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  • Saccharomyces cerevisiae  (734)
  • Currents
  • Springer  (739)
  • American Meteorological Society  (36)
  • John Wiley & Sons  (2)
  • Elsevier B.V.  (1)
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  • 1
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    Response to a steady poleward outflow. Part I : the linear, quasigeostrophic problem (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): 1541-1550, doi:10.1175/2008JPO3999.1.
    Description: The response of a zonal channel to a uniform, switched-on but subsequently steady poleward outflow is presented. An eastward coastal current with a Kelvin wave’s cross-shore structure is found to be generated instantly upon initiation of the outflow. The current is essentially in geostrophic balance everywhere except for the vicinity of the outflow channel mouth, where the streamlines must cross planetary vorticity contours to feed the current. The adjustment of this region generates a plume that propagates westward at Rossby wave speeds. The cross-shore structure of the plume varies with longitude, and at any given longitude it evolves with time. The authors show that the plume evolution can be understood both conceptually and quantitatively as the westward propagation of the Kelvin current’s meridional spectrum, with each spectral element propagating at its own Rossby wave group velocity.
    Description: This work was completed at Woods Hole Oceanographic Institution while T.S. Durland was supported by the Ocean and Climate Change Institute. M.A. Spall was supported by NSF Grant OCE-0423975, and J. Pedlosky by NSF Grant OCE-0451086. T.S. Durland acknowledges additional report preparation support from NASA Grant NNG05GN98G.
    Keywords: Coastal flows ; Estuaries ; Currents ; Vorticity ; Plumes
    Repository Name: Woods Hole Open Access Server
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  • 2
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    Performance of a new generation of acoustic current meters (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): 148–161, doi:10.1175/JPO3003.1.
    Description: As part of a program aimed at developing a long-duration, subsurface mooring, known as Ultramoor, several modern acoustic current meters were tested. The instruments with which the authors have the most experience are the Aanderaa RCM11 and the Nortek Aquadopp, which measure currents using the Doppler shift of backscattered acoustic signals, and the Falmouth Scientific ACM, which measures changes in travel time of acoustic signals between pairs of transducers. Some results from the Doppler-based Sontek Argonaut and the travel-time-based Nobska MAVS are also reported. This paper concentrates on the fidelity of the speed measurement but also presents some results related to the accuracy of the direction measurement. Two procedures were used to compare the instruments. In one, different instruments were placed close to one another on three different deep-ocean moorings. These tests showed that the RCM11 measures consistently lower speeds than either a vector averaging current meter or a vector measuring current meter, both more traditional instruments with mechanical velocity sensors. The Aquadopp in use at the time, but since updated to address accuracy problems in low scattering environments, was biased high. A second means of testing involved comparing the appropriate velocity component of each instrument with the rate of change of pressure when they were lowered from a ship. Results from this procedure revealed no depth dependence or measurable bias in the RCM11 data, but did show biases in both the Aquadopp and Argonaut Doppler-based instruments that resulted from low signal-to-noise ratios in the clear, low scattering conditions beneath the thermocline. Improvements in the design of the latest Aquadopp have reduced this bias to a level that is not significant.
    Description: This material is based upon work supported by the National Science Foundation under Grant 9810641.
    Keywords: Currents ; Acoustic measurements ; In situ sensors
    Repository Name: Woods Hole Open Access Server
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  • 3
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    Shelf circulation and cross-shelf transport out of a bay driven by eddies from an open-ocean current. Part I : interaction between a barotropic vortex and a steplike topography (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): 889–910, doi:10.1175/2010JPO4496.1.
    Description: This paper examines interaction between a barotropic point vortex and a steplike topography with a bay-shaped shelf. The interaction is governed by two mechanisms: propagation of topographic Rossby waves and advection by the forcing vortex. Topographic waves are supported by the potential vorticity (PV) jump across the topography and propagate along the step only in one direction, having higher PV on the right. Near one side boundary of the bay, which is in the wave propagation direction and has a narrow shelf, waves are blocked by the boundary, inducing strong out-of-bay transport in the form of detached crests. The wave–boundary interaction as well as out-of-bay transport is strengthened as the minimum shelf width is decreased. The two control mechanisms are related differently in anticyclone- and cyclone-induced interactions. In anticyclone-induced interactions, the PV front deformations are moved in opposite directions by the point vortex and topographic waves; a topographic cyclone forms out of the balance between the two opposing mechanisms and is advected by the forcing vortex into the deep ocean. In cyclone-induced interactions, the PV front deformations are moved in the same direction by the two mechanisms; a topographic cyclone forms out of the wave–boundary interaction but is confined to the coast. Therefore, anticyclonic vortices are more capable of driving water off the topography. The anticyclone-induced transport is enhanced for smaller vortex–step distance or smaller topography when the vortex advection is relatively strong compared to the wave propagation mechanism.
    Description: Y. Zhang acknowledges the support of theMIT-WHOI Joint Programin Physical Oceanography, NSF OCE-9901654 and OCE-0451086. J. Pedlosky acknowledges the support of NSF OCE- 9901654 and OCE-0451086.
    Keywords: Transport ; Eddies ; Barotropic flow ; Topographic effects ; Vortices ; Currents ; Potential vorticity ; Rossby waves
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  • 4
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    Improving HF radar estimates of surface currents using signal quality metrics, with application to the MVCO high-resolution radar system (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 Atmospheric and Oceanic Technology 29 (2012): 1377–1390, doi:10.1175/JTECH-D-11-00160.1.
    Description: Estimates of surface currents over the continental shelf are now regularly made using high-frequency radar (HFR) systems along much of the U.S. coastline. The recently deployed HFR system at the Martha’s Vineyard Coastal Observatory (MVCO) is a unique addition to these systems, focusing on high spatial resolution over a relatively small coastal ocean domain with high accuracy. However, initial results from the system showed sizable errors and biased estimates of M2 tidal currents, prompting an examination of new methods to improve the quality of radar-based velocity data. The analysis described here utilizes the radial metric output of CODAR Ocean Systems’ version 7 release of the SeaSonde Radial Site Software Suite to examine both the characteristics of the received signal and the output of the direction-finding algorithm to provide data quality controls on the estimated radial currents that are independent of the estimated velocity. Additionally, the effect of weighting spatial averages of radials falling within the same range and azimuthal bin is examined to account for differences in signal quality. Applied to two month-long datasets from the MVCO high-resolution system, these new methods are found to improve the rms difference comparisons with in situ current measurements by up to 2 cm s−1, as well as reduce or eliminate observed biases of tidal ellipses estimated using standard methods.
    Description: 2013-03-01
    Keywords: Coastal flows ; Currents ; Data processing ; Data quality control ; In situ atmospheric observations ; Remote sensing
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Wind-driven cross-equatorial flow in the Indian Ocean (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): 2234–2253, doi:10.1175/JPO-D-12-033.1.
    Description: Meridional velocity, mass, and heat transport in the equatorial oceans are difficult to estimate because of the nonapplicability of the geostrophic balance. For this purpose a steady-state model is utilized in the equatorial Indian Ocean using NCEP wind stress and temperature and salinity data from the World Ocean Atlas 2005 (WOA05) and Argo. The results show a Somali Current flowing to the south during the winter monsoon carrying −11.5 ± 1.3 Sv (1 Sv ≡ 106 m3 s−1) and −12.3 ± 0.3 Sv from WOA05 and Argo, respectively. In the summer monsoon the Somali Current reverses to the north transporting 16.8 ± 1.2 Sv and 19.8 ± 0.6 Sv in the WOA05 and Argo results. Transitional periods are considered together and in consequence, there is not a clear Somali Current present in this period. Model results fit with in situ measurements made around the region, although Argo data results are quite more realistic than WOA05 data results.
    Description: This study has been partly funded by the MOC Project (CTM 2008- 06438) and the Spanish contribution to the Argo network (AC2009 ACI2009-0998), financed by the Spanish Government and Feder.
    Description: 2013-06-01
    Keywords: Indian Ocean ; Subtropics ; Currents ; Ocean circulation ; Transport ; Wind stress
    Repository Name: Woods Hole Open Access Server
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  • 6
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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
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  • 7
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    Laboratory experiments on the interaction of a buoyant coastal current with a canyon : application to the East Greenland Current (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): 1258-1271, doi:10.1175/2008JPO4028.1.
    Description: This paper presents a set of laboratory experiments focused on how a buoyant coastal current flowing over a sloping bottom interacts with a canyon and what controls the separation, if any, of the current from the upstream canyon bend. The results show that the separation of a buoyant coastal current depends on the current width W relative to the radius of curvature of the bathymetry ρc. The flow moved across the mouth of the canyon (i.e., separated) for W/ρc 〉 1, in agreement with previous results. The present study extends previous work by examining both slope-controlled and surface-trapped currents, and using a geometry specific to investigating buoyant current–canyon interaction. The authors find that, although bottom friction is important in setting the position of the buoyant front, the separation process driven by the inertia of the flow could overcome even the strongest bathymetric influence. Application of the laboratory results to the East Greenland Current (EGC), an Arctic-origin buoyant current that is observed to flow in two branches south of Denmark Strait, suggests that the path of the EGC is influenced by the large canyons cutting across the shelf, as the range of W/ρc in the ocean spans those observed in the laboratory. What causes the formation of a two-branched EGC structure downstream of the Kangerdlugssuaq Canyon (68°N, 32°W) is still unclear, but potential mechanisms are discussed.
    Description: This work was partially funded by NSF Grant OCE-0450658. DS also received support from the Academic Programs Office of the Woods Hole Oceanographic Institution, while CC had partial support from NSF OCE-0350891.
