the surveys, with the highest values found in northern Drake Passage, where water mass variability is the most pronounced. Using the density ratio, evidence for double-diffusive instability is presented. Subject to double-diffusive physics, the estimates of diffusivity using the Osborn–Cox method are larger than ensemble statistics based on ε and the buoyancy frequency.
    Description: This work was supported by grants from the U.S. National Science Foundation.
    Description: 2016-10-05
    Keywords: Geographic location/entity ; Southern Ocean ; Circulation/ Dynamics ; Diapycnal mixing ; Mixing ; Turbulence ; Atm/Ocean Structure/ Phenomena ; Fronts ; Observational techniques and algorithms ; Profilers, oceanic
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    Stratified turbulence and mixing efficiency in a salt wedge estuary (2016)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    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): 1769-1783, doi:10.1175/JPO-D-15-0193.1.
    Description: High-resolution observations of velocity, salinity, and turbulence quantities were collected in a salt wedge estuary to quantify the efficiency of stratified mixing in a high-energy environment. During the ebb tide, a midwater column layer of strong shear and stratification developed, exhibiting near-critical gradient Richardson numbers and turbulent kinetic energy (TKE) dissipation rates greater than 10−4 m2 s−3, based on inertial subrange spectra. Collocated estimates of scalar variance dissipation from microconductivity sensors were used to estimate buoyancy flux and the flux Richardson number Rif. The majority of the samples were outside the boundary layer, based on the ratio of Ozmidov and boundary length scales, and had a mean Rif = 0.23 ± 0.01 (dissipation flux coefficient Γ = 0.30 ± 0.02) and a median gradient Richardson number Rig = 0.25. The boundary-influenced subset of the data had decreased efficiency, with Rif = 0.17 ± 0.02 (Γ = 0.20 ± 0.03) and median Rig = 0.16. The relationship between Rif and Rig was consistent with a turbulent Prandtl number of 1. Acoustic backscatter imagery revealed coherent braids in the mixing layer during the early ebb and a transition to more homogeneous turbulence in the midebb. A temporal trend in efficiency was also visible, with higher efficiency in the early ebb and lower efficiency in the late ebb when the bottom boundary layer had greater influence on the flow. These findings show that mixing efficiency of turbulence in a continuously forced, energetic, free shear layer can be significantly greater than the broadly cited upper bound from Osborn of 0.15–0.17.
    Description: Holleman was supported by the Devonshire Scholars program. The field study and the coauthors’ contributions were supported by NSF Grant OCE 0926427.
    Description: 2016-11-24
    Keywords: Circulation/ Dynamics ; Mixing ; Shear structure/flows ; Turbulence ; Observational techniques and algorithms ; Ship observations
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    Comparison of direct covariance flux measurements from an offshore tower and a buoy (2016)
    American Meteorological Society
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Atmospheric and Oceanic Technology 33 (2016): 873-890, doi:10.1175/JTECH-D-15-0109.1.
    Description: Direct covariance flux (DCF) measurements taken from floating platforms are contaminated by wave-induced platform motions that need to be removed before computation of the turbulent fluxes. Several correction algorithms have been developed and successfully applied in earlier studies from research vessels and, most recently, by the use of moored buoys. The validation of those correction algorithms has so far been limited to short-duration comparisons against other floating platforms. Although these comparisons show in general a good agreement, there is still a lack of a rigorous validation of the method, required to understand the strengths and weaknesses of the existing motion-correction algorithms. This paper attempts to provide such a validation by a comparison of flux estimates from two DCF systems, one mounted on a moored buoy and one on the Air–Sea Interaction Tower (ASIT) at the Martha’s Vineyard Coastal Observatory, Massachusetts. The ASIT was specifically designed to minimize flow distortion over a wide range of wind directions from the open ocean for flux measurements. The flow measurements from the buoy system are corrected for wave-induced platform motions before computation of the turbulent heat and momentum fluxes. Flux estimates and cospectra of the corrected buoy data are found to be in very good agreement with those obtained from the ASIT. The comparison is also used to optimize the filter constants used in the motion-correction algorithm. The quantitative agreement between the buoy data and the ASIT demonstrates that the DCF method is applicable for turbulence measurements from small moving platforms, such as buoys.
    Description: This work was funded by the National Science Foundation Grant OCE04-24536 as part of the CLIVAR Mode Water Dynamic Experiment (CLIMODE).
    Keywords: Circulation/ Dynamics ; Turbulence ; Atm/Ocean Structure/ Phenomena ; Boundary layer ; Physical Meteorology and Climatology ; Air-sea interaction ; Observational techniques and algorithms ; Buoy observations ; Quality assurance/control
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    Shear turbulence in the high-wind Southern Ocean using direct measurements (2022)
    American Meteorological Society
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    Publication Date: 2022-10-12
    Description: Author Posting. © American Meteorological Society, 2022. 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 52(10), (2022): 2325–2341, https://doi.org/10.1175/jpo-d-21-0015.1.
    Description: The ocean surface boundary layer is a gateway of energy transfer into the ocean. Wind-driven shear and meteorologically forced convection inject turbulent kinetic energy into the surface boundary layer, mixing the upper ocean and transforming its density structure. In the absence of direct observations or the capability to resolve subgrid-scale 3D turbulence in operational ocean models, the oceanography community relies on surface boundary layer similarity scalings (BLS) of shear and convective turbulence to represent this mixing. Despite their importance, near-surface mixing processes (and ubiquitous BLS representations of these processes) have been undersampled in high-energy forcing regimes such as the Southern Ocean. With the maturing of autonomous sampling platforms, there is now an opportunity to collect high-resolution spatial and temporal measurements in the full range of forcing conditions. Here, we characterize near-surface turbulence under strong wind forcing using the first long-duration glider microstructure survey of the Southern Ocean. We leverage these data to show that the measured turbulence is significantly higher than standard shear-convective BLS in the shallower parts of the surface boundary layer and lower than standard shear-convective BLS in the deeper parts of the surface boundary layer; the latter of which is not easily explained by present wave-effect literature. Consistent with the CBLAST (Coupled Boundary Layers and Air Sea Transfer) low winds experiment, this bias has the largest magnitude and spread in the shallowest 10% of the actively mixing layer under low-wind and breaking wave conditions, when relatively low levels of turbulent kinetic energy (TKE) in surface regime are easily biased by wave events.
    Description: This paper is VIMS Contribution 4103. Computational resources were provided by the VIMS Ocean-Atmosphere and Climate Change Research Fund. AUSSOM was supported by the OCE Division of the National Science Foundation (1558639).
    Keywords: Turbulence ; Wind shear ; Boundary layer ; Parameterization
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    Surf Zone Turbulence and suspended sediment dynamics-a review (2022)
    MDPI
    Details
    Publication Date: 2022-10-20
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Aagaard, T., Brinkkemper, J., Christensen, D. F., Hughes, M. G., & Ruessink, G. Surf Zone Turbulence and suspended sediment dynamics-a review. Journal of Marine Science and Engineering, 9(11), (2021): 1300, https://doi.org/10.3390/jmse9111300.
    Description: The existence of sandy beaches relies on the onshore transport of sand by waves during post-storm conditions. Most operational sediment transport models employ wave-averaged terms, and/or the instantaneous cross-shore velocity signal, but the models often fail in predictions of the onshore-directed transport rates. An important reason is that they rarely consider the phase relationships between wave orbital velocity and the suspended sediment concentration. This relationship depends on the intra-wave structure of the bed shear stress and hence on the timing and magnitude of turbulence production in the water column. This paper provides an up-to-date review of recent experimental advances on intra-wave turbulence characteristics, sediment mobilization, and suspended sediment transport in laboratory and natural surf zones. Experimental results generally show that peaks in the suspended sediment concentration are shifted forward on the wave phase with increasing turbulence levels and instantaneous near-bed sediment concentration scales with instantaneous turbulent kinetic energy. The magnitude and intra-wave phase of turbulence production and sediment concentration are shown to depend on wave (breaker) type, seabed configuration, and relative wave height, which opens up the possibility of more robust predictions of transport rates for different wave and beach conditions.
    Description: This research received no external funding.
    Keywords: Turbulence ; Suspended sediment ; Sediment transport ; Breaking waves ; Beach recovery
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    Microstructure mixing observations and finescale parameterizations in the Beaufort Sea (2021)
    American Meteorological Society
    Details
    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 Journal of Physical Oceanography 51(1), (2021): 19-35, https://doi.org/10.1175/JPO-D-19-0233.1.
    Description: In the Beaufort Sea in September of 2015, concurrent mooring and microstructure observations were used to assess dissipation rates in the vicinity of 72°35′N, 145°1′W. Microstructure measurements from a free-falling profiler survey showed very low [O(10−10) W kg−1] turbulent kinetic energy dissipation rates ε. A finescale parameterization based on both shear and strain measurements was applied to estimate the ratio of shear to strain Rω and ε at the mooring location, and a strain-based parameterization was applied to the microstructure survey (which occurred approximately 100 km away from the mooring site) for direct comparison with microstructure results. The finescale parameterization worked well, with discrepancies ranging from a factor of 1–2.5 depending on depth. The largest discrepancies occurred at depths with high shear. Mean Rω was 17, and Rω showed high variability with values ranging from 3 to 50 over 8 days. Observed ε was slightly elevated (factor of 2–3 compared with a later survey of 11 profiles taken over 3 h) from 25 to 125 m following a wind event which occurred at the beginning of the mooring deployment, reaching a maximum of ε= 6 × 10−10 W kg−1 at 30-m depth. Velocity signals associated with near-inertial waves (NIWs) were observed at depths greater than 200 m, where the Atlantic Water mass represents a reservoir of oceanic heat. However, no evidence of elevated ε or heat fluxes was observed in association with NIWs at these depths in either the microstructure survey or the finescale parameterization estimates.
    Description: This work was supported by NSF Grants PLR 14-56705 and PLR-1303791 and by NSF Graduate Research Fellowship Grant DGE-1650112.
    Keywords: Ocean ; Arctic ; Internal waves ; Turbulence ; Diapycnal mixing
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    Mixing and transformation in a deep western boundary current: a case study (2021)
    American Meteorological Society
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Spingys, C. P., Garabato, A. C. N., Legg, S., Polzin, K. L., Abrahamsen, E. P., Buckingham, C. E., Forryan, A., & Frajka-Williams, E. E. Mixing and transformation in a deep western boundary current: a case study. Journal of Physical Oceanography, 51(4), (2021): 1205-1222, https://doi.org/10.1175/JPO-D-20-0132.1
    Description: Water-mass transformation by turbulent mixing is a key part of the deep-ocean overturning, as it drives the upwelling of dense waters formed at high latitudes. Here, we quantify this transformation and its underpinning processes in a small Southern Ocean basin: the Orkney Deep. Observations reveal a focusing of the transport in density space as a deep western boundary current (DWBC) flows through the region, associated with lightening and densification of the current’s denser and lighter layers, respectively. These transformations are driven by vigorous turbulent mixing. Comparing this transformation with measurements of the rate of turbulent kinetic energy dissipation indicates that, within the DWBC, turbulence operates with a high mixing efficiency, characterized by a dissipation ratio of 0.6 to 1 that exceeds the common value of 0.2. This result is corroborated by estimates of the dissipation ratio from microstructure observations. The causes of the transformation are unraveled through a decomposition into contributions dependent on the gradients in density space of the: dianeutral mixing rate, isoneutral area, and stratification. The transformation is found to be primarily driven by strong turbulence acting on an abrupt transition from the weakly stratified bottom boundary layer to well-stratified off-boundary waters. The reduced boundary layer stratification is generated by a downslope Ekman flow associated with the DWBC’s flow along sloping topography, and is further regulated by submesoscale instabilities acting to restratify near-boundary waters. Our results provide observational evidence endorsing the importance of near-boundary mixing processes to deep-ocean overturning, and highlight the role of DWBCs as hot spots of dianeutral upwelling.
    Description: CS, ACNG, AF, and EFW were supported by the U.K. Natural Environment Research Council (NERC) Grant NE/K013181/1. ACNG was supported by the Royal Society and Wolfson Foundation. EPA and CEB were supported by NERC Grant NE/K012843/1. CEB was funded by an MSCA grant (No. 798319) from the European Union’s Horizon 2020 program. EPA was supported by NERC Grant NE/N018095/1. SL and KP were supported by U.S. National Science Foundation Grants OCE-1536453 and OCE-1536779. SL acknowledges support of Award NA18OAR4320123 from the National Oceanic and Atmospheric Administration, U.S. Department of Commerce. The statements, findings, conclusions, and recommendations are those of the authors, and do not necessarily reflect the views of the National Oceanic and Atmospheric Administration, or the U.S. Department of Commerce.
    Keywords: Bottom currents ; Diapycnal mixing ; Turbulence ; Southern Ocean
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    Kinetic energy transfers between mesoscale and submesoscale motions in the open ocean’s upper layers (2022)
    American Meteorological Society
    Details
    Publication Date: 2022-09-15
    Description: Author Posting. © American Meteorological Society, 2022. 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 52(1),(2022): 75–97, https://doi.org/10.1175/JPO-D-21-0099.1.