    Keywords: Coastal flows ; Buoyancy ; Currents ; Experimental design ; Topographic effects
    Repository Name: Woods Hole Open Access Server
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  • 8
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    Interannual variability in the pathways of the North Atlantic Current over the Mid-Atlantic Ridge and the impact of topography (2010)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2008. 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 38 (2008): 104–120, doi:10.1175/2007JPO3686.1.
    Description: Recent studies have indicated that the North Atlantic Ocean subpolar gyre circulation undergoes significant interannual-to-decadal changes in response to variability in atmospheric forcing. There are also observations, however, suggesting that the southern limb of the subpolar gyre, namely, the eastward-flowing North Atlantic Current (NAC), may be quasi-locked to particular latitudes in the central North Atlantic by fracture zones (gaps) in the Mid-Atlantic Ridge. This could constrain the current’s ability to respond to variability in forcing. In the present study, subsurface float trajectories at 100–1000 m collected during 1997–99 and satellite-derived surface geostrophic velocities from 1992 to 2006 are used to provide an improved description of the detailed pathways of the NAC over the ridge and their relationship to bathymetry. Both the float and satellite observations indicate that in 1997–99, the northern branch of the NAC was split into two branches as it crossed the ridge, one quasi-locked to the Charlie–Gibbs Fracture Zone (CGFZ; 52°–53°N) and the other to the Faraday Fracture Zone (50°–51°N). The longer satellite time series shows, however, that this pattern did not persist outside the float sampling period and that other branching modes persisted for one or more years, including an approximately 12-month time period in 2002–03 when the strongest eastward flow over the ridge was at 49°N. Schott et al. showed how northward excursions of the NAC can temporarily block the westward flow of the Iceland–Scotland Overflow Water through the CGFZ. From the 13-yr time series of surface geostrophic velocity, it is estimated that such blocking may occur on average 6% of the time, although estimates for any given 12-month period range from 0% to 35%.
    Description: This research was supported by National Science Foundation Grants OCE-9531877 to the Woods Hole Oceanographic Institution (WHOI) and OCE-9906775 to the University of Rhode Island, by the WHOI Summer Student Fellowship Program, and by the Lawrence J. Pratt and Melinda M. Hall Endowed Fund for Interdisciplinary Research at the Woods Hole Oceanographic Institution.
    Keywords: Currents ; Topographic effects ; Interannual variability ; Forcing ; Gyres
    Repository Name: Woods Hole Open Access Server
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  • 9
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    Observations and a model of the mean circulation over the Middle Atlantic Bight continental shelf (2010)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2008. 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 38 (2008): 1203–1221, doi:10.1175/2007JPO3768.1.
    Description: Analyses of current time series longer than 200 days from 33 sites over the Middle Atlantic Bight continental shelf reveal a consistent mean circulation pattern. The mean depth-averaged flow is equatorward, alongshelf, and increases with increasing water depth from 3 cm s−1 at the 15-m isobath to 10 cm s−1 at the 100-m isobath. The mean cross-shelf circulation exhibits a consistent cross-shelf and vertical structure. The near-surface flow is typically offshore (positive, range −3 to 6 cm s−1). The interior flow is onshore and remarkably constant (−0.2 to −1.4 cm s−1). The near-bottom flow increases linearly with increasing water depth from −1 cm s−1 (onshore) in shallow water to 4 cm s−1 (offshore) at the 250-m isobath over the slope, with the direction reversal near the 50-m isobath. A steady, two-dimensional model (no along-isobath variations in the flow) reproduces the main features of the observed circulation pattern. The depth-averaged alongshelf flow is primarily driven by an alongshelf pressure gradient (sea surface slope of 3.7 × 10−8 increasing to the north) and an opposing mean wind stress that also drives the near-surface offshore flow. The alongshelf pressure gradient accounts for both the increase in the alongshelf flow with water depth and the geostrophic balance onshore flow in the interior. The increase in the near-bottom offshore flow with water depth is due to the change in the relative magnitude of the contributions from the geostrophic onshore flow that dominates in shallow water and the offshore flow driven by the bottom stress that dominates in deeper water.
    Description: This research was funded by Ocean Sciences Division of the National Science Foundation under Grants OCE-820773, OCE-841292, and OCE-848961.
    Keywords: Ocean models ; Ocean circulation ; Continental shelf ; Currents ; In situ observations
    Repository Name: Woods Hole Open Access Server
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  • 10
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    Western Arctic shelfbreak eddies : formation and transport (2010)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2008. 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 38 (2008): 1644-1668, doi:10.1175/2007JPO3829.1.
    Description: The mean structure and time-dependent behavior of the shelfbreak jet along the southern Beaufort Sea, and its ability to transport properties into the basin interior via eddies are explored using high-resolution mooring data and an idealized numerical model. The analysis focuses on springtime, when weakly stratified winter-transformed Pacific water is being advected out of the Chukchi Sea. When winds are weak, the observed jet is bottom trapped with a low potential vorticity core and has maximum mean velocities of O(25 cm s−1) and an eastward transport of 0.42 Sv (1 Sv ≡ 106 m3 s−1). Despite the absence of winds, the current is highly time dependent, with relative vorticity and twisting vorticity often important components of the Ertel potential vorticity. An idealized primitive equation model forced by dense, weakly stratified waters flowing off a shelf produces a mean middepth boundary current similar in structure to that observed at the mooring site. The model boundary current is also highly variable, and produces numerous strong, small anticyclonic eddies that transport the shelf water into the basin interior. Analysis of the energy conversion terms in both the mooring data and the numerical model indicates that the eddies are formed via baroclinic instability of the boundary current. The structure of the eddies in the basin interior compares well with observations from drifting ice platforms. The results suggest that eddies shed from the shelfbreak jet contribute significantly to the offshore flux of heat, salt, and other properties, and are likely important for the ventilation of the halocline in the western Arctic Ocean. Interaction with an anticyclonic basin-scale circulation, meant to represent the Beaufort gyre, enhances the offshore transport of shelf water and results in a loss of mass transport from the shelfbreak jet.
    Description: This study was supported by the National Science Foundation Office of Polar Programs under Grants 0421904 and 035268 (MS), and by the Office of Naval Research Grant N00014-02-1-0317 (RP and PF). Analysis by AJP was supported by the Office of Naval Research under Grant N00014-97-1-0135 and by the National Science Foundation under Grant OPP-9815303.
    Keywords: Arctic ; Eddies ; Transport ; Currents ; Jets
    Repository Name: Woods Hole Open Access Server
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  • 11
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    The western North Atlantic shelfbreak current system in summer (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): 2509-2533, doi:10.1175/JPO3123.1.
    Description: Twelve years of historical hydrographic data, spanning the period 1990–2001, are analyzed to examine the along-stream evolution of the western North Atlantic Ocean shelfbreak front and current, following its path between the west coast of Greenland and the Middle Atlantic Bight. Over 700 synoptic sections are used to construct a mean three-dimensional description of the summer shelfbreak front and to quantify the along-stream evolution in properties, including frontal strength and grounding position. Results show that there are actually two fronts in the northern part of the domain—a shallow front located near the shelf break and a deeper front centered in the core of Irminger Water over the upper slope. The properties of the deeper Irminger front erode gradually to the south, and the front disappears entirely near the Grand Banks of Newfoundland. The shallow shelfbreak front is identifiable throughout the domain, and its properties exhibit large variations from north to south, with the largest changes occurring near the Tail of the Grand Banks. Despite these structural changes, and large variations in topography, the foot of the shelfbreak front remains within 20 km of the shelf break. The hydrographic sections are also used to examine the evolution of the baroclinic velocity field and its associated volume transport. The baroclinic velocity structure consists of a single velocity core that is stronger and penetrates deeper where the Irminger front is present. The baroclinic volume transport decreases by equal amounts at the southern end of the Labrador Shelf and at the Tail of the Grand Banks. Overall, the results suggest that the Grand Banks is a geographically critical location in the North Atlantic shelfbreak system.
    Description: This work was supported by the National Science Foundation under Grants OCE00- 95261 (PF) and OCE-0450658 (RP).
    Keywords: Continental shelf ; Currents ; Atlantic Ocean ; Fronts ; Transport
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  • 12
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    Strengthening of the Pacific Equatorial Undercurrent in the SODA reanalysis : mechanisms, ocean dynamics, and implications (2014)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2014. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 27 (2014): 2405–2416, doi:10.1175/JCLI-D-13-00359.1.
    Description: Several recent studies utilizing global climate models predict that the Pacific Equatorial Undercurrent (EUC) will strengthen over the twenty-first century. Here, historical changes in the tropical Pacific are investigated using the Simple Ocean Data Assimilation (SODA) reanalysis toward understanding the dynamics and mechanisms that may dictate such a change. Although SODA does not assimilate velocity observations, the seasonal-to-interannual variability of the EUC estimated by SODA corresponds well with moored observations over a ~20-yr common period. Long-term trends in SODA indicate that the EUC core velocity has increased by 16% century−1 and as much as 47% century−1 at fixed locations since the mid-1800s. Diagnosis of the zonal momentum budget in the equatorial Pacific reveals two distinct seasonal mechanisms that explain the EUC strengthening. The first is characterized by strengthening of the western Pacific trade winds and hence oceanic zonal pressure gradient during boreal spring. The second entails weakening of eastern Pacific trade winds during boreal summer, which weakens the surface current and reduces EUC deceleration through vertical friction. EUC strengthening has important ecological implications as upwelling affects the thermal and biogeochemical environment. Furthermore, given the potential large-scale influence of EUC strength and depth on the heat budget in the eastern Pacific, the seasonal strengthening of the EUC may help reconcile paradoxical observations of Walker circulation slowdown and zonal SST gradient strengthening. Such a process would represent a new dynamical “thermostat” on CO2-forced warming of the tropical Pacific Ocean, emphasizing the importance of ocean dynamics and seasonality in understanding climate change projections.