    Description: Mesoscale eddies contain the bulk of the ocean’s kinetic energy (KE), but fundamental questions remain on the cross-scale KE transfers linking eddy generation and dissipation. The role of submesoscale flows represents the key point of discussion, with contrasting views of submesoscales as either a source or a sink of mesoscale KE. Here, the first observational assessment of the annual cycle of the KE transfer between mesoscale and submesoscale motions is performed in the upper layers of a typical open-ocean region. Although these diagnostics have marginal statistical significance and should be regarded cautiously, they are physically plausible and can provide a valuable benchmark for model evaluation. The cross-scale KE transfer exhibits two distinct stages, whereby submesoscales energize mesoscales in winter and drain mesoscales in spring. Despite this seasonal reversal, an inverse KE cascade operates throughout the year across much of the mesoscale range. Our results are not incompatible with recent modeling investigations that place the headwaters of the inverse KE cascade at the submesoscale, and that rationalize the seasonality of mesoscale KE as an inverse cascade-mediated response to the generation of submesoscales in winter. However, our findings may challenge those investigations by suggesting that, in spring, a downscale KE transfer could dampen the inverse KE cascade. An exploratory appraisal of the dynamics governing mesoscale–submesoscale KE exchanges suggests that the upscale KE transfer in winter is underpinned by mixed layer baroclinic instabilities, and that the downscale KE transfer in spring is associated with frontogenesis. Current submesoscale-permitting ocean models may substantially understate this downscale KE transfer, due to the models’ muted representation of frontogenesis.
    Description: The OSMOSIS experiment was funded by the U.K. Natural Environment Research Council (NERC) through Grants NE/1019999/1 and NE/101993X/1. ACNG acknowledges the support of the Royal Society and the Wolfson Foundation, and XY that of a China Scholarship Council PhD studentship.
    Keywords: Ageostrophic circulations ; Dynamics ; Eddies ; Energy transport ; Frontogenesis/frontolysis ; Instability ; Mesoscale processes ; Nonlinear dynamics ; Ocean circulation ; Ocean dynamics ; Small scale processes ; Turbulence
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    Seasonality of the mesoscale inverse cascade as inferred from global scale-dependent eddy energy observations (2022)
    American Meteorological Society
    Details
    Publication Date: 2022-09-01
    Description: Author Posting. © American Meteorological Society, 2022. 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 52(8), (2022): 1677-1691, https://doi.org/10.1175/jpo-d-21-0269.1.
    Description: Oceanic mesoscale motions including eddies, meanders, fronts, and filaments comprise a dominant fraction of oceanic kinetic energy and contribute to the redistribution of tracers in the ocean such as heat, salt, and nutrients. This reservoir of mesoscale energy is regulated by the conversion of potential energy and transfers of kinetic energy across spatial scales. Whether and under what circumstances mesoscale turbulence precipitates forward or inverse cascades, and the rates of these cascades, remain difficult to directly observe and quantify despite their impacts on physical and biological processes. Here we use global observations to investigate the seasonality of surface kinetic energy and upper-ocean potential energy. We apply spatial filters to along-track satellite measurements of sea surface height to diagnose surface eddy kinetic energy across 60–300-km scales. A geographic and scale-dependent seasonal cycle appears throughout much of the midlatitudes, with eddy kinetic energy at scales less than 60 km peaking 1–4 months before that at 60–300-km scales. Spatial patterns in this lag align with geographic regions where an Argo-derived estimate of the conversion of potential to kinetic energy is seasonally varying. In midlatitudes, the conversion rate peaks 0–2 months prior to kinetic energy at scales less than 60 km. The consistent geographic patterns between the seasonality of potential energy conversion and kinetic energy across spatial scale provide observational evidence for the inverse cascade and demonstrate that some component of it is seasonally modulated. Implications for mesoscale parameterizations and numerical modeling are discussed.
    Description: This work was generously funded by NSF Grants OCE-1912302, OCE-1912125 (Drushka), and OCE-1912325 (Abernathey) as part of the Ocean Energy and Eddy Transport Climate Process Team.
    Keywords: Eddies ; Energy transport ; Mesoscale processes ; Turbulence ; Oceanic mixed layer ; Altimetry ; Seasonal cycle
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    Observations of the transfer of energy and momentum to the oceanic surface boundary layer beneath breaking waves (2016)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    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): 1823-1837, doi:10.1175/JPO-D-15-0165.1.
    Description: Measurements just beneath the ocean surface demonstrate that the primary mechanism by which energy from breaking waves is transmitted into the water column is through the work done by the covariance of turbulent pressure and velocity fluctuations. The convergence in the vertical transport of turbulent kinetic energy (TKE) balances the dissipation rate of TKE at first order and is nearly an order of magnitude greater than the sum of the integrated Eulerian and Stokes shear production. The measured TKE transport is consistent with a simple conceptual model that assumes roughly half of the surface flux of TKE by wave breaking is transmitted to depths greater than the significant wave height. During conditions when breaking waves are inferred, the direction of momentum flux is more aligned with the direction of wave propagation than with the wind direction. Both the energy and momentum fluxes occur at frequencies much lower than the wave band, consistent with the time scales associated with wave breaking. The largest instantaneous values of momentum flux are associated with strong downward vertical velocity perturbations, in contrast to the pressure work, which is associated with strong drops in pressure and upward vertical velocity perturbations.
    Description: Funding for this research was provided by the National Science Foundation Grants OCE-1339032 and OCE-1338518
    Keywords: Circulation/ Dynamics ; Energy transport ; Mixing ; Momentum ; Turbulence ; Wave breaking ; Waves, oceanic
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    Ekman veering, internal waves, and turbulence observed under Arctic sea ice (2014)
    American Meteorological Society
    Details
    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): 1306–1328, doi:10.1175/JPO-D-12-0191.1.
    Description: The ice–ocean system is investigated on inertial to monthly time scales using winter 2009–10 observations from the first ice-tethered profiler (ITP) equipped with a velocity sensor (ITP-V). Fluctuations in surface winds, ice velocity, and ocean velocity at 7-m depth were correlated. Observed ocean velocity was primarily directed to the right of the ice velocity and spiraled clockwise while decaying with depth through the mixed layer. Inertial and tidal motions of the ice and in the underlying ocean were observed throughout the record. Just below the ice–ocean interface, direct estimates of the turbulent vertical heat, salt, and momentum fluxes and the turbulent dissipation rate were obtained. Periods of elevated internal wave activity were associated with changes to the turbulent heat and salt fluxes as well as stratification primarily within the mixed layer. Turbulent heat and salt fluxes were correlated particularly when the mixed layer was closest to the freezing temperature. Momentum flux is adequately related to velocity shear using a constant ice–ocean drag coefficient, mixing length based on the planetary and geometric scales, or Rossby similarity theory. Ekman viscosity described velocity shear over the mixed layer. The ice–ocean drag coefficient was elevated for certain directions of the ice–ocean shear, implying an ice topography that was characterized by linear ridges. Mixing length was best estimated using the wavenumber of the beginning of the inertial subrange or a variable drag coefficient. Analyses of this and future ITP-V datasets will advance understanding of ice–ocean interactions and their parameterizations in numerical models.
    Description: Support for this study and the overall ITP program was provided by the National Science Foundation and Woods Hole Oceanographic Institution. Support for S. Cole was partially though the Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution, with funding provided by the Devonshire Foundation.
    Description: 2014-11-01
    Keywords: Geographic location/entity ; Arctic ; Sea ice ; Circulation/ Dynamics ; Ekman pumping/transport ; Internal waves ; Turbulence ; Atm/Ocean Structure/ Phenomena ; Oceanic mixed layer
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    Moored turbulence measurements using pulse-coherent doppler sonar (2022)
    American Meteorological Society
    Details
    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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    Double diffusion, shear instabilities, and heat impacts of a pacific summer water intrusion in the Beaufort Sea (2022)
    American Meteorological Society
    Details
    Publication Date: 2022-06-13
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Fine, E., MacKinnon, J., Alford, M., Middleton, L., Taylor, J., Mickett, J., Cole, S., Couto, N., Boyer, A., & Peacock, T. Double diffusion, shear instabilities, and heat impacts of a pacific summer water intrusion in the Beaufort Sea. Journal of Physical Oceanography, 52(2), (2022): 189–203, https://doi.org/10.1175/jpo-d-21-0074.1.
    Description: Pacific Summer Water eddies and intrusions transport heat and salt from boundary regions into the western Arctic basin. Here we examine concurrent effects of lateral stirring and vertical mixing using microstructure data collected within a Pacific Summer Water intrusion with a length scale of ∼20 km. This intrusion was characterized by complex thermohaline structure in which warm Pacific Summer Water interleaved in alternating layers of O(1) m thickness with cooler water, due to lateral stirring and intrusive processes. Along interfaces between warm/salty and cold/freshwater masses, the density ratio was favorable to double-diffusive processes. The rate of dissipation of turbulent kinetic energy (ε) was elevated along the interleaving surfaces, with values up to 3 × 10−8 W kg−1 compared to background ε of less than 10−9 W kg−1. Based on the distribution of ε as a function of density ratio Rρ, we conclude that double-diffusive convection is largely responsible for the elevated ε observed over the survey. The lateral processes that created the layered thermohaline structure resulted in vertical thermohaline gradients susceptible to double-diffusive convection, resulting in upward vertical heat fluxes. Bulk vertical heat fluxes above the intrusion are estimated in the range of 0.2–1 W m−2, with the localized flux above the uppermost warm layer elevated to 2–10 W m−2. Lateral fluxes are much larger, estimated between 1000 and 5000 W m−2, and set an overall decay rate for the intrusion of 1–5 years.
    Description: This work was supported by ONR Grant N00014-16-1-2378 and NSF Grants PLR 14-56705 and PLR-1303791, NSF Graduate Research Fellowship Grant DGE-1650112, as well as by the Postdoctoral Scholar Program at Woods Hole Oceanographic Institution, with funding provided by the Weston Howland Jr. Postdoctoral Scholarship.
    Keywords: Arctic ; Diapycnal mixing ; Diffusion ; Fluxes ; Instability ; Mixing ; Turbulence
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    Observed eddy-internal wave interactions in the Southern Ocean (2021)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cusack, J. M., Brearley, J. A., Garabato, A. C. N., Smeed, D. A., Polzin, K. L., Velzeboer, N., & Shakespeare, C. J. Observed eddy-internal wave interactions in the Southern Ocean. Journal of Physical Oceanography, 50(10), (2020): 3042-3062, doi:10.1175/JPO-D-20-0001.1.
    Description: The physical mechanisms that remove energy from the Southern Ocean’s vigorous mesoscale eddy field are not well understood. One proposed mechanism is direct energy transfer to the internal wave field in the ocean interior, via eddy-induced straining and shearing of preexisting internal waves. The magnitude, vertical structure, and temporal variability of the rate of energy transfer between eddies and internal waves is quantified from a 14-month deployment of a mooring cluster in the Scotia Sea. Velocity and buoyancy observations are decomposed into wave and eddy components, and the energy transfer is estimated using the Reynolds-averaged energy equation. We find that eddies gain energy from the internal wave field at a rate of −2.2 ± 0.6 mW m−2, integrated from the bottom to 566 m below the surface. This result can be decomposed into a positive (eddy to wave) component, equal to 0.2 ± 0.1 mW m−2, driven by horizontal straining of internal waves, and a negative (wave to eddy) component, equal to −2.5 ± 0.6 mW m−2, driven by vertical shearing of the wave spectrum. Temporal variability of the transfer rate is much greater than the mean value. Close to topography, large energy transfers are associated with low-frequency buoyancy fluxes, the underpinning physics of which do not conform to linear wave dynamics and are thereby in need of further research. Our work suggests that eddy–internal wave interactions may play a significant role in the energy balance of the Southern Ocean mesoscale eddy and internal wave fields.
    Description: Funding for DIMES was provided by U.K. Natural Environment Research Council (NERC) Grants NE/E007058/1 and NE/E005667/1. JMC acknowledges the support of a NERC PhD studentship, and ACNG that of the Royal Society and the Wolfson Foundation. NV acknowledges support from the ARC Centre of Excellence for Climate Extremes (CLEX) Honours Scholarship and the ANU PBSA Partnership - Spotless Scholarship. CJS acknowledges support from an ARC Discovery Early Career Researcher Award DE180100087 and an Australian National University Futures Scheme award. Numerical simulations were conducted on the National Computational Infrastructure (NCI) facility, Canberra, Australia. This study has been conducted using E.U. Copernicus Marine Service Information. We thank two anonymous reviewers for their comments which helped to improve the manuscript significantly. Codes and output files are available online at the project repository (https://github.com/jessecusack/DIMES_eddy_wave_interactions).
    Keywords: Southern Ocean ; Eddies ; Internal waves ; Turbulence
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    Can we detect submesoscale motions in drifter pair dispersion? (2019)
    American Meteorological Society
    Details
    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(9), (2019): 2237-2254, doi: 10.1175/JPO-D-18-0181.1.
    Description: A cluster of 45 drifters deployed in the Bay of Bengal is tracked for a period of four months. Pair dispersion statistics, from observed drifter trajectories and simulated trajectories based on surface geostrophic velocity, are analyzed as a function of drifter separation and time. Pair dispersion suggests nonlocal dynamics at submesoscales of 1–20 km, likely controlled by the energetic mesoscale eddies present during the observations. Second-order velocity structure functions and their Helmholtz decomposition, however, suggest local dispersion and divergent horizontal flow at scales below 20 km. This inconsistency cannot be explained by inertial oscillations alone, as has been reported in recent studies, and is likely related to other nondispersive processes that impact structure functions but do not enter pair dispersion statistics. At scales comparable to the deformation radius LD, which is approximately 60 km, we find dynamics in agreement with Richardson’s law and observe local dispersion in both pair dispersion statistics and second-order velocity structure functions.
    Description: This research was supported by the Air Sea Interaction Regional Initiative (ASIRI) under ONR Grant N00014-13-1-0451 (SE and AM) and ONR Grant N00014-13-1-0477 (VH and LC). Additionally, AM and SE thank NSF (Grant OCE-I434788) and ONR (Grant N00014-16-1-2470) for support; VH and LC were further supported by ONR Grant N00014-15-1-2286 and NOAA GDP Grant NA10OAR4320156. We thank Joe LaCasce, Dhruv Balwada, and one anonymous reviewer for helpful comments and discussions that significantly improved this manuscript. The authors thank the captain and crew of the R/V Roger Revelle. The SVP-type drifters are part of the Global Drifter Program and supported by ONR Grant N00014-15-1-2286 and NOAA GDP Grant NA10OAR4320156 and are available under http://www.aoml.noaa.gov/phod/dac/. The Ssalto/Duacs altimeter products were produced and distributed by the Copernicus Marine and Environment Monitoring Service (CMEMS, http://www.marine.copernicus.eu).