    Description: EJDis supported by NSFGrantsOCE-1031971 and OCE-1233282. KBK is supported by NSF Grant OCE-1233282.
    Description: 2014-09-15
    Keywords: Tropics ; Currents ; Ocean dynamics ; Atmosphere-ocean interaction ; Climate variability ; Reanalysis data
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  • 13
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    The Equatorial Undercurrent and TAO sampling bias from a decade at SEA (2014)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2014. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 21 (2014): 2015–2025, doi:10.1175/JTECH-D-13-00262.1.
    Description: The NOAA Tropical Atmosphere Ocean (TAO) moored array has, for three decades, been a valuable resource for monitoring and forecasting El Niño–Southern Oscillation and understanding physical oceanographic as well as coupled processes in the tropical Pacific influencing global climate. Acoustic Doppler current profiler (ADCP) measurements by TAO moorings provide benchmarks for evaluating numerical simulations of subsurface circulation including the Equatorial Undercurrent (EUC). Meanwhile, the Sea Education Association (SEA) has been collecting data during repeat cruises to the central equatorial Pacific Ocean (160°–126°W) throughout the past decade that provide useful cross validation and quantitative insight into the potential for stationary observing platforms such as TAO to incur sampling biases related to the strength of the EUC. This paper describes some essential sampling characteristics of the SEA dataset, compares SEA and TAO velocity measurements in the vicinity of the EUC, shares new insight into EUC characteristics and behavior only observable in repeat cross-equatorial sections, and estimates the sampling bias incurred by equatorial TAO moorings in their estimates of the velocity and transport of the EUC. The SEA high-resolution ADCP dataset compares well with concurrent TAO measurements (RMSE = 0.05 m s−1; R2 = 0.98), suggests that the EUC core meanders sinusoidally about the equator between ±0.4° latitude, and reveals a mean sampling bias of equatorial measurements (e.g., TAO) of the EUC’s zonal velocity of −0.14 ± 0.03 m s−1 as well as a ~10% underestimation of EUC volume transport. A bias-corrected monthly record and climatology of EUC strength at 140°W for 1990–2010 is presented.
    Description: The authors thank the NSF Physical Oceanography program (OCE-1233282) and the WHOI Academic Programs Office for funding.
    Description: 2015-03-01
    Keywords: Pacific Ocean ; Tropics ; Currents ; Ocean dynamics ; Buoy observations ; Sampling
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  • 14
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    Absolute velocity estimates from autonomous underwater gliders equipped with Doppler current profilers (2017)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 34 (2017): 309-333, doi:10.1175/JTECH-D-16-0156.1.
    Description: Doppler current profilers on autonomous underwater gliders measure water velocity relative to the moving glider over vertical ranges of O(10) m. Measurements obtained with 1-MHz Nortek acoustic Doppler dual current profilers (AD2CPs) on Spray gliders deployed off Southern California, west of the Galápagos Archipelago, and in the Gulf Stream are used to demonstrate methods of estimating absolute horizontal velocities in the upper 1000 m of the ocean. Relative velocity measurements nearest to a glider are used to infer dive-dependent flight parameters, which are then used to correct estimates of absolute vertically averaged currents to account for the accumulation of biofouling during months-long glider missions. The inverse method for combining Doppler profiler measurements of relative velocity with absolute references to estimate profiles of absolute horizontal velocity is reviewed and expanded to include additional constraints on the velocity solutions. Errors arising from both instrumental bias and decreased abundance of acoustic scatterers at depth are considered. Though demonstrated with measurements from a particular combination of platform and instrument, these techniques should be applicable to other combinations of gliders and Doppler current profilers.
    Description: Spray glider missions were supported by the National Science Foundation (OCE-1232971, OCE-1233282), the National Oceanic and Atmospheric Administration (NA10OAR4320156, NA15OAR4320071), Eastman Chemical Company, the Oceans and Climate Change Institute at WHOI, and the W. Van Alan Clark Jr. Chair for Excellence in Oceanography at WHOI. RET acknowledges additional support for analysis and publication from the National Science Foundation (OCE-1633911).
    Description: 2017-07-31
    Keywords: Currents ; Acoustic measurements/effects ; Data processing ; Data quality control ; Profilers ; Inverse methods
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  • 15
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    The occurrence, drivers, and implications of submesoscale eddies on the Martha’s Vineyard Inner Shelf (2016)
    American Meteorological Society
    Details
    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): 2645-2662, doi:10.1175/JPO-D-15-0191.1.
    Description: The occurrence, drivers, and implications of small-scale O(2–5) km diameter coherent vortices, referred to as submesoscale eddies, over the inner shelf south of Martha’s Vineyard, Massachusetts, are examined using high-frequency (HF), radar-based, high-resolution (400 m) observations of surface currents. Within the 300 km2 study area, eddies occurred at rates of 1 and 4 day−1 in winter and summer, respectively. Most were less than 5 h in duration, smaller than 4 km in diameter, and rotated less than once over their lifespan; 60% of the eddies formed along the eastern edge of study area, adjacent to Wasque Shoal, and moved westward into the interior, often with relative vorticity greater than f. Eddy generation was linked to vortex stretching on the ebb and flood tide as well as the interaction of the spatially variable tide and the wind-driven currents; however, these features had complex patterns of surface divergence and stretching. Eddies located away from Wasque Shoal were related to the movement of wind-driven surface currents, as wind direction controlled where eddies formed as well as density effects. Using an analysis of particles advected within the radar-based surface currents, the observed eddies were found to be generally leaky, losing 60%–80% of particles over their lifespan, but still more retentive than the background flow. As a result, the combined translation and rotational effects of the observed eddies were an important source of lateral exchange for surface waters over the inner shelf.
    Description: The HF radar data utilized here were obtained using internal funding from the Woods Hole Oceanographic Institution. The analysis was supported by NSF OCE Grant 1332646.
    Description: 2017-02-19
    Keywords: Geographic location/entity ; Continental shelf/slope ; Circulation/ Dynamics ; Currents ; Eddies ; Observational techniques and algorithms ; Radars/Radar observations
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  • 16
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    Observing the Galápagos–EUC interaction : insights and challenges (2011)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2010. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 40 (2010): 2768–2777, doi:10.1175/2010JPO4461.1.
    Description: Although sustained observations yield a description of the mean equatorial current system from the western Pacific to the eastern terminus of the Tropical Atmosphere Ocean (TAO) array, a comprehensive observational dataset suitable for describing the structure and pathways of the Equatorial Undercurrent (EUC) east of 95°W does not exist and therefore climate models are unconstrained in a region that plays a critical role in ocean–atmosphere coupling. Furthermore, ocean models suggest that the interaction between the EUC and the Galápagos Islands (92°W) has a striking effect on the basic state and coupled variability of the tropical Pacific. To this end, the authors interpret historical measurements beginning with those made in conjunction with the discovery of the Pacific EUC in the 1950s, analyze velocity measurements from an equatorial TAO mooring at 85°W, and analyze a new dataset from archived shipboard ADCP measurements. Together, the observations yield a possible composite description of the EUC structure and pathways in the eastern equatorial Pacific that may be useful for model validation and guiding future observation.
    Description: Karnauskas acknowledges the WHOI Penzance Endowed Fund in Support of Assistant Scientists.
    Keywords: Atmosphere-ocean interaction ; Currents ; In situ observations ; Model evaluation/performance ; Pacific Ocean ; Tropics
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    Anisotropic material transport by eddies and eddy-driven currents in a model of the North Atlantic (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): 3162-3175, doi:10.1175/2009JPO4239.1.
    Description: This study analyzes anisotropic properties of the material transport by eddies and eddy-driven zonal jets in a general circulation model of the North Atlantic through the analysis of Lagrangian particle trajectories. Spreading rates—defined here as half the rate of change in the particle dispersion—in the zonal direction systematically exceed the meridional rates by an order of magnitude. Area-averaged values for the upper-ocean zonal and meridional spreading rates are approximately 8100 and 1400 m2 s−1, respectively, and in the deep ocean they are 2400 and 200 m2 s−1. The results demonstrate that this anisotropy is mainly due to the action of the transient eddies and not to the shear dispersion associated with the time-mean jets. This property is consistent with the fact that eddies in this study have zonally elongated shapes. With the exception of the upper-ocean subpolar gyre, eddies also cause the superdiffusive zonal spreading, significant variations in the spreading rate in the vertical and meridional directions, and the difference between the westward and eastward spreading.
    Description: Funding for IK was provided by NSF Grants OCE 0346178, 0749722, and 0842834. Funding for PB was provided by NSF Grants OCE 0344094 and OCE 0725796 and by the research grant from the Newton Trust of the University of Cambridge. For JP the acknowledgement is to NSF OCE-0451086.
    Keywords: Eddies ; Transport ; Currents ; North Atlantic Ocean
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    An oceanic current against the wind : how does Taiwan island steer warm water into the East China Sea? (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): 2563-2569, doi:10.1175/JPO3134.1.
    Description: Along the Taiwan Strait (〈100 m in depth) a northeastward flow persists in all seasons despite the annually averaged wind stress that is strongly southwestward. The forcing mechanism of this countercurrent is examined by using a simple ocean model. The results from a suite of experiments demonstrate that it is the Kuroshio that plays the deciding role for setting the flow direction along the Taiwan Strait. The momentum balance along the strait is mainly between the wind stress, friction, and pressure gradient. Since both wind stress and friction act against the northward flow, it is most likely the pressure gradient that forces the northward flow, as noted in some previous studies. What remains unknown is why there is a considerable pressure difference between the southern and northern strait. The Kuroshio flows along the east coast of Taiwan, and thus the western boundary current layer dynamics applies there. Integrating the momentum equation along Taiwan’s east coast shows that there must be a pressure difference between the southern and the northern tip of Taiwan to counter a considerable friction exerted by the mighty Kuroshio. This same pressure difference is also felt on the other side of the island where it forces the northward flow through Taiwan Strait. The model shows that the local wind stress acts to dampen this northward flow. This mechanism can be illustrated by an integral constraint for flow around an island.
    Description: This study has been supported by National Science Foundation through Grant OCE-0351055.
    Keywords: Ocean circulation ; Wind ; Currents
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  • 19
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    Transport and dynamics of the Panay Sill overflow in the Philippine Seas (2011)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2010. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 40 (2010): 2679–2695, doi:10.1175/2010JPO4395.1.
    Description: Observations of stratification and currents between June 2007 and March 2009 reveal a strong overflow between 400- and 570-m depth from the Panay Strait into the Sulu Sea. The overflow water is derived from approximately 400 m deep in the South China Sea. Temporal mean velocity is greater than 0.75 m s−1 at 50 m above the 570-m Panay Sill. Empirical orthogonal function analysis of a mooring time series shows that the flow is dominated by the bottom overflow current with little seasonal variance. The overflow does not descend below 1250 m in the Sulu Sea but rather settles above high-salinity deep water derived from the Sulawesi Sea. The mean observed overflow transport at the sill is 0.32 × 106 m3 s−1. The observed transport was used to calculate a bulk diapycnal diffusivity of 4.4 × 10−4 m2 s−1 within the Sulu Sea slab (575–1250 m) ventilated from Panay Strait. Analysis of Froude number variation across the sill shows that the flow is hydraulically controlled. A suitable hydraulic control model shows overflow transport equivalent to the observed overflow. Thorpe-scale estimates show turbulent dissipation rates up to 5 × 10−7 W kg−1 just downstream of the supercritical to subcritical flow transition, suggesting a hydraulic jump downstream of the sill.
    Description: This work was supported by the Office of Naval Research Grant N00014-09-1-0582 to Lamont-Doherty Earth Observatory of Columbia University; Grants ONR-13759000 and N00014-09-1-0582 to the Woods Hole Oceanographic Institution; Grant ONR-N00014-06-1-0690 to Scripps Institute of Oceanography; and a National Defense Science and Engineering Graduate Fellowship.
    Keywords: Transport ; Dynamics ; Topographic effects ; Currents ; Empirical orthogonal functions
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  • 20
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    Near-surface transport pathways in the north Atlantic Ocean : looking for throughput from the subtropical to the subpolar gyre (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): 911–925, doi:10.1175/2011JPO4498.1.
    Description: Motivated by discrepancies between Eulerian transport estimates and the behavior of Lagrangian surface drifters, near-surface transport pathways and processes in the North Atlantic are studied using a combination of data, altimetric surface heights, statistical analysis of trajectories, and dynamical systems techniques. Particular attention is paid to the issue of the subtropical-to-subpolar intergyre fluid exchange. The velocity field used in this study is composed of a steady drifter-derived background flow, upon which a time-dependent altimeter-based perturbation is superimposed. This analysis suggests that most of the fluid entering the subpolar gyre from the subtropical gyre within two years comes from a narrow region lying inshore of the Gulf Stream core, whereas fluid on the offshore side of the Gulf Stream is largely prevented from doing so by the Gulf Stream core, which acts as a strong transport barrier, in agreement with past studies. The transport barrier near the Gulf Stream core is robust and persistent from 1992 until 2008. The qualitative behavior is found to be largely independent of the Ekman drift.
    Description: This work was supported by the National Science Foundation Grants CMG-82469600 and CMG-82579600 and by the Office of Naval Research Grant ONR-13108700.
    Keywords: Atlantic Ocean ; Transport ; Gyres ; Lagrangian circulation/transport ; Tracers ; Currents ; Meridional overturning circulation
    Repository Name: Woods Hole Open Access Server
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  • 21
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    Coral reef drag coefficients – water depth dependence (2017)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 47 (2017): 1061-1075, doi:10.1175/JPO-D-16-0248.1.
    Description: A major challenge in modeling the circulation over coral reefs is uncertainty in the drag coefficient because existing estimates span two orders of magnitude. Current and pressure measurements from five coral reefs are used to estimate drag coefficients based on depth-average flow, assuming a balance between the cross-reef pressure gradient and the bottom stress. At two sites wind stress is a significant term in the cross-reef momentum balance and is included in estimating the drag coefficient. For the five coral reef sites and a previous laboratory study, estimated drag coefficients increase as the water depth decreases consistent with open channel flow theory. For example, for a typical coral reef hydrodynamic roughness of 5 cm, observational estimates, and the theory indicate that the drag coefficient decreases from 0.4 in 20 cm of water to 0.005 in 10 m of water. Synthesis of results from the new field observations with estimates from previous field and laboratory studies indicate that coral reef drag coefficients range from 0.2 to 0.005 and hydrodynamic roughnesses generally range from 2 to 8 cm. While coral reef drag coefficients depend on factors such as physical roughness and surface waves, a substantial fraction of the scatter in estimates of coral reef drag coefficients is due to variations in water depth.
    Description: The Red Sea field program was supported by Awards USA 00002 and KSA 00011 made by KAUST to S. Lentz and J. Churchill. The Palau field program was funded by NSF Award OCE-1220529.
    Keywords: Ocean ; Currents ; Wind stress ; Boundary layer ; Sea level ; Tides
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    Deep eddies in the Gulf of Mexico observed with floats (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): 2703-2719, doi:10.1175/JPO-D-17-0245.1.
    Description: A new set of deep float trajectory data collected in the Gulf of Mexico from 2011 to 2015 at 1500- and 2500-m depths is analyzed to describe mesoscale processes, with particular attention paid to the western Gulf. Wavelet analysis is used to identify coherent eddies in the float trajectories, leading to a census of the basinwide coherent eddy population and statistics of the eddies’ kinematic properties. The eddy census reveals a new formation region for anticyclones off the Campeche Escarpment, located northwest of the Yucatan Peninsula. These eddies appear to form locally, with no apparent direct connection to the upper layer. Once formed, the eddies drift westward along the northern edge of the Sigsbee Abyssal Gyre, located in the southwestern Gulf of Mexico over the abyssal plain. The formation mechanism and upstream sources for the Campeche Escarpment eddies are explored: the observational data suggest that eddy formation may be linked to the collision of a Loop Current eddy with the western boundary of the Gulf. Specifically, the disintegration of a deep dipole traveling under the Loop Current eddy Kraken, caused by the interaction with the northwestern continental slope, may lead to the acceleration of the abyssal gyre and the boundary current in the Bay of Campeche region.
    Description: The authors were supported by the Department of the Interior, Bureau of Ocean Energy Management (BOEM), Contract M10PC00112 to Leidos, Inc., Raleigh, North Carolina.
    Description: 2019-05-07
    Keywords: Abyssal circulation ; Currents ; Eddies ; Mesoscale processes ; Trajectories ; In situ oceanic observations
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  • 23
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    Influence of the meridional shifts of the Kuroshio and the Oyashio Extensions on the atmospheric circulation (2011)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    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 Climate 24 (2011): 762-777, doi:10.1175/2010JCLI3731.1.
    Description: The meridional shifts of the Oyashio Extension (OE) and of the Kuroshio Extension (KE), as derived from high-resolution monthly sea surface temperature (SST) anomalies in 1982–2008 and historical temperature profiles in 1979–2007, respectively, are shown based on lagged regression analysis to significantly influence the large-scale atmospheric circulation. The signals are independent from the ENSO teleconnections, which were removed by seasonally varying, asymmetric regression onto the first three principal components of the tropical Pacific SST anomalies. The response to the meridional shifts of the OE front is equivalent barotropic and broadly resembles the North Pacific Oscillation/western Pacific pattern in a positive phase for a northward frontal displacement. The response may reach 35 m at 250 hPa for a typical OE shift, a strong sensitivity since the associated SST anomaly is 0.5 K. However, the amplitude, but not the pattern or statistical significance, strongly depends on the lag and an assumed 2-month atmospheric response time. The response is stronger during fall and winter and when the front is displaced southward. The response to the northward KE shifts primarily consists of a high centered in the northwestern North Pacific and hemispheric teleconnections. The response is also equivalent barotropic, except near Kamchatka, where it tilts slightly westward with height. The typical amplitude is half as large as that associated with OE shifts.
    Description: This work was supported in part by the L’Institut universitaire de France (CF), the WHOI Heyman fellowship, and the NASAGrant withAwardNNX09AF35G(Y.-O. K), and grants through NOAA’s Climate Variability and Predictability Program (MAA).
    Keywords: Atmospheric circulation ; Currents
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    Four current meter models compared in strong currents in Drake Passage (2014)
    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 Atmospheric and Oceanic Technology 30 (2013): 2465–2477, doi:10.1175/JTECH-D-13-00032.1.