    Keywords: Dispersion ; Fronts ; Mesoscale processes ; Subgrid-scale processes ; Trajectories ; Turbulence
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    Persistent turbulence in the Samoan Passage (2020)
    American Meteorological Society
    Details
    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 Cusack, J. M., Voet, G., Alford, M. H., Girton, J. B., Carter, G. S., Pratt, L. J., Pearson-Potts, K. A., & Tan, S. Persistent turbulence in the Samoan Passage. Journal of Physical Oceanography, 49(12), (2019): 3179-3197, doi: 10.1175/JPO-D-19-0116.1.
    Description: Abyssal waters forming the lower limb of the global overturning circulation flow through the Samoan Passage and are modified by intense mixing. Thorpe-scale-based estimates of dissipation from moored profilers deployed on top of two sills for 17 months reveal that turbulence is continuously generated in the passage. Overturns were observed in a density band in which the Richardson number was often smaller than ¼, consistent with shear instability occurring at the upper interface of the fast-flowing bottom water layer. The magnitude of dissipation was found to be stable on long time scales from weeks to months. A second array of 12 moored profilers deployed for a shorter duration but profiling at higher frequency was able to resolve variability in dissipation on time scales from days to hours. At some mooring locations, near-inertial and tidal modulation of the dissipation rate was observed. However, the modulation was not spatially coherent across the passage. The magnitude and vertical structure of dissipation from observations at one of the major sills is compared with an idealized 2D numerical simulation that includes a barotropic tidal forcing. Depth-integrated dissipation rates agree between model and observations to within a factor of 3. The tide has a negligible effect on the mean dissipation. These observations reinforce the notion that the Samoan Passage is an important mixing hot spot in the global ocean where waters are being transformed continuously.
    Description: The authors thank Zhongxiang Xao and Jody Klymak, who provided earlier setups of the numerical model, and also Arjun Jagannathan for insightful discussions on the subject of flow over topography. We also thank John Mickett and Eric Boget for their assistance in designing, deploying, and recovering the moorings. In addition, we also thank the crew and scientists aboard the R/V Revelle and R/V Thompson, without whom the data presented in this paper could not have been gathered. Ilker Fer and two anonymous reviewers provided thoughtful feedback that improved the paper. This work was supported by the National Science Foundation under Grants OCE-1029268, OCE-1029483, OCE-1657264, OCE-1657795, OCE-1657870, and OCE-1658027.
    Keywords: Gravity waves ; Turbulence ; Abyssal circulation ; Mixing ; Tides
    Repository Name: Woods Hole Open Access Server
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    Transformation and upwelling of bottom water in fracture zone valleys (2020)
    American Meteorological Society
    Details
    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 Physical Oceanography 50(3), (2020): 715-726, doi:10.1175/JPO-D-19-0021.1.
    Description: Closing the overturning circulation of bottom water requires abyssal transformation to lighter densities and upwelling. Where and how buoyancy is gained and water is transported upward remain topics of debate, not least because the available observations generally show downward-increasing turbulence levels in the abyss, apparently implying mean vertical turbulent buoyancy-flux divergence (densification). Here, we synthesize available observations indicating that bottom water is made less dense and upwelled in fracture zone valleys on the flanks of slow-spreading midocean ridges, which cover more than one-half of the seafloor area in some regions. The fracture zones are filled almost completely with water flowing up-valley and gaining buoyancy. Locally, valley water is transformed to lighter densities both in thin boundary layers that are in contact with the seafloor, where the buoyancy flux must vanish to match the no-flux boundary condition, and in thicker layers associated with downward-decreasing turbulence levels below interior maxima associated with hydraulic overflows and critical-layer interactions. Integrated across the valley, the turbulent buoyancy fluxes show maxima near the sidewall crests, consistent with net convergence below, with little sensitivity of this pattern to the vertical structure of the turbulence profiles, which implies that buoyancy flux convergence in the layers with downward-decreasing turbulence levels dominates over the divergence elsewhere, accounting for the net transformation to lighter densities in fracture zone valleys. We conclude that fracture zone topography likely exerts a controlling influence on the transformation and upwelling of bottom water in many areas of the global ocean.
    Description: The data used in this study were collected in the context of several projects funded by the U.S. National Science Foundation (NSF), in particular BBTRE (OCE-9415589 and OCE-9415598) and DoMORE (OCE-1235094). Funding for the analysis was provided as part of the NSF DoMORE and DECIMAL (OCE-1735618) projects. Author Ijichi is a Japan Society for the Promotion of Science (JSPS) Overseas Research Fellow. Comments on an early draft of this paper by Jim Ledwell and Bryan Kaiser, as well as topical discussions with Jörn Callies and Trevor McDougall, are gratefully acknowledged. The paper was greatly improved during the review process, in particular because of the critical comments from one of the two anonymous reviewers.
    Keywords: Diapycnal mixing ; Topographic effects ; Turbulence ; Upwelling/downwelling ; Bottom currents/bottom water
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    Dynamics of a turbulent buoyant plume in a stratified fluid : an idealized model of subglacial discharge in Greenland fjords (2017)
    American Meteorological Society
    Details
    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): 2611-2630, doi:10.1175/JPO-D-16-0259.1.
    Description: This study reports the results of large-eddy simulations of an axisymmetric turbulent buoyant plume in a stratified fluid. The configuration used is an idealized model of the plume generated by a subglacial discharge at the base of a tidewater glacier with an ambient stratification typical of Greenland fjords. The plume is discharged from a round source of various diameters and characteristic stratifications for summer and winter are considered. The classical theory for the integral parameters of a turbulent plume in a homogeneous fluid gives accurate predictions in the weakly stratified lower layer up to the pycnocline, and the plume dynamics are not sensitive to changes in the source diameter. In winter, when the stratification is similar to an idealized two-layer case, turbulent entrainment and generation of internal waves by the plume top are in agreement with the theoretical and numerical results obtained for turbulent jets in a two-layer stratification. In summer, instead, the stratification is more complex and turbulent entrainment by the plume top is significantly reduced. The subsurface layer in summer is characterized by a strong density gradient and the oscillating plume generates internal waves that might serve as an indicator of submerged plumes not penetrating to the surface.
    Description: This work was supported by Linné FLOW Centre at KTH and the Academy of Finland Centre of Excellence program (Grant 307331) (E. E.) and VR Swedish Research Council, Outstanding Young Researcher Award, Grant VR 2014-5001 (L. B.). Support to C. C. was given by the NSF Project OCE-1434041.
    Description: 2018-04-26
    Keywords: Buoyancy ; Internal waves ; Turbulence ; Jets ; Oscillations ; Large eddy simulations
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    Eddy vertical structure and variability: deepglider observations in the North Atlantic (2023)
    American Meteorological Society
    Details
    Publication Date: 2023-02-28
    Description: Author Posting. © American Meteorological Society, 2022. 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 52(6), (2022): 1091–1110, https://doi.org/10.1175/JPO-D-21-0068.1.
    Description: Hundreds of full-depth temperature and salinity profiles collected by Deepglider autonomous underwater vehicles (AUVs) in the North Atlantic reveal robust signals in eddy isopycnal vertical displacement and horizontal current throughout the entire water column. In separate glider missions southeast of Bermuda, subsurface-intensified cold, fresh coherent vortices were observed with velocities exceeding 20 cm s−1 at depths greater than 1000 m. With vertical resolution on the order of 20 m or less, these full-depth glider slant profiles newly permit estimation of scaled vertical wavenumber spectra from the barotropic through the 40th baroclinic mode. Geostrophic turbulence theory predictions of spectral slopes associated with the forward enstrophy cascade and proportional to inverse wavenumber cubed generally agree with glider-derived quasi-universal spectra of potential and kinetic energy found at a variety of locations distinguished by a wide range of mean surface eddy kinetic energy. Water-column average spectral estimates merge at high vertical mode number to established descriptions of internal wave spectra. Among glider mission sites, geographic and seasonal variability implicate bottom drag as a mechanism for dissipation, but also the need for more persistent sampling of the deep ocean.
    Description: This work was funded by NSF Grant 1736217 and would not have been possible without the help of Kirk O’Donnell, James Bennett, Noel Pelland, and all contributors to Deepglider development. We additionally thank the captain crew of the R/V Atlantic Explorer and the BATS team at the Bermuda Institute of Ocean Sciences, particularly Rod Johnson, as well as Seakeepers International for their professionalism, capability, and generous assistance in deploying and recovering gliders.
    Keywords: North Atlantic Ocean ; Eddies ; Mesoscale processes ; Turbulence ; Energy transport ; In situ oceanic observations ; Oceanic variability
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  • 46
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    Improved protein refolding using hollow-fibre membrane dialysis (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 57 (1998), S. 590-599 
    Details
    ISSN: 0006-3592
    Keywords: protein refolding ; hollow-fibre membrane ; dialysis ; carbonic anhydrase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: We have used a cellulose acetate, hollow-fibre (HF) ultrafiltration membrane to refold bovine carbonic anhydrase, loaded into the lumen space, by removing the denaturant through controlled dialysis via the shell side space. When challenged with GdnHCl-denatured carbonic anhydrase, 70% of the loaded protein reptated through the membrane into the circulating dialysis buffer. Reptation occurred because the protein, in its fully unfolded configuration, was able to pass through the pores. The loss of carbonic anhydrase through the membrane was controlled by the dialysis conditions. Dialysis against 0.05 M Tris-HCl for 30 min reduced the denaturant around the protein to a concentration that allowed the return of secondary structure, increasing the hydrodynamic radius, thus preventing protein transmission. Under these conditions a maximum of 42% of carbonic anhydrase was recovered (from a starting concentration of 5 mg/mL) with 94% activity. This is an improvement over refolding carbonic anhydrase by simple batch dilution, which gave a maximum reactivation of 85% with 35% soluble protein yield. The batch refolding of carbonic anhydrase is very sensitive to temperature; however, during HF refolding between 0 and 25°C the temperature sensitivity was considerably reduced. In order to reduce the convection forces that give rise to aggregation and promote refolding the dialyzate was slowly heated from 4 to 25°C. This slow, temperature-controlled refolding gave an improved soluble protein recovery of 55% with a reactivation yield of 90%. The effect of a number of additives on the refolding system performance were tested: the presence of PEG improved both the protein recovery and the recovered activity from the membrane, while the detergents Tween 20 and IGEPAL CA-630 increased only the refolding yield. ©1998 John Wiley & Sons, Inc. Biotechnol Bioeng 57: 590-599, 1998.
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    Metabolic engineering (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 58 (1998), S. 119-120 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: No abstract.
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    Activity losses among T4 lysozyme variants after adsorption to colloidal silica (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 58 (1998), S. 658-662 
    Details
    ISSN: 0006-3592
    Keywords: T4 lysozyme ; silica nanoparticles ; synthetic enzyme variants ; surface-induced conformational change ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Maintaining a specific molecular conformation is essential for the proper functioning of an enzyme. A substantial loss of catalytic activity can occur from the displacement caused by even a single amino acid substitution. Activity may also be lost as an enzyme undergoes a conformational change during adsorption. In this study, we investigated the effect of thermostability on the activities of three T4 lysozyme variants after adsorption to 9 nm colloidal silica particles. Less-stable T4 lysozyme variants lost more activity after adsorption than did more stable variants, apparently because they experienced more extensive structural alteration. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58: 658-662, 1998.
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    On-line metabolic pathway analysis based on metabolic signal flow diagram (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 58 (1998), S. 139-148 
    Details
    ISSN: 0006-3592
    Keywords: metabolic engineering ; pathway analysis ; metabolic and energetic model ; physiological state ; Saccharomyces cerevisiae ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: In this work, an integrated modeling approach based on a metabolic signal flow diagram and cellular energetics was used to model the metabolic pathway analysis for the cultivation of yeast on glucose. This approach enables us to make a clear analysis of the flow direction of the carbon fluxes in the metabolic pathways as well as of the degree of activation of a particular pathway for the synthesis of biomaterials for cell growth. The analyses demonstrate that the main metabolic pathways of Saccharomyces cerevisiae change significantly during batch culture. Carbon flow direction is toward glycolysis to satisfy the increase of requirement for precursors and energy. The enzymatic activation of TCA cycle seems to always be at normal level, which may result in the overflow of ethanol due to its limited capacity. The advantage of this approach is that it adopts both virtues of the metabolic signal flow diagram and the simple network analysis method, focusing on the investigation of the flow directions of carbon fluxes and the degree of activation of a particular pathway or reaction loop. All of the variables used in the model equations were determined on-line; the information obtained from the calculated metabolic coefficients may result in a better understanding of cell physiology and help to evaluate the state of the cell culture process. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:139-148, 1998.
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    Experimental determination of group flux control coefficients in metabolic networks (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 58 (1998), S. 149-153 
    Details
    ISSN: 0006-3592
    Keywords: Metabolic Control Analysis ; flux control coefficients ; top down MCA ; metabolic engineering ; Corynebacterium glutamicum ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Grouping of reactions around key metabolite branch points can facilitate the study of metabolic control of complex metabolic networks. This top-down Metabolic Control Analysis is exemplified through the introduction of group (flux, as well as concentration) control coefficients whose magnitudes provide a measure of the relative impact of each reaction group on the overall network flux, as well as on the overall network stability, following enzymatic amplification. In this article, we demonstrate the application of previously developed theory to the determination of group flux control coefficients. Experimental data for the changes in metabolic fluxes obtained in response to the introduction of six different environmental perturbations are used to determine the group flux control coefficients for three reaction groups formed around the phosphoenolpyruvate/pyruvate branch point. The consistency of the obtained group flux control coefficient estimates is systematically analyzed to ensure that all necessary conditions are satisfied. The magnitudes of the determined control coefficients suggest that the control of lysine production flux in Corynebacterium glutamicum cells at a growth base state resides within the lysine biosynthetic pathway that begins with the PEP/PYR carboxylation anaplorotic pathway. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:149-153, 1998.