    Description: Seven current meters representing four models on a stiffly buoyed mooring were placed for an 11-month deployment to intercompare their velocity measurements: two vector-measuring current meters (VMCMs), two Aanderaa recording current meter (RCM) 11s, two Aanderaa SEAGUARDs, and a Nortek Aquadopp. The current meters were placed 6-m apart from each other at about 4000-m depth in an area of Drake Passage expected to have strong currents, nearly independent of depth near the bottom. Two high-current events occurred in bursts of semidiurnal pulses lasting several days, one with peak speeds up to 67 cm s−1 and the other above 35 cm s−1. The current-speed measurements all agreed within 7% of the median value when vector averaged over simultaneous time intervals. The VMCMs, chosen as the reference measurements, were found to measure the median of the mean-current magnitudes. The RCM11 and SEAGUARD current speeds agreed within 2% of the median at higher speeds (35–67 cm s−1), whereas in lower speed ranges (0–35 cm s−1) the vector-averaged speeds for the RCM11 and SEAGUARD were 4%–5% lower and 3%–5% higher than the median, respectively. The shorter-record Aquadopp current speeds were about 6% higher than the VMCMs over the range (0–40 cm s−1) encountered.
    Description: This work was supported by U.S. National Science Foundation Grants ANT-0635437 and ANT-0636493.
    Description: 2014-04-01
    Keywords: Currents ; Acoustic measurements/effects ; In situ oceanic observations ; Instrumentation/sensors
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    Eulerian and Lagrangian correspondence of high-frequency radar and surface drifter data : effects of radar resolution and flow components (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 Atmospheric and Oceanic Technology 31 (2014): 945–966, doi:10.1175/JTECH-D-13-00146.1.
    Description: This study investigated the correspondence between the near-surface drifters from a mass drifter deployment near Martha’s Vineyard, Massachusetts, and the surface current observations from a network of three high-resolution, high-frequency radars to understand the effects of the radar temporal and spatial resolution on the resulting Eulerian current velocities and Lagrangian trajectories and their predictability. The radar-based surface currents were found to be unbiased in direction but biased in magnitude with respect to drifter velocities. The radar systematically underestimated velocities by approximately 2 cm s−1 due to the smoothing effects of spatial and temporal averaging. The radar accuracy, quantified by the domain-averaged rms difference between instantaneous radar and drifter velocities, was found to be about 3.8 cm s−1. A Lagrangian comparison between the real and simulated drifters resulted in the separation distances of roughly 1 km over the course of 10 h, or an equivalent separation speed of approximately 2.8 cm s−1. The effects of the temporal and spatial radar resolution were examined by degrading the radar fields to coarser resolutions, revealing the existence of critical scales (1.5–2 km and 3 h) beyond which the ability of the radar to reproduce drifter trajectories decreased more rapidly. Finally, the importance of the different flow components present during the experiment—mean, tidal, locally wind-driven currents, and the residual velocities—was analyzed, finding that, during the study period, a combination of tidal, locally wind-driven, and mean currents were insufficient to reliably reproduce, with minimal degradation, the trajectories of real drifters. Instead, a minimum combination of the tidal and residual currents was required.
    Description: I.R. was supported by the WHOI Coastal Ocean Institute Project 27040148 and by the WHOI Access to the Sea Program 27500036. I.R. and A.K. acknowledge support fromthe NSF project 83264600. A.K. acknowledges support from the Massachusetts Clean Energy Center (MassCEC) via the New England Marine Renewable Energy Center (MREC).
    Description: 2014-10-01
    Keywords: Coastal flows ; Currents ; Lagrangian circulation/transport ; Trajectories ; Radars/Radar observations
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  • 26
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    Wave-driven along-channel subtidal flows in a well-mixed ocean inlet (2014)
    John Wiley & Sons
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Geophysical Union, 2014. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 119 (2014): 2987–3001, doi:10.1002/2014JC009839.
    Description: Observations of waves, flows, and water levels collected for a month in and near a long, narrow, shallow (∼ 3000 m long, 1000 m wide, and 5 m deep), well-mixed ocean inlet are used to evaluate the subtidal (periods 〉 30 h) along-inlet momentum balance. Maximum tidal flows in the inlet were about 1.5 m/s and offshore significant wave heights ranged from about 0.5 to 2.5 m. The dominant terms in the local (across the km-wide ebb shoal) along-inlet momentum balance are the along-inlet pressure gradient, the bottom stress, and the wave radiation-stress gradient. Estimated nonlinear advective acceleration terms roughly balance in the channel. Onshore radiation-stress gradients owing to breaking waves enhance the flood flows into the inlet, especially during storms.
    Description: Funding was provided by the Office of Naval Research, the Office of the Assistant Secretary of Defense for Research and Engineering, and a National Defense Science and Engineering Graduate Fellowship.
    Description: 2014-11-20
    Keywords: Inlet ; Wind waves ; Currents ; Radiation stress
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    The equatorial current system west of the Galapagos Islands during the 2014-16 El Niño as observed by underwater gliders (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): 3-17, https://doi.org/10.1175/JPO-D-20-0064.1.
    Description: The strong El Niño of 2014–16 was observed west of the Galápagos Islands through sustained deployment of underwater gliders. Three years of observations began in October 2013 and ended in October 2016, with observations at longitudes 93° and 95°W between latitudes 2°N and 2°S. In total, there were over 3000 glider-days of data, covering over 50 000 km with over 12 000 profiles. Coverage was superior closer to the Galápagos on 93°W, where gliders were equipped with sensors to measure velocity as well as temperature, salinity, and pressure. The repeated glider transects are analyzed to produce highly resolved mean sections and maps of observed variables as functions of time, latitude, and depth. The mean sections reveal the structure of the Equatorial Undercurrent (EUC), the South Equatorial Current, and the equatorial front. The mean fields are used to calculate potential vorticity Q and Richardson number Ri. Gradients in the mean are strong enough to make the sign of Q opposite to that of planetary vorticity and to have Ri near unity, suggestive of mixing. Temporal variability is dominated by the 2014–16 El Niño, with the arrival of depressed isopycnals documented in 2014 and 2015. Increases in eastward velocity advect anomalously salty water and are uncorrelated with warm temperatures and deep isopycnals. Thus, vertical advection is important to changes in heat, and horizontal advection is relevant to changes in salt. Implications of this work include possibilities for future research, model assessment and improvement, and sustained observations across the equatorial Pacific.
    Description: We gratefully acknowledge the support of the National Science Foundation (OCE-1232971, OCE-1233282) and the Ocean Observing and Monitoring Division of the National Oceanographic and Atmospheric Administration (NA13OAR4830216).
    Keywords: Ocean ; Tropics ; Currents ; El Nino ; In situ oceanic observations
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    On the predictability of sea surface height around Palau (2021)
    American Meteorological Society
    Details
    Publication Date: 2022-05-27
    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(11), (2020): 3267–3294, https://doi.org/10.1175/JPO-D-19-0310.1.
    Description: As part of the Flow Encountering Abrupt Topography (FLEAT) program, an array of pressure-sensor equipped inverted echo sounders (PIESs) was deployed north of Palau where the westward-flowing North Equatorial Current encounters the southern end of the Kyushu–Palau Ridge in the tropical North Pacific. Capitalizing on concurrent observations from satellite altimetry, FLEAT Spray gliders, and shipboard hydrography, the PIESs’ 10-month duration hourly bottom pressure p and round-trip acoustic travel time τ records are used to examine the magnitude and predictability of sea level and pycnocline depth changes and to track signal propagations through the array. Sea level and pycnocline depth are found to vary in response to a range of ocean processes, with their magnitude and predictability strongly process dependent. Signals characterized here comprise the barotropic tides, semidiurnal and diurnal internal tides, southeastward-propagating superinertial waves, westward-propagating mesoscale eddies, and a strong signature of sea level increase and pycnocline deepening associated with the region’s relaxation from El Niño to La Niña conditions. The presence of a broad band of superinertial waves just above the inertial frequency was unexpected and the FLEAT observations and output from a numerical model suggest that these waves detected near Palau are forced by remote winds east of the Philippines. The PIES-based estimates of pycnocline displacement are found to have large uncertainties relative to overall variability in pycnocline depth, as localized deep current variations arising from interactions of the large-scale currents with the abrupt topography around Palau have significant travel time variability.
    Description: Support for this research was provided by Office of Naval Research Grants N00014-16-1-2668, N00014-18-1-2406, N00014-15-1-2488, and N00014-15-1-2622. R.C.M. was additionally supported by the Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution, with funding provided by the Weston Howland Jr. Postdoctoral Scholarship.
    Keywords: Tropics ; Currents ; Eddies ; ENSO ; Internal waves ; Mesoscale processes
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    Kinematic structure and dynamics of the Denmark Strait Overflow from ship-based observations (2021)
    American Meteorological Society
    Details
    Publication Date: 2022-05-27
    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(11), (2020): 3235–3251, https://doi.org/10.1175/JPO-D-20-0095.1.
    Description: The dense outflow through Denmark Strait is the largest contributor to the lower limb of the Atlantic meridional overturning circulation, yet a description of the full velocity field across the strait remains incomplete. Here we analyze a set of 22 shipboard hydrographic–velocity sections occupied along the Látrabjarg transect at the Denmark Strait sill, obtained over the time period 1993–2018. The sections provide the first complete view of the kinematic components at the sill: the shelfbreak East Greenland Current (EGC), the combined flow of the separated EGC, and the North Icelandic Jet (NIJ), and the northward-flowing North Icelandic Irminger Current (NIIC). The total mean transport of overflow water is 3.54 ± 0.29 Sv (1 Sv ≡ 106 m3 s−1), comparable to previous estimates. The dense overflow is partitioned in terms of water mass constituents and flow components. The mean transports of the two types of overflow water—Atlantic-origin Overflow Water and Arctic-origin Overflow Water—are comparable in Denmark Strait, while the merged NIJ–separated EGC transports 55% more water than the shelfbreak EGC. A significant degree of water mass exchange takes place between the branches as they converge in Denmark Strait. There are two dominant time-varying configurations of the flow that are characterized as a cyclonic state and a noncyclonic state. These appear to be wind-driven. A potential vorticity analysis indicates that the flow through Denmark Strait is subject to symmetric instability. This occurs at the top of the overflow layer, implying that the mixing/entrainment process that modifies the overflow water begins at the sill.
    Description: Funding for the study was provided by National Science Foundation (NSF) Grants OCE-1259618, OCE-1756361, and OCE-1558742. The German research cruises were financially supported through various EU Projects (e.g. THOR, NACLIM) and national projects (most recently TRR 181 “Energy Transfer in Atmosphere and Ocean” funded by the German Research Foundation and RACE II “Regional Atlantic Circulation and Global Change” funded by the German Federal Ministry for Education and Research). GWKM acknowledges the support of the Natural Sciences and Engineering Research Council of Canada. LP was supported by NSF Grant OCE-1657870.
    Keywords: Currents ; Instability ; Ocean circulation ; Ocean dynamics ; Potential vorticity
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    Role of the Gulf Stream and Kuroshio–Oyashio systems in large-scale atmosphere–ocean interaction : a review (2010)
    American Meteorological Society
    Details
    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 Climate 23 (2010): 3249-3281, doi:10.1175/2010JCLI3343.1.
    Description: Ocean–atmosphere interaction over the Northern Hemisphere western boundary current (WBC) regions (i.e., the Gulf Stream, Kuroshio, Oyashio, and their extensions) is reviewed with an emphasis on their role in basin-scale climate variability. SST anomalies exhibit considerable variance on interannual to decadal time scales in these regions. Low-frequency SST variability is primarily driven by basin-scale wind stress curl variability via the oceanic Rossby wave adjustment of the gyre-scale circulation that modulates the latitude and strength of the WBC-related oceanic fronts. Rectification of the variability by mesoscale eddies, reemergence of the anomalies from the preceding winter, and tropical remote forcing also play important roles in driving and maintaining the low-frequency variability in these regions. In the Gulf Stream region, interaction with the deep western boundary current also likely influences the low-frequency variability. Surface heat fluxes damp the low-frequency SST anomalies over the WBC regions; thus, heat fluxes originate with heat anomalies in the ocean and have the potential to drive the overlying atmospheric circulation. While recent observational studies demonstrate a local atmospheric boundary layer response to WBC changes, the latter’s influence on the large-scale atmospheric circulation is still unclear. Nevertheless, heat and moisture fluxes from the WBCs into the atmosphere influence the mean state of the atmospheric circulation, including anchoring the latitude of the storm tracks to the WBCs. Furthermore, many climate models suggest that the large-scale atmospheric response to SST anomalies driven by ocean dynamics in WBC regions can be important in generating decadal climate variability. As a step toward bridging climate model results and observations, the degree of realism of the WBC in current climate model simulations is assessed. Finally, outstanding issues concerning ocean–atmosphere interaction in WBC regions and its impact on climate variability are discussed.
    Description: Funding for LT was provided by the NASA-sponsored Ocean Surface Topography Science Team, under Contract 1267196 with the University of Washington, administered by the Jet Propulsion Laboratory. HN was supported in part by the Grant-in-Aid 18204044 by the Japan Society for Promotion for Science (JSPS) and the Global Environment Research Fund (S-5) of the Japanese Ministry of Environment. YK was supported by the Kerr Endowed Fund and Penzance Endowed Fund.
    Keywords: Currents ; Sea surface temperature ; Anomalies ; Large-scale motions ; Oceanic mixed layer ; Northern Hemisphere
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    Diapycnal mixing in the Antarctic Circumpolar Current (2011)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    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): 241-246, doi:10.1175/2010JPO4557.1.
    Description: The vertical dispersion of a tracer released on a density surface near 1500-m depth in the Antarctic Circumpolar Current west of Drake Passage indicates that the diapycnal diffusivity, averaged over 1 yr and over tens of thousands of square kilometers, is (1.3 ± 0.2) × 10−5 m2 s−1. Diapycnal diffusivity estimated from turbulent kinetic energy dissipation measurements about the area occupied by the tracer in austral summer 2010 was somewhat less, but still within a factor of 2, at (0.75 ± 0.07) × 10−5 m2 s−1. Turbulent diapycnal mixing of this intensity is characteristic of the midlatitude ocean interior, where the energy for mixing is believed to derive from internal wave breaking. Indeed, despite the frequent and intense atmospheric forcing experienced by the Southern Ocean, the amplitude of finescale velocity shear sampled about the tracer was similar to background amplitudes in the midlatitude ocean, with levels elevated to only 20%–50% above the Garrett–Munk reference spectrum. These results add to a long line of evidence that diapycnal mixing in the interior middepth ocean is weak and is likely too small to dictate the middepth meridional overturning circulation of the ocean.
    Description: This material is based upon work supported by the National Science Foundation Grants OCE-0622825,OCE-0622670, OCE-0622630, and OCE-0623177.
    Keywords: Diapycnal mixing ; Currents ; Antarctica ; Ocean circulation ; Meridional overturning circulation
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    The use (and misuse) of sediment traps in coral reef environments : theory, observations, and suggested protocols (2011)
    Springer
    Details
    Publication Date: 2022-05-26
    Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Coral Reefs 30 (2011): 23-38, doi:10.1007/s00338-010-0705-3.
    Description: Sediment traps are commonly used as standard tools for monitoring “sedimentation” in coral reef environments. In much of the literature where sediment traps were used to measure the effects of “sedimentation” on corals, it is clear from deployment descriptions and interpretations of the resulting data that information derived from sediment traps has frequently been misinterpreted or misapplied. Despite their widespread use in this setting, sediment traps do not provide quantitative information about “sedimentation” on coral surfaces. Traps can provide useful information about the relative magnitude of sediment dynamics if trap deployment standards are used. This conclusion is based first on a brief review of the state of knowledge of sediment trap dynamics, which has primarily focused on traps deployed high above the seabed in relatively deep water, followed by our understanding of near-bed sediment dynamics in shallow-water environments that characterize coral reefs. This overview is followed by the first synthesis of near-bed sediment trap data collected with concurrent hydrodynamic information in coral reef environments. This collective information is utilized to develop nine protocols for using sediment traps in coral reef environments, which focus on trap parameters that researchers can control such as trap height (H), trap mouth diameter (D), the height of the trap mouth above the substrate (z o ), and the spacing between traps. The hydrodynamic behavior of sediment traps and the limitations of data derived from these traps should be forefront when interpreting sediment trap data to infer sediment transport processes in coral reef environments.
    Keywords: Sediment trap ; Coral reefs ; Sedimentation ; Waves ; Currents ; Shear stress
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    3D structure of striations in the North Pacific (2022)
    American Meteorological Society
    Details
    Publication Date: 2022-06-06
    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(12),(2021): 3651–3662, https://doi.org/10.1175/JPO-D-21-0076.1.
    Description: Ocean striations are composed of alternating quasi-zonal band-like flows; this kind of organized structure of currents can be found in all the world’s oceans and seas. Previous studies have mainly been focused on the mechanisms of their generation and propagation. This study uses the spatial high-pass filtering to obtain the three-dimensional structure of ocean striations in the North Pacific in both the z coordinate and σ coordinate based on 10-yr averaged Simple Ocean Data Assimilation version 3 (SODA3) data. First, we identify an ideal-fluid potential density domain where the striations are undisturbed by the surface forcing and boundary effects. Second, using the isopycnal layer analysis, we show that on isopycnal surfaces the orientations of striations nearly follow the potential vorticity (PV) contours, while in the meridional–vertical plane the central positions of striations are generally aligned with the latitude of zero gradient of the relative PV. Our analysis provides a simple dynamical interpretation and better understanding for the role of ocean striations.
    Description: This work is supported by the National Natural Science Foundation of China (42076025, 41676021), the Key Special Project for introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) (GML2019ZD0306), the National Basic Research Program (973 Program) of China (2013CB956201). The numerical simulation is supported by the High Performance Computing Division in the South China Sea Institute of Oceanography. The authors thank Tingjin Guan for the help in enhancing drawing quality.
    Keywords: Currents ; Jets ; Mesoscale processes ; Potential vorticity ; Isopycnal coordinates
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  • 34
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    Whither the Chukchi Slope Current? (2021)
    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(6),(2020): 1717-1732, doi:10.1175/JPO-D-19-0273.1.
    Description: Recent measurements and modeling indicate that roughly half of the Pacific-origin water exiting the Chukchi Sea shelf through Barrow Canyon forms a westward-flowing current known as the Chukchi Slope Current (CSC), yet the trajectory and fate of this current is presently unknown. In this study, through the combined use of shipboard velocity data and information from five profiling floats deployed as quasi-Lagrangian particles, we delve further into the trajectory and the fate of the CSC. During the period of observation, from early September to early October 2018, the CSC progressed far to the north into the Chukchi Borderland. The northward excursion is believed to result from the current negotiating Hanna Canyon on the Chukchi slope, consistent with potential vorticity dynamics. The volume transport of the CSC, calculated using a set of shipboard transects, decreased from approximately 2 Sv (1 Sv ≡ 106 m3 s−1) to near zero over a period of 4 days. This variation can be explained by a concomitant change in the wind stress curl over the Chukchi shelf from positive to negative. After turning northward, the CSC was disrupted and four of the five floats veered offshore, with one of the floats permanently leaving the current. It is hypothesized that the observed disruption was due to an anticyclonic eddy interacting with the CSC, which has been observed previously. These results demonstrate that, at times, the CSC can get entrained into the Beaufort Gyre.