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    Application of mathematical tools for metabolic design of microbial ethanol production (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 58 (1998), S. 154-161 
    Details
    ISSN: 0006-3592
    Keywords: central carbon pathways ; metabolic optimization ; ethanol production ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Many attempts to engineer cellular metabolism have failed due to the complexity of cellular functions. Mathematical and computational methods are needed that can organize the available experimental information, and provide insight and guidance for successful metabolic engineering. Two such methods are reviewed here. Both methods employ a (log)linear kinetic model of metabolism that is constructed based on enzyme kinetics characteristics. The first method allows the description of the dynamic responses of metabolic systems subject to spatiotemporal variations in their parameters. The second method considers the product-oriented, constrained optimization of metabolic reaction networks using mixed-integer linear programming methods. The optimization framework is used in order to identify the combinations of the metabolic characteristics of the glycolytic enzymes from yeast and bacteria that will maximize ethanol production. The methods are also applied to the design of microbial ethanol production metabolism. The results of the calculations are in qualitative agreement with experimental data presented here. Experiments and calculations suggest that, in resting Escherichia coli cells, ethanol production and glucose uptake rates can be increased by 30% and 20%, respectively, by overexpression of a deregulated pyruvate kinase, while increase in phosphofructokinase expression levels has no effect on ethanol production and glucose uptake rates. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:154-161, 1998.
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    Multiple mechanisms controlling carbon metabolism in bacteria (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 58 (1998), S. 170-174 
    Details
    ISSN: 0006-3592
    Keywords: catabolite repression ; phosphotransferase system ; inducer exclusion ; inducer expulsion ; protein kinase ; transcriptional regulation ; transport regulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Catabolite repression is a universal phenomenon, found in virtually all living organisms. These organisms range from the simplest bacteria to higher fungi, plants, and animals. A mechanism involving cyclic AMP and its receptor protein (CRP) in Escherichia coli was established years ago, and this mechanism has been assumed by many to serve as the prototype for catabolite repression in all organisms. However, recent studies have shown that this mechanism is restricted to enteric bacteria and their close relatives. Cyclic AMP-independent mechanisms of catabolite repression occur in other bacteria, yeast, plants, and even E. coli. In fact, single-celled organisms such as E. coli, Bacillus subtilis, and Saccharomyces cerevisiae exhibit multiple mechanisms of catabolite repression, and most of these are cyclic AMP-independent. The mechanistic features of the best of such characterized processes are briefly reviewed, and references are provided that will allow the reader to delve more deeply into these subjects. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:170-174, 1998.
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    How will bioinformatics influence metabolic engineering? (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 58 (1998), S. 162-169 
    Details
    ISSN: 0006-3592
    Keywords: bioinformatics ; metabolic engineering ; genetic engineering ; mathematical analysis ; stoichiometry ; enzyme kinetics ; modal analysis ; genetic circuits ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Ten microbial genomes have been fully sequenced to date, and the sequencing of many more genomes is expected to be completed before the end of the century. The assignment of function to open reading frames (ORFs) is progressing, and for some genomes over 70% of functional assignments have been made. The majority of the assigned ORFs relate to metabolic functions. Thus, the complete genetic and biochemical functions of a number of microbial cells may be soon available. From a metabolic engineering standpoint, these developments open a new realm of possibilities. Metabolic analysis and engineering strategies can now be built on a sound genomic basis. An important question that now arises; how should these tasks be approached? Flux-balance analysis (FBA) has the potential to play an important role. It is based on the fundamental principle of mass conservation. It requires only the stoichiometric matrix, the metabolic demands, and some strain specific parameters. Importantly, no enzymatic kinetic data is required. In this article, we show how the genomically defined microbial metabolic genotypes can be analyzed by FBA. Fundamental concepts of metabolic genotype, metabolic phenotype, metabolic redundancy and robustness are defined and examples of their use given. We discuss the advantage of this approach, and how FBA is expected to find uses in the near future. FBA is likely to become an important analysis tool for genomically based approaches to metabolic engineering, strain design, and development. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:162-169, 1998.
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    Artificial promoters for metabolic optimization (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 58 (1998), S. 191-195 
    Details
    ISSN: 0006-3592
    Keywords: control analysis ; Lactococcus lactis ; gene expression ; flux ; oligonucleotide ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: In this article, we review some of the expression systems that are available for Metabolic Control Analysis and Metabolic Engineering, and examine their advantages and disadvantages in different contexts. In a recent approach, artificial promoters for modulating gene expression in micro-organisms were constructed using synthetic degenerated oligonucleotides. From this work, a promoter library was obtained for Lactococcus lactis, containing numerous individual promoters and covering a wide range of promoter activities. Importantly, the range of promoter activities was covered in small steps of activity change. Promoter libraries generated by this approach allow for optimization of gene expression and for experimental control analysis in a wide range of biological systems by choosing from the promoter library promoters giving, e.g., 25%, 50%, 200%, and 400% of the normal expression level of the gene in question. If the relevant variable (e.g., the flux or yield) is then measured with each of these constructs, then one can calculate the control coefficient and determine the optimal expression level. One advantage of the method is that the construct which is found to have the optimal expression level is then, in principle, ready for use in the industrial fermentation process; another advantage is that the system can be used to optimize the expression of different enzymes within the same cell. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:191-195, 1998.
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    Engineering protein-based machines to emulate key steps of metabolism (biological energy conversion) (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 58 (1998), S. 175-190 
    Details
    ISSN: 0006-3592
    Keywords: protein-based polymers ; inverse temperature transitions ; hydrophobic-induced pKa shifts ; waters of hydrophobic hydration ; five axioms for protein engineering; microwave dielectric relaxation ; a universal mechanism for biological energy conversion ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Metabolism is the conversion of available energy sources to those energy forms required for sustaining and propagating living organisms; this is simply biological energy conversion. Proteins are the machines of metabolism; they are the engines of motility and the other machines that interconvert energy forms not involving motion. Accordingly, metabolic engineering becomes the use of natural protein-based machines for the good of society. In addition, metabolic engineering can utilize the principles, whereby proteins function, to design new protein-based machines to fulfill roles for society that proteins have never been called upon throughout evolution to fulfill.This article presents arguments for a universal mechanism whereby proteins perform their diverse energy conversions; it begins with background information, and then asserts a set of five axioms for protein folding, assembly, and function and for protein engineering. The key process is the hydrophobic folding and assembly transition exhibited by properly balanced amphiphilic protein sequences. The fundamental molecular process is the competition for hydration between hydrophobic and polar, e.g., charged, residues. This competition determines Tt, the onset temperature for the hydrophobic folding and assembly transition, Nhh, the numbers of waters of hydrophobic hydration, and the pKa of ionizable functions.Reported acid-base titrations and pH dependence of microwave dielectric relaxation data simultaneously demonstrate the interdependence of Tt, Nhh and the pKa using a series of microbially prepared protein-based poly(30mers) with one glutamic acid residue per 30mer and with an increasing number of more hydrophobic phenylalanine residues replacing valine residues. Also, reduction of nicotinamides and flavins is shown to lower Tt, i.e., to increase hydrophobicity.Furthermore, the argument is presented, and related to an extended Henderson-Hasselbalch equation, wherein reduction of nicotinamides represents an increase in hydrophobicity and resulting hydrophobic-induced pKa shifts become the basis for understanding a primary energy conversion (proton transport) process of mitochondria. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:175-190, 1998.
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    Generating controlled reducing environments in aerobic recombinant Escherichia coli fermentations: Effects on cell growth, oxygen uptake, heat shock protein expression, and in vivo CAT activity (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 59 (1998), S. 248-259 
    Details
    ISSN: 0006-3592
    Keywords: Escherichia coli ; Chloramphenicol Acetyltransferase (CAT) ; Culture Redox Potential (CRP) ; Dithiothreitol (DTT) ; reducing agents ; molecular chaperones ; proteases ; heat shock ; stress response ; protein folding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The independent control of culture redox potential (CRP) by the regulated addition of a reducing agent, dithiothreitol (DTT) was demonstrated in aerated recombinant Escherichia coli fermentations. Moderate levels of DTT addition resulted in minimal changes to specific oxygen uptake, growth rate, and dissolved oxygen. Excessive levels of DTT addition were toxic to the cells resulting in cessation of growth. Chloramphenicol acetyltransferase (CAT) activity (nmoles/μg total protein min.) decreased in batch fermentation experiments with respect to increasing levels of DTT addition. To further investigate the mechanisms affecting CAT activity, experiments were performed to assay heat shock protein expression and specific CAT activity (nmoles/μg CAT min.). Expression of such molecular chaperones as GroEL and DnaK were found to increase after addition of DTT. Additionally, sigma factor 32 (σ32) and several proteases were seen to increase dramatically during addition of DTT. Specific CAT activity (nmoles/μg CAT min.) varied greatly as DTT was added, however, a minimum in activity was found at the highest level of DTT addition in E. coli strains RR1 [pBR329] and JM105 [pROEX-CAT]. In conjunction, cellular stress was found to reach a maximum at the same levels of DTT. Although DTT addition has the potential for directly affecting intracellular protein folding, the effects felt from the increased stress within the cell are likely the dominant effector. That the effects of DTT were measured within the cytoplasm of the cell suggests that the periplasmic redox potential was also altered. The changes in specific CAT activity, molecular chaperones, and other heat shock proteins, in the presence of minimal growth rate and oxygen uptake alterations, suggest that the ex vivo control of redox potential provides a new process for affecting the yield and conformation of heterologous proteins in aerated E. coli fermentations. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59: 248-259, 1998.
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    A review of experimental measurements of effective diffusive permeabilities and effective diffusion coefficients in biofilms (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 59 (1998), S. 261-272 
    Details
    ISSN: 0006-3592
    Keywords: effective diffusive permeability ; diffusion coefficient ; biofilm ; cell density ; review ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Experimental measurements of effective diffusive permeabilities and effective diffusion coefficients in biofilms are reviewed. Effective diffusive permeabilities, the parameter appropriate to the analysis of reaction-diffusion interactions, depend on solute type and biofilm density. Three categories of solute physical chemistry with distinct diffusive properties were distinguished by the present analysis. In order of descending mean relative effective diffusive permeability (De/Daq) these were inorganic anions or cations (0.56), nonpolar solutes with molecular weights of 44 or less (0.43), and organic solutes of molecular weight greater than 44 (0.29). Effective diffusive permeabilities decrease sharply with increasing biomass volume fraction suggesting a serial resistance model of diffusion in biofilms as proposed by Hinson and Kocher (1996). A conceptual model of biofilm structure is proposed in which each cell is surrounded by a restricted permeability envelope. Effective diffusion coefficients, which are appropriate to the analysis of transient penetration of nonreactive solutes, are generally similar to effective diffusive permeabilities in biofilms of similar composition. In three studies that examine diffusion of very large molecular weight solutes ( 〉 5000) in biofilms, the average ratio of the relative effective diffusion coefficient of the large solute to the relative effective diffusion coefficient of either sucrose or fluorescein was 0.64, 0.61, and 0.36. It is proposed that large solutes are effectively excluded from microbial cells, that small solutes partition into and diffuse within cells, and that ionic solutes are excluded from cells but exhibit increased diffusive permeability (but decreased effective diffusion coefficients) due to sorption to the biofilm matrix. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:261-272, 1998.
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    II. Electrostatic effect in the aggregation of heat-denatured RNase A and implications for protein additive design (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 59 (1998), S. 281-285 
    Details
    ISSN: 0006-3592
    Keywords: protein aggregation ; RNase A ; protein formulation ; protein additives ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: In the previous study (part I), heat-denatured RNase A aggregation was shown to depend on the solution pH. Interestingly, at pH 3.0, the protein did not aggregate even when exposed to 75°C for 24 h. In this study, electrostatic repulsion was shown to be responsible for the absence of aggregates at that pH. While RNase A aggregation was prevented at the extremely acidic pH, this is not an environment conducive to maintaining protein function in general. Therefore, attempts were made to confer electrostatic repulsion near neutral pH. In this study, heat-denatured RNase A was mixed with charged polymers at pH 7.8 in an attempt to provide the protein with excess surface cations or anions. At 75°C, SDS and dextran sulfate were successful in preventing RNase A aggregation, whereas their cationic, nonionic, and zwitterionic analogs did not do so. We believe that the SO3- groups present in both additives transformed the protein into polyanionic species, and this may have provided a sufficient level of electrostatic repulsion at pH 7.8 and 75°C to prevent aggregation from proceeding. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:281-285, 1998.
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    An experimental and modeling study on the removal of mono-chlorobenzene vapor in biotrickling filters (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 59 (1998), S. 328-343 
    Details
    ISSN: 0006-3592
    Keywords: biotrickling filters ; biotrickling filter modeling ; mono-chlorobenzene ; biodegradation kinetics of mono-chlorobenzene ; chlorinated VOC emissions ; biofiltration ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Removal of mono-chlorobenzene (m-CB) vapor from airstreams was studied in a biotrickling filter (BTF) operating under counter-current flow of the air and liquid streams. Experiments were performed under various values of inlet m-CB concentration, air and/or liquid volumetric flow rates, and pH of the recirculating liquid. Conversion of m-CB was never below 70% and at low concentrations exceeded 90%. A maximum removal rate of about 60 gm-3-reactor h-1 was observed. Conversion of m-CB was found to increase as the values of liquid and air flow rate increase and decrease, respectively. The effects of pH and frequency of medium replenishment on BTF performance were also investigated. The process was successfully described with a detailed mathematical model, which accounts for mass transfer and kinetic effects based on m-CB and oxygen availability. Solution of the model equations yielded m-CB and oxygen concentration profiles in all three phases (airstream, liquid, biofilm). It is predicted that oxygen has a controling effect on the process at high inlet m-CB concentrations. From independent, suspended culture, experiments it was found that m-CB biodegradation follows Andrews inhibitory kinetics. The kinetic constants were found to remain practically unchanged after the culture was used in BTF experiments for 8 months. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:328-343, 1998.