    Description: This work was principally supported by the Stratified Ocean Dynamics of the Arctic (SODA) program under ONR Grant N000141612450. S.B. wants to thank Labex iMust for supporting his research. R.S.P. acknowledges U.S. National Science Foundation Grants OPP-1702371, OPP-1733564, and PLR-1303617. P.L. acknowledges National Oceanic and Atmospheric Administration Grant NA14-OAR4320158. M.L. acknowledges National Natural Science Foundation of China Grants 41706025 and 41506018. T.P. thanks ENS de Lyon for travel support funding. The authors gratefully acknowledge the support of Steve Jayne, Pelle Robins, and Alex Ekholm at the Woods Hole Oceanographic Institution for preparation, deployment, and data provision for the ALTO floats. Chanhyung Jeon assisted in preparing and deploying the floats. The invaluable support of the crew of the R/V Sikuliaq is also gratefully acknowledged.
    Keywords: Arctic ; Continental shelf/slope ; Currents ; Mixing
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    Structure and variability of the shelfbreak East Greenland Current north of Denmark Strait (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): 2631-2646, doi:10.1175/JPO-D-17-0062.1.
    Description: Data from a mooring array deployed north of Denmark Strait from September 2011 to August 2012 are used to investigate the structure and variability of the shelfbreak East Greenland Current (EGC). The shelfbreak EGC is a surface-intensified current situated just offshore of the east Greenland shelf break flowing southward through Denmark Strait. This study identified two dominant spatial modes of variability within the current: a pulsing mode and a meandering mode, both of which were most pronounced in fall and winter. A particularly energetic event in November 2011 was related to a reversal of the current for nearly a month. In addition to the seasonal signal, the current was associated with periods of enhanced eddy kinetic energy and increased variability on shorter time scales. The data indicate that the current is, for the most part, barotropically stable but subject to baroclinic instability from September to March. By contrast, in summer the current is mainly confined to the shelf break with decreased eddy kinetic energy and minimal baroclinic conversion. No other region of the Nordic Seas displays higher levels of eddy kinetic energy than the shelfbreak EGC north of Denmark Strait during fall. This appears to be due to the large velocity variability on mesoscale time scales generated by the instabilities. The mesoscale variability documented here may be a source of the variability observed at the Denmark Strait sill.
    Description: Support for this work was provided by the Norwegian Research Council under Grant Agreement 231647 (LH and KV) and the Bergen Research Foundation under Grant BFS2016REK01 (KV). Additional funding was provided by the National Science Foundation under Grants OCE-0959381 and OCE-1558742 (RP).
    Keywords: Ocean ; Arctic ; Boundary currents ; Currents ; Stability ; Oceanic variability
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    Iceland-Scotland Overflow Water transport variability through the Charlie-Gibbs Fracture Zone and the impact of the North Atlantic Current (2017)
    John Wiley & Sons
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Geophysical Union, 2017. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 122 (2017): 6989–7012, doi:10.1002/2017JC012698.
    Description: The Charlie-Gibbs Fracture Zone (CGFZ), a deep and wide gap in the Mid-Atlantic Ridge near 52°N, is a gateway between the eastern and western subpolar regions for the Atlantic Meridional Overturning Circulation (AMOC). In 2010–2012, an eight-mooring array of current meters and temperature/salinity sensors was installed across the CGFZ between 500 m and the sea floor to measure the mean transport of westward-flowing Iceland-Scotland Overflow Water (ISOW) and investigate the impact of the eastward-flowing North Atlantic Current (NAC) on ISOW transport variability. The 22 month record mean ISOW transport through the CGFZ, −1.7 ± 0.5 Sv (95% confidence interval), is 30% lower than the previously published estimate based on 13 months of current-only measurements, −2.4 ± 1.2 Sv. The latter mean estimate may have been biased high due to the lack of continuous salinity measurements, although the two estimates are not statistically different due to strong mesoscale variability in both data sets. Empirical Orthogonal Function analysis and maps of satellite-derived absolute dynamic topography show that weak westward ISOW transport events and eastward reversals are caused by northward meanders of the NAC, with its deep-reaching eastward velocities. These results add to growing evidence that a significant fraction of ISOW exits the Iceland Basin by routes other than the CGFZ.
    Description: U.S. National Science Foundation Grant Number: OCE-0926656; Woods Hole Oceanographic Institution
    Description: 2018-03-01
    Keywords: Currents ; Eddies and mesoscale processes ; Topographic/bathymetric interactions
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  • 37
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    Sedimentation processes in a coral reef embayment : Hanalei Bay, Kauai (2009)
    Elsevier B.V.
    Details
    Publication Date: 2022-05-26
    Description: This paper is not subject to U.S. copyright. The definitive version was published in Marine Geology 264 (2009): 140-151, doi:10.1016/j.margeo.2009.05.002.
    Description: Oceanographic measurements and sediment samples were collected during the summer of 2006 as part of a multi-year study of coastal circulation and the fate of terrigenous sediment on coral reefs in Hanalei Bay, Kauai. The goal of this study was to better understand sediment dynamics in a coral reef-lined embayment where winds, ocean surface waves, and river floods are important processes. During a summer period that was marked by two wave events and one river flood, we documented significant differences in sediment trap collection rates and the composition, grain size, and magnitude of sediment transported in the bay. Sediment trap collection rates were well correlated with combined wave-current near-bed shear stresses during the non-flood periods but were not correlated during the flood. The flood's delivery of fine-grained sediment to the bay initially caused high turbidity and sediment collection rates off the river mouth but the plume dispersed relatively quickly. Over the next month, the flood deposit was reworked by mild waves and currents and the fine-grained terrestrial sediment was advected around the bay and collected in sediment traps away from the river mouth, long after the turbid surface plume was gone. The reworked flood deposits, due to their longer duration of influence and proximity to the seabed, appear to pose a greater long-term impact to benthic coral reef communities than the flood plumes themselves. The results presented here display how spatial and temporal differences in hydrodynamic processes, which result from variations in reef morphology and orientation, cause substantial variations in the deposition, residence time, resuspension, and advection of both reef-derived and fluvial sediment over relatively short spatial scales in a coral reef embayment.
    Keywords: Coral reefs ; Winds ; Waves ; Currents ; Sediment traps ; Sedimentation ; USA ; Hawaii ; Kauai
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  • 38
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    Hurricane Sally (2020) shifts the ocean thermal structure across the inner core during rapid intensification over the shelf (2023)
    American Meteorological Society
    Details
    Publication Date: 2023-02-25
    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(11), (2022): 2841–2852, https://doi.org/10.1175/jpo-d-22-0025.1.
    Description: Prediction of rapid intensification in tropical cyclones prior to landfall is a major societal issue. While air–sea interactions are clearly linked to storm intensity, the connections between the underlying thermal conditions over continental shelves and rapid intensification are limited. Here, an exceptional set of in situ and satellite data are used to identify spatial heterogeneity in sea surface temperatures across the inner core of Hurricane Sally (2020), a storm that rapidly intensified over the shelf. A leftward shift in the region of maximum cooling was observed as the hurricane transited from the open gulf to the shelf. This shift was generated, in part, by the surface heat flux in conjunction with the along- and across-shelf transport of heat from storm-generated coastal circulation. The spatial differences in the sea surface temperatures were large enough to potentially influence rapid intensification processes suggesting that coastal thermal features need to be accounted for to improve storm forecasting as well as to better understand how climate change will modify interactions between tropical cyclones and the coastal ocean.
    Description: This research was made possible by the NOAA RESTORE Science Program (NA17NOS4510101 and NA19NOS4510194) and the NASA Physical Oceanography program (80NSSC21K0553 and WBS 281945.02.25.04.67) and NOAA IOOS program via GCOOS (NA16NOS0120018). The authors declare that they have no competing interests.
    Keywords: Seas/gulfs/bays ; Atmosphere–ocean interaction ; Currents ; Tropical cyclones ; Buoy observations ; In situ oceanic observations
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    Turbulent thermal-wind driven coastal upwelling: current observations and dynamics (2022)
    American Meteorological Society
    Details
    Publication Date: 2022-12-21
    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(12), (2022): 2909-2921, https://doi.org/10.1175/jpo-d-22-0063.1.
    Description: A remarkably consistent Lagrangian upwelling circulation at monthly and longer time scales is observed in a 17-yr time series of current profiles in 12 m of water on the southern New England inner shelf. The upwelling circulation is strongest in summer, with a current magnitude of ∼1 cm s−1, which flushes the inner shelf in ∼2.5 days. The average winter upwelling circulation is about one-half of the average summer upwelling circulation, but with larger month-to-month variations driven, in part, by cross-shelf wind stresses. The persistent upwelling circulation is not wind-driven; it is driven by a cross-shelf buoyancy force associated with less-dense water near the coast. The cross-shelf density gradient is primarily due to temperature in summer, when strong surface heating warms shallower nearshore water more than deeper offshore water, and to salinity in winter, caused by fresher water near the coast. In the absence of turbulent stresses, the cross-shelf density gradient would be in a geostrophic, thermal-wind balance with the vertical shear in the along-shelf current. However, turbulent stresses over the inner shelf attributable to strong tidal currents and wind stress cause a partial breakdown of the thermal-wind balance that releases the buoyancy force, which drives the observed upwelling circulation. The presence of a cross-shelf density gradient has a profound impact on exchange across this inner shelf. Many inner shelves are characterized by turbulent stresses and cross-shelf density gradients with lighter water near the coast, suggesting turbulent thermal-wind-driven coastal upwelling may be a broadly important cross-shelf exchange mechanism.