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    Effect of some operating variables on citrate recovery from model solutions by electrodialysis (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 59 (1998), S. 344-350 
    Details
    ISSN: 0006-3592
    Keywords: electrodialysis ; citric acid ; pH ; temperature ; Faraday efficiency ; solute recovery efficiency ; specific energy consumption ; solute flux ; water flux ; feed solute concentration ; electric current density ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The effect of pH and temperature (θ) on the overall performance indicators (i.e., solute recovery, ρ, and Faraday, η, efficiencies; specific energy consumption, ε, solute, JS, and water, JW, fluxes) of batch electrodialytic recovery of citric acid from model solutions was assessed at different values of feed solute concentration (cSf) and electric current density (j). Regardless of the initial feed concentration used, ρ and JS were found to be independent of θ; η and JW exhibited a positive trend with respect to θ, while ε a negative one. At the maximum temperature tested (33°C), as the pH of the feed solution was varied from 3 to 7, ρ increased from 0.90 ± 0.08 to 0.97 ± 0.02, η grew from 0.09 ± 0.02 to 0.50 ± 0.01, JS practically doubled, ε reduced about 8 times, but JW increased from 3 to 4 times. So, the optimal conditions for this technique are to be determined by balancing the savings in the investment and maintenance costs against the energy costs. © John Wiley & Sons, Inc. Biotechnol Bioeng 59:344-350, 1998.
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    Stability and activity modulation of chymotrypsins in AOT reversed micelles by protein-interface interaction: Interaction of α-chymotrypsin with a negative interface leads to a cooperative breakage of a salt bridge that keeps the catalytic active conformation (Ile16-Asp194) (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 59 (1998), S. 360-363 
    Details
    ISSN: 0006-3592
    Keywords: chymotrypsin ; enzyme stability ; reversed micelles ; interface ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The stability of α-chymotrypsin and δ-chymotrypsin was studied in reversed micelles of sodium bis(2-ethylhexyl)sulfosuccinate (AOT) in isooctane. α-Chymotrypsin is inactivated at the interface and at the water pool, while δ-chymotrypsin is inactivated only at the water pool. The mechanism of inactivation at the interface is related to the interaction of N-terminal group alanine 149 (absent in δ-chymotrypsin) with the negative interface. The dependence of enzyme activity on water content of these two enzymes in reversed micelles of AOT is also related with the interface interaction, since δ-chymotrypsin does not have a bell-shaped curve as observed for α-chymotrypsin. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:360-363, 1998.
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    High-density perfusion culture of insect cells with a BioSep ultrasonic filter (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 59 (1998), S. 351-359 
    Details
    ISSN: 0006-3592
    Keywords: bioreactor ; high density ; insect cells ; perfusion ; Sf9 ; ultrasonic filter ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The baculovirus/insect cell expression system has provided a vital tool to produce a high level of active proteins for many applications. We have developed a very high-density insect cell perfusion process with an ultrasonic filter as a cell retention device. The separation efficiency of the filter was studied under various operating conditions. A cell density of over 30 million cells/mL was achieved in a controlled perfusion bioreactor and cell viability remained greater than 90%. Sf9 cells from a high-density culture and a spinner culture were infected with two recombinant baculoviruses expressing genes for the production of human chitinase and monocyte-colony inhibition factor. The protein yield on a cell basis from infecting high-density Sf9 cells was the same as or higher than that from the spinner Sf9 culture. Virus production from the high-density culture was similar to that from the spinner culture. The results show that the ultrasonic filter did not affect insect cells' ability to support protein expression and virus production following infection with baculovirus. The potential applications of the high-density perfusion culture for large-scale protein expression from Sf9 cells are also highlighted. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:351-359, 1998.
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    Prevention of marine biofouling using a conductive paint electrode (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 59 (1998), S. 374-378 
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    ISSN: 0006-3592
    Keywords: conductive paint electrode ; prevention of marine biofouling ; fishing net ; alternating potential ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Conductive paint electrode was used for marine biofouling on fishing nets by electrochemical disinfection. When a potential of 1.2 V vs. a saturated calomel electrode (SCE) was applied to the conductive paint electrode, Vibrio alginolyticus cells attached on the electrode were completely killed. By applying a negative potential, the attached cells were removed from the surface of the electrode. Changes in pH and chlorine concentration were not observed at potentials in the range -0.6 ∼1.2 V vs. SCE. In a field experiment, accumulation of the bacterial cells and formation of biofilms on the electrode were prevented by application of an alternating potential, and 94% of attachment of the biofouling organisms was inhibited electrically on yarn used for fishing net coated with conductive paint. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:374-378, 1998.
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    Mass transfer studies on immobilized α-chymotrypsin biocatalysts prepared by deposition for use in organic medium (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 59 (1998), S. 364-373 
    Details
    ISSN: 0006-3592
    Keywords: porous supports ; internal and external diffusion ; active site accessibility ; enzyme loading ; kinetically controlled dipeptide synthesis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Mass transfer limitations were studied in enzyme preparations of α-chymotrypsin made by deposition on different porous support materials such as controlled pore glasses, Celite, and polyamides of different particle sizes. It is the onset of mass transfer limitations that determines the position of the activity optimum with respect to enzyme loading on each support. The evidence of various experiments indicates that internal diffusional limitations are the important mechanism for the observed mass transfer limitations. External diffusion was not found to play an important role under the conditions used, and it was also found that when immobilizing multilayers of enzyme the buried enzyme molecules are active to a large extent. An extreme situation is observed on Celite at very high loadings. Under these conditions, this support is expected to have its pores completely filled with packed enzyme molecules, and then it is the diffusion within the enzyme layer that determines the observed rate. As the enzyme loading increases, the area of contact between the deposited enzyme layers and the liquid solution inside the pores diminishes, causing a decrease on the observed rate of an intrinsically fast reaction which apparently is incongruous with the presence of more enzyme in the system. This work shows that mass transfer limitations can be an important factor when working with immobilized enzymes in organic media, and its study should be carried out in order to avoid undesired reduced enzyme activities and specificities. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:364-373, 1998.
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    Degradation of perchloroethylene and dichlorophenol by pulsed-electric discharge and bioremediation (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 59 (1998), S. 438-444 
    Details
    ISSN: 0006-3592
    Keywords: bioremediation ; plasma discharge ; dichlorophenol degradation ; perchloroethylene degradation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Pulsed electric discharge (PED) and bioremediation were combined to create a novel two-stage system which dechlorinates the halogenated pollutants, 2,4-dichlorophenol and perchloroethylene, with repetitive (0.1-1 kHz), short pulse (∼100 ns), low voltage (40-80 kV) discharges and then mineralizes the less chlorinated products with aerobic bacteria. A 6.1 mM aqueous dichlorophenol sample was cycled through the PED reactor (60 kV of applied pulsed voltage and 300 Hz) 6 times, resulting in the release of 55% of the initial dichlorophenol chloride ions (1 mM Cl- removed each cycle). The respective average specific efficiency is 0.4-0.6 keV/(Cl- molecule). Pseudomonas mendocina KR1, which grows in minimal medium supplemented with phenol but not with dichlorophenol, increased in cell density in all cultures supplemented with the PED-treated DCP samples and yielded a maximum of two-fold additional Cl- released compared to the PED-related alone. The number of PED-treatment cycles, voltage, and frequency were also varied, showing that both cell densities and overall dichlorophenol dechlorination were highly dependent upon the number of PED-treatment cycles, rather than the tested voltages and frequencies. Using this two-stage treatment system, PED released 31% of the initial chloride ions from dichlorophenol (after three cycles at 40-45 kV and 1.2 kHz) while P. mendocina KR1 in the second stage increased dechlorination to 90%. These results were corroborated by the 35% additional chloride release found with activated sludge cultures. Perchloroethylene (0.6 mM) was similarly treated in a first-stage PED reactor (80% chloride removal after four cycles) followed by biodegradation of the dechlorinated products with a recombinant toluene o-monooxygenase-expressing Pseudomonas fluorescens strain. Gas chromatographic analysis showed that the PED reactor created less-chlorinated byproducts (i.e., trichloroethylene) that were removed (74%) upon exposure to the recombinant bacterium. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:438-444, 1998.
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    Antisense strategies for glycosylation engineering of Chinese hamster ovary (CHO) cells (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 59 (1998), S. 445-450 
    Details
    ISSN: 0006-3592
    Keywords: CHO cells ; glycosylation engineering ; antisense ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Novel glycoproteins, inaccessible by other techniques, can be obtained by metabolic engineering of the oligosaccharide biosynthesis pathway. Furthermore, alteration of cell-surface oligosaccharides can change the properties of receptors involved in cell-cell adhesion. Sialyl Lewis X (sLex) is a cell-surface oligosaccharide determinant which is specifically expressed on granulocytes and monocytes and which interacts with selectins to influence leukocyte trafficking, thrombosis, inflammation, and cancer. Antisense technology targeting fucosyltransferase VI (Fuc-TVI), an enzyme necessary for the synthesis of the sLex in engineered Chinese hamster ovary (CHO) cells, has reduced Fuc-TVI activity, sLex synthesis, and adhesion to endothelial cells. Antisense methodology to reduce targeted activity in oligosaccharide biosynthesis or other pathways is an important addition to CHO cell metabolic engineering capabilities. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:445-450, 1998.
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    Analysis of protein fouling during ultrafiltration using a two-layer membrane model (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 59 (1998), S. 451-460 
    Details
    ISSN: 0006-3592
    Keywords: protein fouling ; membrane transport ; ultrafiltration ; adsorption ; filtration ; composite membrane ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Protein fouling can significantly alter both the flux and retention characteristics of ultrafiltration membranes. There has, however, been considerable controversy over the nature of this fouling layer. In this study, hydraulic permeability and dextran sieving data were obtained both before and after albumin adsorption and/or filtration using polyethersulfone ultrafiltration membranes. The dextran molecular weight distributions were analyzed by gel permeation chromatography to evaluate the sieving characteristics over a broad range of solute size. Protein fouling caused a significant reduction in the dextran sieving coefficients, with very different effects seen for the diffusive and convective contributions to dextran transport. The changes in dextran sieving coefficients and diffusive permeabilities were analyzed using a two-layer membrane model in which a distinct protein layer is assumed to form on the upstream surface of the membrane. The data suggest that the protein layer formed during filtration was more tightly packed than that formed by simple static adsorption. Hydrodynamic calculations indicated that the pore size of the protein layer remained relatively constant throughout the adsorption or filtration, but the thickness of this layer increased with increasing exposure time. These results provide important insights into the nature of protein fouling during ultrafiltration and its effects on membrane transport. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:451-460, 1998.
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    Contribution of protein charge to partitioning in aqueous two-phase systems (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 59 (1998), S. 461-470 
    Details
    ISSN: 0006-3592
    Keywords: aqueous two-phase separation ; protein partitioning ; T4 lysozyme ; electrochemical partitioning ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Protein partitioning in aqueous two-phase systems based on phase-forming polymers is strongly affected by the net charge of the protein, but a thermodynamic description of the charge effects has been hindered by conflicting results. Many of the difficulties could be because of problems in isolating electrochemical effects from other interactions of phase components.We explored charge effects on protein partitioning in poly(ethylene glycol)-dextran two-phase systems by using two series of genetically engineered charge modifications of bacteriophage T4 lysozyme produced in Escherichia coli. The two series, one in the form of charged-fusion tails and the other in the form of charge-change point mutations, provided matching net charges but very different polarity. Partition coefficients of both series were obtained and interfacial potential differences of the phase systems were measured. Multi-angle laser light scattering measurements were also performed to determine second virial coefficients. A semi-empirical model accounting for the roles of both charge and non-charge effects on protein partitioning behavior is proposed, and the results predicted from the model are compared to the results from the experiments. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:461-470, 1998.
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    Adaptive on-line model for aerobic Saccharomyces cerevisiae fermentation (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 48 (1995), S. 631-638 
    Details
    ISSN: 0006-3592
    Keywords: Saccharomyces cerevisiae ; fermentation ; on-line simulation ; state estimation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: In order to study and control fermentation processes, indirect on-tine measurements and mathematical models can be used. In this article we present a mathematical on-line model for fermentation processes. The model is based on atom and partial mass balances as well as on equations describing the acid-base system. The model is brought into an adaptive form by including transport equations for mass transfer and unstructured expressions for the fermentation kinetics. The state of the process, i.e., the concentrations of biomass, substrate, and products, can be estimated on-line using the balance part of the model completed with measurement equations for the input and output flows of the process. Adaptivity is realized by means of on-line estimation of parameters in the transport and kinetic expressions using recursive regression analysis. These expressions can thus be used in the model as valid equations enabling prediction of the process. This makes model-based automation of the process and testing of the validity of the measurement variables possible. The model and the on-line principles are applied to a 3.5-L laboratory tormentor in which Saccharomyces cerevisiae is cultivated. The experimental results show that the model-based estimation of the state and the predictions of the process correlate closely with high-performance liquid chromatography (HPLC) analyses. © 1995 John Wiley & Sons, Inc.
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    Kinetics of chlorinated ethylene dehalogenation under methanogenic conditions (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 48 (1995), S. 659-666 
    Details
    ISSN: 0006-3592
    Keywords: methanogenic activity ; ethylene ; dechlorination ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Kinetics were determined for methanogenic activity and chlorinated ethylene dehalogenation by a methanol-enriched, anaerobic sediment consortium. The culture reductively dechlorinated perchloroethylene (PCE) to trichloroethylene (TCE), 1,1-dichloroethylene (1,1-DCE), vinylchloride (VC), and ethylene and ethane. The absence : of methanol or the addition of 2-bromoethanesulfonic. acid in the presence of methanol suppressed both methanogenic activity and dechlorination. In contrast, acetate production continued in the presence of 2-bromoethanesulfonic acid. These results suggest that dechlorination was strongly linked to methane formation and not to acetate production. A kinetic model, developed to describe both methanogenesis and dechlorination, successfully predicted experimentally measured concentrations of biomass, methane, substrate, and chlorinated ethylenes. The average maximum specific dehalogenation rates for PCE, TCE, 1,1-DCE, and VC were 0.9 ± 0.6, 0.4 ± 0.1, 12 ± 0.1, and 2.5 ± 1.7 μmol contaminant/ g. DW/day, respectively. This pattern for dechlorination rates is distinctly different than that reported for transition metal cofactors, where rates drop by approximately one order of magnitude as each successive chlorine is removed. The experimental results and kinetic analysis suggest that it will be impractical to targeting methanol consuming methanogenic organisms for in situ ground-water restoration. © 1995 John Wiley & Sons, Inc.
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    Enhancement of antibody production by growth factor addition in perfusion and hollow-fiber culture systems (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 48 (1995), S. 673-680 
    Details
    ISSN: 0006-3592
    Keywords: bovine serum albumin ; growth factor ; hollow-fiber culture ; perfusion culture ; antibody production rate ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The effects of the high-molecular-weight growth factors, transferrin and bovine serum albumin (BSA), on antibody production were analyzed quantitatively in continuous hollow-fiber cultivation over a period of 60 days. Transferrin enhanced cell growth but had no significant effect on the specific antibody production rate, whereas BSA significantly enhanced antibody production. The antibody production rate was increased 4- and 14-fold respectively by feeding BSA at 2 and 5 g L-1 into the EC side of the system (the side connected to the cell-containing outer part of the hollow-fiber unit) compared with the production achieved without BSA. Addition of 5 g L1 BSA into the IC side of the system (the side connected to the inner part of the hollow-fiber unit) resulted in a 2.5-fold increase in the antibody production rate. The effect of BSA was also analyzed using the perfusion culture system with a separation unit. When fresh medium containing either 2 or 5 g L-1 BSA was fed into the reactor, both the specific growth rate and specific death rate increased, while the specific antibody production rate was increased 2- and 25-fold, respectively, by feeding BSA at these two concentrations compared with no addition. Comparing the two systems, the increase in the antibody production rate achieved with the hollow-fiber system was threefold greater than that in the perfusion culture system with the same concentration of BSA feeding. © 1995 John Wiley & Sons, Inc.
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    Influence of the nature of modifier in the enzymatic activity of chemical modified semipurified lipase from Candida rugosa (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 55 (1997), S. 252-260 
    Details
    ISSN: 0006-3592
    Keywords: lipase ; chemical modification ; stability ; esterification ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Semipurified lipase of Candida rugosa (CRSL) was subjected to chemical modification, and the activities of the modified lipase, in hydrolysis and esterification reactions, were examined. The esterification reactions were carried out in the absence and presence of isooctane. When the enzyme was modified with polyethylene glycol (PEG), two methodologies were studied. The activation of PEG with p-NO2-phenylchloroformate gives better biocatalysts than those obtained with cyanuric chloride-PEG. The chemical modification with PEG increases the stability of pure lipases in isooctane at 50°C (extreme conditions). The chemically modified enzymes are useful for biotransformations in organic solvents. In addition the nitration of tyrosines with tetranitromethane was also studied. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 55: 252-260, 1997.
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    Ion exchange purification of G6PDH from unclarified yeast cell homogenates using expanded bed adsorption (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 49 (1996), S. 204-216 
    Details
    ISSN: 0006-3592
    Keywords: expanded bed adsorption ; bakers' yeast ; G6PDH ; STREAMLINE ion exchange adsorbents ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The use of expanded beds of STREAMLINE ion exchange adsorbents for the direct extraction of an intracellular enzyme glucose-6-phosphate dehydrogenase (G6PDH) from unclarified yeast cell homogenates has been investigated. It has been demonstrated that such crude feedstocks can be applied to the bed without prior clarification steps. The purification of G6PDH from an unclarified yeast homogenate was chosen as a model system containing the typical features of a direct extraction technique. Optimal conditions for the purification were determined in small scale, packed bed experiments conducted with clarified homogenates. Results from these experiments were used to develop a preparative scale separation of G6PDH in a STREAMLINE 50 EBA apparatus. The use of an on-line rotameter for measuring and controlling the height of the expanded bed when operated in highly turbid feedstocks was demonstrated. STREAMLINE DEAE has been shown to be successful in achieving isolation of G6PDH from an unclarified homogenate with a purification factor of 12 and yield of 98% in a single step process. This ion exchange adsorbent is readily cleaned using simple cleaning-in-place procedures without affecting either adsorption or the bed expansion properties of the adsorbent after many cycles of operation. The ability of combining clarification, capture, and purification in a single step will greatly simplify downstream processing flowsheets and reduce the costs of protein purification. © 1996 John Wiley & Sons, Inc.
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    Rat hepatocyte morphology and function on lactose-derivatized polystyrene surfaces (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 49 (1996), S. 259-265 
    Details
    ISSN: 0006-3592
    Keywords: hepatocytes ; lactose-derivatized polystyrene ; polystyrene ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Hepatocytes isolated from male Fisher 344VF rats were cultured on two substrates, collagen I and a lactose-derivatized polystyrene (PS-lactose), to compare morphological and functional differences. Hepatocyte morphology changed dramatically depending upon the substrate, shown through actin cytoskeletal staining and scanning electron microscopy. Functional assays performed included albumin secretion, reduced glutathione content, UDP-glucuronosyl transferase, and cytochrome P4501A1 activity. The presence of dexamethasone and dimethylsulfoxide (DMSO) in the media was required for the maintenance of several differentiated functions for cells cultured on collagen. In general, cells cultured on the PS-lactose substrate showed a much slower loss of function over the same period of time. The maintenance of differentiated function of cells on PS-lactose was enhanced with the addition of dexamethasone and DMSO. This is the first report of a culture system in which hepatocytes, cultured on a polymer substrate without additional protein coatings or media additives, have been able to maintain differentiated functions for up to 1 week. © 1996 John Wiley & Sons, Inc.
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    Conservative chemical modification of proteins to study the effects of a single protein property on partitioning in aqueous two-phase systems (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 49 (1996), S. 290-299 
    Details
    ISSN: 0006-3592
    Keywords: proteins, modified ; partitioning in aqueous system ; thaumatin ; β-lactoglobulin ; BSA ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Relatively conservative modifications of three proteins were carried out to alter their surface properties. The protein properties modified were hydrophobicity and charge. This was done by acylation of amino groups with anhydrides. For the hydrophobic modification experiments, two proteins (β-lactoglobulin and bovine serum albumin [BSA]) and four anhydrides (hexanoic, butyric, succinic, acetic) were used. For the modification of surface charge the protein thaumatin was selected and various proportions of the free amino groups were blocked with acetic anhydride to give a series of proteins with differing isoelectric points. Detailed characterization and purification of selected modified proteins was carried out including molecular weight measurements and conformational analysis. The criteria used for selecting the modified proteins for subsequent investigation of their partitioning in aqueous two-phase systems (ATPS) is described. With a judicious choice of starting material it was found that limited chemical modifications to proteins could effectively alter surface hydrophobicity or charge almost independently, with little effect on other molecular properties. It appears, however, that the method for chemical modification and the reaction conditions must also be carefully controlled. © 1996 John Wiley & Sons, Inc.
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    Use of chemically modified proteins to study the effect of a single protein property on partitioning in aqueous two-phase systems: Effect of surface charge (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 49 (1996), S. 309-315 
    Details
    ISSN: 0006-3592
    Keywords: surface charge ; proteins, modified ; partitioning in aqueous system ; thaumatin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A series of charge-modified thaumatins with different values of surface charge were partitioned in aqueous two-phase systems (ATPS) to study the effect of surface charge as a single property on partitioning. Electrophoretic mobility of the proteins in titration curves was used as a measure of surface charge. Four modified proteins derived from thaumatin with the following values of isoelectric point: 8.70, 8.15, 5.60, and 4.50 were used for partitioning. The resolution of the systems in terms of protein surface charge was calculated. Partitioning of modified thaumatins in PEG 4000/dextran systems with phosphate buffer, Tris buffer, NaCl, KCl, and sulfate salts was carried out. Among the sulfate salts tested, the addition of 50 mM Li2SO4 to the system buffered with phosphate gave the highest value of resolution for differences in surface protein charge (RSPC). It shows a decrease in the value of K (partition coefficient) with an increase in the protein's charge. The addition of 100 mM KCl to the system promoted the opposite effect on the RSPC value. Charge-modified proteins were partitioned in PEG/salt systems to investigate the ability of these systems for resolving differences in surface charge. The PEG/citrate system seemed to have almost no ability for resolving proteins on the basis of surface charge differences; PEG/phosphate systems had some capability for resolving differently charged proteins. The more negative proteins tended to have higher values of K than the more positively charged fractions. The use of charge-modified proteins allowed the investigation of the effect of protein surface charge on partitioning in aqueous two-phase systems independently from other protein parameters as they were prepared from a common parent protein thaumatin. This technique provides an interesting novel tool to investigate the effect of protein surface charge on partitioning in ATPS taking protein charge as an independent parameter. © 1996 John Wiley & Sons, Inc.
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    A versatile oxygenator and perfusion system for magnetic resonance studies (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 49 (1996), S. 348-354 
    Details
    ISSN: 0006-3592
    Keywords: oxygenator ; NMR spectroscopy ; organ perfusion ; mammalian cell culture ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A compact, reusable membrane oxygenator has been constructed for the perfusion of cultured cells and isolated organs. While the oxygenator was designed to be compatible with nuclear magnetic resonance (NMR) spectroscopy studies, it can also be used for any experiment which requires warming and oxygenation of perfusates. For the NMR studies, the oxygenator can be positioned at the opening of the magnet bore which allows oxygenation and warming of the perfusate immediately prior to delivery to the tissue, therefore eliminating problems with heat or oxygen loss which may occur with the long perfusion lines. © 1996 John Wiley & Sons, Inc.
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    Fluid shear stress induction of the transcriptional activator c-fos in human and bovine endothelial cells, HeLa, and Chinese hamster ovary cells (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 49 (1996), S. 383-390 
    Details
    ISSN: 0006-3592
    Keywords: c-fos protein ; endothelium ; hemodynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The c-fos protein belongs to a family of transcriptional cofactors that can complex with proteins of the Jun family and activate mRNA transcription from gene promoters containing an activator protein 1 (AP-1) binding element. The shear stress inducibility of the c-fos protein was studied in human and animal cell lines of vastly different origins. Primary human umbilical vein endothelial cells (HUVEC), bovine aortic endothelial cells (BAEC, passage 2-14), HeLa cells, and Chinese hamster ovary (CHO) cells were subjected to steady laminar shear stress using a parallel plate flow apparatus. After 1 h of flow exposure at 25 dyn/cm2, the c-fos levels in nuclei of shear stress HUVEC, BAEC, HeLa, and CHO were 5.4 ± 2.0 (n = 3), 2.25 ± 1.38 (n = 6), 2.14 ± 0.07 (n = 8), 1.92 ± 0.58 (n = 2) times higher, respectively, than in matched stationary controls. Flow exposure at 4 dyn/cm2 caused no enhancement of c-fos levels in any of the cell lines tested, but caused significant reduction in c-fos expression in the HeLa cells. The c-fos induction by shear stress could be blocked by pharmacological agents. For example, the flow induction of the c-fos protein levels was blocked by 50% with the preincubation of HUVEC with a protein kinase C inhibitor, H7 (10 μM) and blocked completely in HeLa cells preincubated with the phospholipase C inhibitor, neomycin (5 mM). The minimum time of shear stress exposure required to induce the c-fos protein expression in HeLa cells was found to be as low as 1 min. By Northern analysis, the c-fos mRNA levels were found to be elevated in BAEC, CHO, and HeLa cells exposed to 25 dyn/cm2 for 30 min. These studies indicate that c-fos induction is a consistent genetic response in a variety of mammalian cells that may alter cellular phenotype in mechanical environments. © 1996 John Wiley & Sons, Inc.
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    Vancomycin production in batch and continuous culture (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 49 (1996), S. 412-420 
    Details
    ISSN: 0006-3592
    Keywords: Amycolatopsis orientalis ; vancomycin production ; chemostat culture ; phosphate inhibition ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Production of the glycopeptide antibiotic vancomycin by two Amycolatopsis orientalis strains was examined in batch shake flask culture in a semidefined medium with peptone as the nitrogen source. Different growth and production profiles were observed with the two strains; specific production (Yp/x) was threefold higher with strain ATCC 19795 than with strain NCIMB 12945. A defined medium with amino acids as the nitrogen source was developed by use of the Plackett-Burman statistical screening method. This technique identified certain amino acids (glycine, phenylalanine, tyrosine, and arginine) that gave significant increased specific production, whereas phosphate was identified as inhibitory for high specific vancomycin production. Experiments made with the improved medium and strain ATCC 19795 showed that vancomycin production kinetics were either growth dissociated or growth associated, depending on the amino acid concentration. In chemostat culture at a constant dilution rate (0.087 h-1), specific vancomycin production rate (qvancomycin) decreased linearly as the medium phosphate concentration was increased from 2 to 8 mM. In both phosphate and glucose limited chemostats, qvancomycin was a function of specific growth rate; the maximum value was observed at D = 0.087 h-1 (52% of the maximum specific growth rate). Under phosphate limited growth conditions, qvancomycin was threefold higher (0.37 mg/g dry weight/h) than under glucose limitation (0.12 mg/g dry weight/h). © 1996 John Wiley & Sons, Inc.
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    On-line monitoring of respiration in recombinant-baculovirus infected and uninfected insect cell bioreactor cultures (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 50 (1996), S. 36-48 
    Details
    ISSN: 0006-3592
    Keywords: insect cell culture ; Sf-9 cells ; respiration ; bioreactor ; on-line monitoring ; baculovirus expression vector system ; recombinant proteins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Respiration rates in Spodoptera frugiperda (Sf-9) cell bioreactor cultures were successfully measured on-line using two methods: The O2 uptake rate (OUR) was determined using gas phase pO2 values imposed by a dissolved oxygen controller and the CO2 evolution rate (CER) was measured using an infrared detector. The measurement methods were accurate, reliable, and relatively inexpensive. The CER was routinely determined in bioreactor cultures used for the production of several recombinant proteins. Simple linear relationships between viable cell densities and both OUR and CER in exponentially growing cultures were used to predict viable cell density. Respiration measurements were also used to follow the progress of baculoviral infections in Sf-9 cultures. Infection led to increases in volumetric and per-cell respiration rates. The relationships between respiration and several other culture parameters, including viable cell density, cell protein, cell volume, glucose consumption, lactate production, viral titer, and recombinant β-galactosidase accumulation, were examined. The extent of the increase in CER following infection and the time postinfection at which maximum CER was attained were negatively correlated with the multiplicity of infection (MOI) at multiplicities below the level required to infect all the cells in a culture. Delays in the respiration peak related to the MOI employed were correlated with delays in the peak in recombinant protein accumulation. DO levels in the range 5-100% did not exert any major effects on viable cell densities, CER, or product titer in cultures infected with a baculovirus expressing recombinant β-galactosidase. © 1996 John Wiley & Sons, Inc.
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    Masthead (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 50 (1996) 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
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    URL: http://dx.doi.org/10.1002/bit.260500101
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    Aggregation of ligand-modified liposomes by specific interactions with proteins. II: Biotinylated liposomes and antibiotin antibody (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 50 (1996), S. 169-183 
    Details
    ISSN: 0006-3592
    Keywords: liposomes ; biotin ; aggregation kinetics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The aggregation of biotinylated phospholipid vesicles (liposomes) cross-linked by antibiotin IgG was studied experimentally and theoretically. The liposomes were either low density liposomes that contained 0.4 mol% biotinylated phospholipid (≈100 exposed biotin molecules per liposome), or high density liposomes that contained 2.7 mol% biotinylated phospholipid (≈1000 exposed biotin molecules per liposome). The solution turbidity and mean particle size measured by quasi-elastic light scattering (QLS) were monitored throughout the aggregation. Three different lots of antibiotin antibodies, each with different association constants and binding heterogeneities, were used. The antibody binding characteristics affected the aggregation rates. The aggregation kinetics were analyzed using a model based on the Smoluchowski theory of aggregation, fractal concepts of aggregate microstructure, and Rayleigh and Mie light scattering theory. The experimental conditions of liposome concentration, protein concentration, and ligand density under which aggregation occurred correlated well with calculated sticking probabilities based on isotherms describing the adsorption of antibiotin antibody to the liposomes. These results are compared with prior observations made when avidin was used as the cross-linking protein. © 1996 John Wiley & Sons, Inc.
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    Masthead (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 50 (1996) 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
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    URL: http://dx.doi.org/10.1002/bit.260500201
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    Collagenase digestion of bone fragments in microgravity (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 50 (1996), S. 211-216 
    Details
    ISSN: 0006-3592
    Keywords: microgravity ; bioprocessing ; sedimentation ; turbulence ; collagenase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The effect of a quiescent microgravity fluid environment on the activity of collagenase directed at demineralized bone fragments was investigated over a period of 10 days. Enzyme treatment resulted in greater mass loss in microgravity, with nearly three times the loss of mass during Space Shuttle mission STS-62 compared to the stationary ground control. Clinorotation enhanced the loss of mass relative to a stationary control, but this increase was still significantly less than the increase with exposure to microgravity. This suggests the detrimental influence of turbulence on the enzyme function and the benefit of using microgravity to provide both low turbulence and uniformity of unequally dense materials within the reaction chamber. The results are considered for their general applicability to a variety of bioprocessing applications that may be enhanced in microgravity. © 1996 John Wiley & Sons, Inc.
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    Mini-review: Mechanical factors affecting cartilage regeneration in vitro (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 50 (1996), S. 430-437 
    Details
    ISSN: 0006-3592
    Keywords: cartilage ; tissue regeneration ; chondrocytes ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: In the last 5 to 10 years, tissue engineering has revolutionized the way in which medical researchers and clinicians are thinking of and, in some cases, actually treating diseases involving tissue damage and destruction. One such disease, osteoarthritis, results from progressive degeneration of articular cartilage, which has a limited ability to repair itself. With tissue engineering, scientists are now able to regenerate cartilage in vitro from isolated mature chondrocytes. While the regeneration process is still not fully understood, enough has been learned that physicians are already implanting cultured chondrocytes into humans and other animals in the hopes of effecting joint repair. One aspect which has not been fully explored is the effect of mechanical stress on developing and implanted cartilage, especially over the long term. This article will review in brief what is now known about the mechanical factors affecting cartilage regeneration in vitro and what still remains to be determined for optimum tissue engineering of cartilage constructs. © 1996 John Wiley & Sons, Inc.
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    Osteoblast migration on poly(α-hydroxy esters) (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 50 (1996), S. 443-451 
    Details
    ISSN: 0006-3592
    Keywords: osteoblast ; migration ; poly(αhydroxy esters) ; poly(DL-lactic-co-glycolic acid) ; PLGA ; biodegradable polymers ; tissue engineering ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: We investigated the migration of rat calvaria osteoblast populations on poly(α-hydroxy ester) films for up to 14 days to determine effects of substrate composition and culture conditions on the migratory characteristics of osteoblasts. Initial osteoblast culture conditions included cell colonies formed by seeding a high (84,000 cells/cm2) or low (42,000 cells/cm2) density of isolated osteoblasts on the polymer films, and bone tissue cultures formed by plating bone chips directly on the substrates. High density osteoblast colonies cultured and allowed to migrate and proliferate radially on 85:15 poly(DL-lactic-co-glycolic acid) (PLGA) films, 75:25 PLGA films, and tissue culture polystyrene controls demonstrated that the copolymer ratio in the polymer films did not affect the rate of increase in substrate surface area (or culture area) covered by the growing cell colony. However, the rate of increase in culture area was dependent on the initial osteoblast seeding density. Initial cell colonies formed with a lower osteoblast seeding density on 75:25 PLGA resulted in a lower rate of increase in culture area, specifically 4.9 ± 0.3 mm2/day, versus 14.1 ± 0.7 mm2/day for colonies seeded with a higher density of cells on the same polymer films. The proliferation rate for osteoblasts in the high and low density seeded osteoblast colonies did not differ, whereas the proliferation rate for the osteoblasts arising from the bone chips was lower than either of these isolated cell colonies. Confocal and light microscopy revealed that the osteoblast migration occurred as a monolayer of individual osteoblasts and not a calcified tissue front. These results demonstrated that cell seeding conditions strongly affect the rates of osteoblast migration and proliferation on biodegradable poly(α-hydroxy esters). © 1996 John Wiley & Sons, Inc.
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    Different measures of human hematopoietic cell culture performance are optimized under vastly different conditions (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 50 (1996), S. 505-513 
    Details
    ISSN: 0006-3592
    Keywords: bone marrow ; hematopoiesis ; perfusion ; culture optimization ; stroma ; stem cells ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Hematopoiesis, the formation of mature blood cells from stem (LTC-IC) and progenitor (CFU-GM) cells in the bone marrow, is a complex tissue-forming process that leads to many important physiological functionalities. Consequently, a functioning ex vivo hematopoietic system has a variety of basic scientific and clinical uses. The design and operation of such a system presents the tissue engineer with challenges and choices. In this study, three culture variables were used to control ex vivo human hematopoiesis. Systematic variation of inoculum density (ID), medium exchange interval (MEI), and the use of preformed stroma (PFS) showed that (1) all three variables significantly influenced culture performance, (2) the three variables interacted strongly, and (3) the variables could be manipulated to achieve the optimization of different performance criteria. Donor-to-donor variability in culture performance was great at low ID but was minimized at higher ID. PFS had a large positive effect on cell and CFU-GM output at low ID, but had minimal effect at higher ID. In fact, PFS caused a decrease in LTC-IC output at high ID. The effects of PFS indicated that stromal cell elements became more limiting than proliferative cell elements as ID was reduced.In cultures without PFS, maximum cell output was obtained with high ID using a short MEI, whereas the greatest cell expansion ratio was obtained at low ID with an intermediate MEI. Maximum CFU-GM output was obtained from cultures with high ID using a short to intermediate MEI, whereas the greatest CFU-GM expansion ratio was obtained at intermediate ID with an intermediate MEI. The addition of PFS altered the locations of these maxima. In general, PFS moved the maxima to lower ID, and culture output became more sensitive to MEI. Therefore, the optimization of one performance criterion always resulted in a decline of the others. This study demonstrates that ex vivo tissue function is sensitive to many culture variables in an interactive fashion and that systematic multivariable studies are required to characterize tissue function. Once the effects of individual variables and their interactions are known, this knowledge can be used to optimize tissue performance with respect to desired criteria. © 1996 John Wiley & Sons, Inc.
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    Masthead (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 50 (1996) 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260500501
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    Effect of hypoosmotic stress on hybridoma cell growth and antibody production (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 55 (1997), S. 565-570 
    Details
    ISSN: 0006-3592
    Keywords: hybridoma ; hypoosmotic stress ; specific antibody productivity ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: To investigate the response of hybridoma cells to hypoosmotic stress, S3H5/γ2bA2 and DB9G8 hybridomas were cultivated in the hypoosmolar medium [Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% serum] resulting from sodium chloride subtraction. Both hybridomas showed similar responses to hypoosmotic stress in regard to cell growth and antibody production. The cell growth and antibody production at 276 mOsm/kg were comparable to those at 329 mOsm/kg (standard DMEM). Both cells grew well at 219 mOsm/kg, though their growth and antibody production were slightly decreased. When the osmolality was further decreased to 168 mOsm/kg, the cell growth did not occur. When subjected to hyperosmotic stress, both cells displayed significantly enhanced specific antibody productivity (qAb). However, the cells subjected to hypoosmotic stress did not display enhanced qAb. Taken together, both hyperosmotic and hypoosmotic stresses depressed the growth of S3H5/γ2bA2 and DB9G8 hybridomas. However, their response to hypoosmotic stress in regard to qAb was different from that to hyperosmotic stress. © 1997 John Wiley & Sons, Inc. Biotechnol Biong 55: 565-570, 1997.
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    Production of recombinant bacterial endoglucanase as a co-product with ethanol during fermentation using derivatives of Escherichia coli KO11 (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 55 (1997), S. 547-555 
    Details
    ISSN: 0006-3592
    Keywords: ethanol ; cellulose ; hemicellulose ; endoglucanase ; cellulase ; lignocellulose ; biomass ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: This study demonstrates a new approach to reduce the amount of fungal cellulase required for the conversion of cellulose into ethanol. Escherichia coli KO11, a biocatalyst developed for the fermentation of hemicellulose syrups, was used to produce recombinant endoglucanase as a co-product with ethanol. Seven different bacterial genes were expressed from plasmids in KO11. All produced cell-associated endoglucanase activity. KO11(pLOI1620) containing Erwinia chrysanthemi celZ (EGZ) produced the highest activity, 3,200 IU endoglucanase/L fermentation broth (assayed at pH 5.2 and 35°C). Recombinant EGZ was solubilized from harvested cells by treatment with dilute sodium dodecyl sulfate (12.5 mg/ml, 10 min, 50°C) and tested in fermentation experiments with commercial fungal cellulase (5 filter paper units/g cellulose) and purified cellulose (100 g/L). Using Klebsiella oxytoca P2 as the biocatalyst, fermentations supplemented with EGZ as a detergent-lysate of KO11(pLOI1620) produced 14%-24% more ethanol than control fermentations supplemented with a detergent-lysate of KO11(pUC18). These results demonstrate that recombinant bacterial endoglucanase can function with fungal cellulase to increase ethanol yield during the simultaneous saccharification and fermentation of cellulose. © 1997 Wiley & Sons, Inc. Biotechnol Bioeng 55: 547-555, 1997.
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    Engineering mRNA stability in E. coli by the addition of synthetic hairpins using a 5′ cassette system (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 55 (1997), S. 577-580 
    Details
    ISSN: 0006-3592
    Keywords: mRNA stability ; hairpins ; gene expression control ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: An expression system has been developed for the introduction of DNA cassettes into the region between the transcription and translation start sites of a gene of interest. This cassette system was used to engineer mRNA stability through the introduction of hairpins at the 5′ end. A synthetic DNA cassette was designed so that the resulting mRNA hairpin would be positioned one nucleotide from the 5′ mRNA end. The hairpin-containing mRNA exhibited a half-life 3 times that of the mRNA with no hairpin, resulting in increases in both mRNA and protein levels. These results indicate that it is possible to engineer mRNA stability as an additional means of controlling gene expression. © 1997 John Wiley & Sons Inc. Biotechnol Bioeng 55: 557-580, 1997
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    Application of membrane-based preferential transport to whole broth processing (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 55 (1997), S. 581-591 
    Details
    ISSN: 0006-3592
    Keywords: adsorptive membranes ; oscillatory flow ; integrated processes ; in situ product recovery ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Preferential transport in adsorptive membranes can be used to selectively remove biochemicals directly from fermentation broths. During preferential transport, an adsorbing solute is selectively transported across the membrane while nonadsorbing solutes and cells are retained by the membrane. This technique was used to separate lysozyme directly from a feed containing lysozyme, myoglobin, and yeast cells. We found that because the oscillatory flows used in preferential transport involve strokes that are close to symmetric, they are very efficient in alleviating cake formation due to cell deposition on the membrane surface. Theoretical results suggest that, by optimizing process variables, preferential transport can lead to a continuous concentrated stream of the adsorbing protein. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 54: 581-591, 1997.
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    In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae: II. Mathematical model (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 55 (1997), S. 592-608 
    Details
    ISSN: 0006-3592
    Keywords: Saccharomyces cerevisiae ; metabolic modeling ; sensitivity analysis ; glycolysis ; compartmentation ; transient response ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A mathematical model of glycolysis in Saccharomyces cerevisiae is presented. The model is based on rate equations for the individual reactions and aims to predict changes in the levels of intra- and extracellular metabolites after a glucose pulse, as described in part I of this study. Kinetic analysis focuses on a time scale of seconds, thereby neglecting biosynthesis of new enzymes. The model structure and experimental observations are related to the aerobic growth of the yeast. The model is based on material balance equations of the key metabolites in the extracellular environment, the cytoplasm and the mitochondria, and includes mechanistically based, experimentally matched rate equations for the individual enzymes. The model includes removal of metabolites from glycolysis and TCC for biosynthesis, and also compartmentation and translocation of adenine nucleotides. The model was verified by in vivo diagnosis of intracellular enzymes, which includes the decomposition of the network of reactions to reduce the number of parameters to be estimated simultaneously. Additionally, sensitivity analysis guarantees that only those parameters are estimated that contribute to systems trajectory with reasonable sensitivity. The model predictions and experimental observations agree reasonably well for most of the metabolites, except for pyruvate and adenine nucleotides. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 55: 592-608, 1997.
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    A novel membrane reactor design for controlled studies of interacting populations (simulation of the interaction between microorganism and plant suspension cultures) (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 55 (1997), S. 609-615 
    Details
    ISSN: 0006-3592
    Keywords: interacting populations ; membrane reactor ; induced metabolic changes ; elicitation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The design of a reactor in which two interacting cell populations (microorganisms and plants) could grow under controlled conditions was considered. In this reactor, the cell populations are separated by a membrane which permits semi-in vivo study of induced interaction-specific changes in metabolism. In this paper, the interaction of suspension culture of Nicotiana tabacum (tobacco) and the Oomycete, Phytophthora nicotiana was simulated. The results of the computer simulation show the induced metabolic changes as a consequence of the biological interaction. The paper introduces a novel approach in the strategy for the study of interacting population in suspension cultures. This type of system has potential applications in studies of the regulation of secondary metabolism and for the production of high values pharmaceuticals. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 55: 609-615, 1997.
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    Application of fluid mechanic and kinetic models to characterize mammalian cell detachment in a radial-flow chamber (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 55 (1997), S. 616-629 
    Details
    ISSN: 0006-3592
    Keywords: cell adhesion ; radial-flow chamber ; hydrodynamic shear ; detachment kinetics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The strength of adhesion and dynamics of detachment of murine 3T3 fibroblasts from self-assembled monolayers were measured in a radial-flow chamber (RFC) by applying models for fluid mechanics, adhesion strength probability distributions, and detachment kinetics. Four models for predicting fluid mechanics in a RFC were compared to evaluate the accuracy of each model and the significance of inlet effects. Analysis of these models indicated an outer region at large radial positions consistent with creeping flow, an intermediate region influenced by inertial dampening, and an inner region dominated by entrance effects from the axially-oriented inlet. In accompanying experiments patterns of the fraction of cells resisting detachment were constructed for individual surfaces as a function of the applied shear stress and evaluated by comparison with integrals of both a normal and a log-normal distribution function. The two functions were equally appropriate, yielding similar estimates of the mean strength of adhesion. Further, varying the Reynolds number in the inlet, Red, between 630 and 1480 (corresponding to volumetric flow rates between 0.9 and 2.1 mL/s) did not affect the mean strength of adhesion. For these same experiments, analysis of the dynamics of detachment revealed three temporal phases: 1) rapid detachment of cells at the onset of flow, consistent with a first-order homogeneous kinetic model; 2) time-dependent rate of detachment during the first 30 sec. of exposure to hydrodynamic shear, consistent with the first-order heterogeneous kinetic model proposed by Dickinson and Cooper (1995); and 3) negligible detachment, indicative of pseudo-steady state after 60 sec. of flow. Our results provide rigorous guidelines for the measurement of adhesive interactions between mammalian cells and prospective biomaterial surfaces using a RFC. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 55: 616-629, 1997.
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    Real-time method for determining the colony-forming cell content of human hematopoietic cell cultures (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 55 (1997), S. 693-700 
    Details
    ISSN: 0006-3592
    Keywords: glucose ; lactate ; real-time determination ; hematopoietic cell culture ; colony-forming cells ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Glucose and lactate metabolic rates were evaluated for cultures of cord blood (CB) mononuclear cell (MNC), peripheral blood (PB) MNC, and PB CD34+ cell cultures carried out in spinner flasks and in T-flasks in both serum-containing and serum-free media. Specific glucose uptake rates (qgluc, in micromoles per cell per hour) and lactate generation rates (qlac) correlated with the percentage of colony-forming cells (CFC) present in the culture for a broad range of culture conditions. Specifically, the time of maximum CFC percentage in each culture coincided with the time of maximum qgluc and qlac in cultures with different seeding densities and cytokine combinations. A two-population model (Qlac = α[CFC] + β([TC] - [CFC]), where [TC] is total cell concentration; Qlac is volumetric lactate production rate in micromoles per milliliter per hour; α is qlac for an average CFC; and β is qlac for an average non-CFC) was developed to describe lactate production. The model described lactate production well for cultures carried out in both T-flasks and spinner flasks and inoculated with either PB or CB MNC or PB CD34+ cells. The values for α and β that were derived from the model varied with both the inoculum density and the cytokine combination. However, preliminary results indicate that cultures carried out under the same conditions from different samples with similar initial CD34+ cell content have similar values for β and β. These findings suggest that it should be possible to use lactate production data to predict the harvest time that corresponds to the maximum number of CFC in culture. The ability to harvest ex vivo hematopoietic cultures for transplantation when CFC are at a maximum has the potential to speed the rate at which immunocompromised patients recover. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 55: 693-700, 1997.
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    A model for light distribution and average solar irradiance inside outdoor tubular photobioreactors for the microalgal mass culture (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 55 (1997), S. 701-714 
    Details
    ISSN: 0006-3592
    Keywords: tubular photobioreactors ; light distribution ; average solar irradiance ; light attenuation ; microalgae mass culture ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A mathematical model to estimate the solar irradiance profile and average light intensity inside a tubular photobioreactor under outdoor conditions is proposed, requiring only geographic, geometric, and solar position parameters. First, the length of the path into the culture traveled by any direct or disperse ray of light was calculated as the function of three variables: day of year, solar hour, and geographic latitude. Then, the phenomenon of light attenuation by biomass was studied considering Lambert-Beer's law (only considering absorption) and the monodimensional model of Cornet et al. (1900) (considering absorption and scattering phenomena). Due to the existence of differential wavelength absorption, none of the literature models are useful for explaining light attenuation by the biomass. Therefore, an empirical hyperbolic expression is proposed. The equations to calculate light path length were substituted in the proposed hyperbolic expression, reproducing light intensity data obtained in the center of the loop tubes. The proposed model was also likely to estimate the irradiance accurately at any point inside the culture. Calculation of the local intensity was thus extended to the full culture volume in order to obtain the average irradiance, showing how the higher biomass productivities in a Phaeodactylum tricornutum UTEX 640 outdoor chemostat culture could be maintained by delaying light limitation. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 55: 701-714, 1997.
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    Effect of agitation intensities on fungal morphology of submerged fermentation (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 55 (1997), S. 715-726 
    Details
    ISSN: 0006-3592
    Keywords: fungal morphology ; pellets ; hyphae ; hair of pellets ; agitation intensity ; fermentation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Both parallel fermentations with Aspergillus awamori (CBS 115.52) and a literature study on several fungi have been carried out to determine a relation between fungal morphology and agitation intensity. The studied parameters include hyphal length, pellet size, surface structure or so-called hairy length of pellets, and dry mass per-wet-pellet volume at different specific energy dissipation rates. The literature data from different strains, different fermenters, and different cultivation conditions can be summarized to say that the main mean hyphal length is proportional to the specific energy dissipation rate according to a power function with an exponent of -0.25 ± 0.08. Fermentations with identical inocula showed that pellet size was also a function of the specific energy dissipation rate and proportional to the specific energy dissipation rate to an exponent of -0.16 ± 0.03. Based on the experimental observations, we propose the following mechanism of pellet damage during submerged cultivation in stirred fermenters. Interaction between mechanical forces and pellets results in the hyphal chip-off from the pellet outer zone instead of the breakup of pellets. By this mechanism, the extension of the hyphae or hair from pellets is restricted so that the size of pellets is related to the specific energy dissipation rate. Hyphae chipped off from pellets contribute free filamentous mycelia and reseed their growth. So the fraction of filamentous mycelial mass in the total biomass is related to the specific energy dissipation rate as well.To describe the surface morphology of pellets, the hyphal length in the outer zone of pellets or the so-called hairy length was measured in this study. A theoretical relation of the hairy length with the specific energy dissipation rate was derived. This relation matched the measured data well. It was found that the porosity of pellets showed an inverse relationship with the specific energy dissipation rate and that the dry biomass per-wet-pellet volume increased with the specific energy dissipation rates. This means that the tensile strength of pellets increased with the increase of specific energy dissipation rate. The assumption of a constant tensile strength, which is often used in literature, is then not valid for the derivation of the relation between pellet size and specific energy dissipation rate. The fraction of free filamentous mycelia in the total biomass appeared to be a function of the specific energy dissipation in stirred bioreactors. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 55: 715-726, 1997.
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    Ammonium ion and glucosamine dependent increases of oligosaccharide complexity in recombinant glycoproteins secreted from cultivated BHK-21 cells (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 57 (1998), S. 518-528 
    Details
    ISSN: 0006-3592
    Keywords: ammonium ; UDP-GlcNAc ; N -glycosylation ; BHK-21 cells ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The effect of different ammonium concentrations and glucosamine on baby hamster kidney (BHK)-21 cell cultures grown in continuously perfused double membrane bioreactors was investigated with respect to the final carbohydrate structures of a secretory recombinant glycoprotein. The human interleukin-2 (IL-2) mutant glycoprotein variant IL-Mu6, which bears a novel N-glycosylation site (created by a single amino acid exchange of Gln100 to Asn), was produced under different defined protein-free culture conditions in the presence or absence of either glutamine, NH4Cl, or glucosamine. Recombinant glycoprotein products were purified and characterized by amino acid sequencing and carbohydrate structural analysis using matrix-assisted laser desorption ionization time of flight mass spectrometry, high-pH anion-exchange chromatography with pulsed amperometric detection, and methylation analysis. In the absence of glutamine, cells secreted glycoprotein forms with preponderantly biantennary, proximal fucosylated carbohydrate chains (85%) with a higher NeuAc content (58%). Under standard conditions in the presence of 7.5 mM glutamine, complex-type N-glycans were found to be mainly biantennary (68%) and triantennary structures (33%) with about 50% containing proximal α1-6-linked fucose; 37% of the antenna were found to be substituted with terminal α2-3-linked N-acetylneuraminic acid. In the presence of 15 mM exogenously added NH4Cl, a significant and reproducible increase in tri- and tetraantennary oligosaccharides (45% of total) was detected in the secretion product. In glutamin-free cultures supplemented with glucosamine, an intermediate amount of high antennary glycans was detected. The increase in complexity of N-linked oligosaccharides is considered to be brought about by the increased levels of intracellular uridine diphosphate-GlcNAc/GalNAc. These nucleotide sugar pools were found to be significantly elevated in the presence of high NH3/NH4+ and glucosamine concentrations. ©1998 John Wiley & Sons, Inc. Biotechnol Bioeng 57: 518-528, 1998.
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    Metabolic modeling of polyhydroxybutyrate biosynthesis (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 57 (1998), S. 557-570 
    Details
    ISSN: 0006-3592
    Keywords: Alcaligenes eutrophus ; polyhydroxyalkanoates ; metabolic engineering ; mathematical modeling ; enzyme kinetics ; regulation of metabolism ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A mathematical model describing intracellular polyhydroxybutyrate (PHB) synthesis in Alcaligenes eutrophus has been constructed. The model allows investigation of issues such as the existence of rate-limiting enzymatic steps, possible regulatory mechanisms in PHB synthesis, and the effects different types of rate expressions have on model behavior. Simulations with the model indicate that activities of all PHB pathway enzymes influence overall PHB flux and that no single enzymatic step can easily be identified as rate limiting. Simulations also support regulatory roles for both thiolase and reductase, mediated through AcCoA/CoASH and NADPH/NADP+ ratios, respectively. To make the model more realistic, complex rate expressions for enzyme-catalyzed reactions were used which reflect both the reversibility of the reactions and the reaction mechanisms. Use of the complex kinetic expressions dramatically changed the behavior of the system compared to a simple model containing only Michaelis-Menten kinetic expressions; the more complicated model displayed different responses to changes in enzyme activities as well as inhibition of flux by the reaction products CoASH and NADP+. These effects can be attributed to reversible rate expressions, which allow prediction of reaction rates under conditions both near and far from equilibrium. ©1998 John Wiley & Sons, Inc. Biotechnol Bioeng 57: 557-570, 1998.
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