    Description: The National Science Foundation, Woods Hole Oceanographic Institution, the Massachusetts Technology Collaborative, and the Office of Naval Research have supported the construction and maintenance of MVCO. The analysis presented here was partially funded by the National Science Foundation under Grants OCE 1558874 and OCE 1655686.
    Keywords: Buoyancy ; Coastal flows ; Currents ; Dynamics ; Lagrangian circulation/transport ; Upwelling/downwelling
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  • 40
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    Potential Vorticity and Instability in the Pacific Equatorial Undercurrent West of the Galápagos Archipelago (2022)
    American Meteorological Society
    Details
    Publication Date: 2023-02-01
    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): 1927-1943, https://doi.org/10.1175/jpo-d-21-0124.1.
    Description: The Galápagos Archipelago lies on the equator in the path of the eastward flowing Pacific Equatorial Undercurrent (EUC). When the EUC reaches the archipelago, it upwells and bifurcates into a north and south branch around the archipelago at a latitude determined by topography. Since the Coriolis parameter (f) equals zero at the equator, strong velocity gradients associated with the EUC can result in Ertel potential vorticity (Q) having sign opposite that of planetary vorticity near the equator. Observations collected by underwater gliders deployed just west of the Galápagos Archipelago during 2013–16 are used to estimate Q and to diagnose associated instabilities that may impact the Galápagos Cold Pool. Estimates of Q are qualitatively conserved along streamlines, consistent with the 2.5-layer, inertial model of the EUC by Pedlosky. The Q with sign opposite of f is advected south of the Galápagos Archipelago when the EUC core is located south of the bifurcation latitude. The horizontal gradient of Q suggests that the region between 2°S and 2°N above 100 m is barotropically unstable, while limited regions are baroclinically unstable. Conditions conducive to symmetric instability are observed between the EUC core and the equator and within the southern branch of the undercurrent. Using 2-month and 3-yr averages, e-folding time scales are 2–11 days, suggesting that symmetric instability can persist on those time scales.
    Description: This work was supported by the National Science Foundation (Grants OCE-1232971 and OCE-1233282), the NASA Earth and Space Science Fellowship Program (Grant 80NSSC17K0443), and the Global Ocean Monitoring and Observing Program of the National Oceanographic and Atmospheric Administration (NA13OAR4830216). Color maps are from Thyng et al. (2016).
    Description: 2023-02-01
    Keywords: Currents ; In situ oceanic observations ; Instability ; Mixing ; Ocean dynamics ; Pacific Ocean ; Potential vorticity ; Tropics
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  • 41
    Electronic Resource
    Electronic Resource
    Biotransformation of aromatic aldehydes bySaccharomyces cerevisiae: Investigation of reaction rates (1989)
    Springer
    Journal of industrial microbiology and biotechnology 4 (1989), S. 49-53 
    Details
    ISSN: 1476-5535
    Keywords: l-Phenylacetyl carbinol ; Saccharomyces cerevisiae ; Yeast ; Benzaldehyde ; Biotransformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary The rate of production ofl-phenylacetyl carbinol bySaccharomyces cerevisiae in reaction mixtures containing benzaldehyde with sucrose or pyruvate as cosubstrate was investigated in short 1 h incubations. The effect of yeast dose rate, sucrose and benzaldehyde concentration and pH on the rate of reaction was determined. Maximum biotransformation rates were obtained with concentrations of benzaldehyde, sucrose and yeast of 6 g, 40 g and 60 g/l, respectively. Negligible biotransformation rates were observed at a concentration of 8 g/l benzaldehyde. The reaction had a pH optimum of 4.0–4.5. Rates of bioconversion of benzaldehyde and selected substituted aromatic aldehydes using both sucrose and sodium pyruvate as cosubstrate were compared. The rate of aromatic alcohol production was much higher when sucrose was used rather than pyruvate.o-Tolualdehyde and 1-chlorobenzaldehyde were poor substrates for aromatic carbinol formation although the latter produced significant aromatic alcohol in sucrose-containing media. Yields of 2.74 and 3.80 g/l phenylacetyl carbinol were produced from sucrose and pyruvate, respectively, in a 1 h reaction period.
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    URL: http://dx.doi.org/10.1007/BF01569693
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    High solids fermentation of hydrolysates of wheat starch B in a continuous dynamic immobilized biocatalyst bioreactor (1989)
    Springer
    Journal of industrial microbiology and biotechnology 4 (1989), S. 81-84 
    Details
    ISSN: 1476-5535
    Keywords: Ethanol fermentation ; Wheat starch ; Saccharomyces cerevisiae ; immobilization ; Continuous dynamic immobilized biocatalyst bioreactor ; Biocatalyst bioreactor
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary A simple and efficient method of conversion of wheat starch B to ethanol was investigated. Employing a two-stage enzymatic saccharification process, 95% of the wheat starch was converted to fermentable sugars in 40 h. From 140 g/l total sugars in the feed solution, 63.6 g/l ethanol was produced continuously with a residence time of 3.3 h in a continuous dynamic immobilized biocatalyst bioreactor by immobilized cells ofSaccharomyces cerevisiae. The advantages and the application of this bioreactor to continuous alcoholic fermentation of industrial substrates are presented.
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    URL: http://dx.doi.org/10.1007/BF01569698
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    Der Einfluß von Cadmium, Zink, Blei und Quecksilber auf die Enzymaktivität beiSaccharomyces cerevisiae in vitro (1983)
    Springer
    European journal of nutrition 22 (1983), S. 205-212 
    Details
    ISSN: 1436-6215
    Keywords: Schwermetallwirkung ; Malatdehydrogenase ; Glutamatdehydrogenase ; Glycerinaldehyd-3-phosphatdehydrogenase ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Medicine
    Description / Table of Contents: Summary The difference between cadmium, zinc, lead, and mercury in regard of their effects on the activity of the enzymes tested is very slight. Concentrations higher than 10−5 M reduce significantly the activity of the enzymes, and concentrations of approximately 10−3 M inhibit it completely. An increase of the activity cannot be detected. The addition of combinations of cadmium, zinc, and lead results in a summing up of the toxic effects, whereas the interaction between mercury and the other three heavy metals shows a cumulative effect, which is appointed nearly completely by the heavy metal more toxic. The findings suggest that under in-vitro conditions there exists a direct interaction between the heavy metals and the enzymes.
    Notes: Zusammenfassung Die vier Schwermetalle Cadmium, Zink, Blei und Quecksilber unterscheiden sich in ihrer Wirkung auf die Aktivität der untersuchten Enzyme nur sehr wenig. Konzentrationen über 10−5 M vermindern die Enzymaktivität signifikant, und Konzentrationen von etwa 10−3 M unterbinden sie völlig. Eine Steigerung der Enzymaktivität läßt sich nicht feststellen. Die Zugabe von Cadmium-, Zink- und Bleikombinationen führt zu einer Addition der toxischen Effekte, während bei der Interaktion zwischen Quecksilber und den anderen drei Schwermetallen die Gesamtwirkung fast ausschließlich durch das stärker hemmende Schwermetall allein bestimmt wird. Die erhaltenen Ergebnisse lassen vermuten, daß es unter Invitro-Bedingungen zu einer direkten Wechselwirkung zwischen den Schwermetallen und den Enzymen kommt.
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    Identification of a fungal triacetylfusarinine C siderophore transport gene (TAF1) in Saccharomyces cerevisiae as a member of the major facilitator superfamily (1999)
    Springer
    BioMetals 12 (1999), S. 301-306 
    Details
    ISSN: 1572-8773
    Keywords: iron ; siderophores ; transport ; Saccharomyces cerevisiae ; fungi
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract Transport proteins of microorganisms may either belong to the ATP-binding cassette (ABC) superfamily or to the major facilitator (MFS)-superfamily. MFS transporters are single-polypeptide membrane transporters that transport small molecules via uniport, symport or antiport mechanisms in response to a chemiosmotic gradient. Although Saccharomyces cerevisiae is a non-siderophore producer, various bacterial and fungal siderophores can be utilized as an iron source. From yeast genome sequencing data six genes of the unknown major facilitator (UMF) family were known of which YEL065w Sce was recently identified as a transporter for the bacterial siderophore ferrioxamine B (Sit1p). The present investigation shows that another UMF gene, YHL047c Sce, encodes a transporter for the fungal siderophore triacetylfusarinine C. The gene YHL047c Sce (designated TAF1) was disrupted using the kanMX disruption module in a fet3 background (strain DEY 1394 Δfet3), possessing a defect in the high affinity ferrous iron transport. Growth promotion assays and transport experiments with 55Fe-labelled triacetylfusarinine C showed a complete loss of iron utilization and uptake in the disrupted strain, indicating that TAF1 is the gene for the fungal triacetylfusarinine transport in Saccharomyces cerevisiae and possibly in other siderophore producing fungi.
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    URL: http://dx.doi.org/10.1023/A:1009252118050
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    A gene of the major facilitator superfamily encodes a transporter for enterobactin (Enb1p) in Saccharomyces cerevisiae (2000)
    Springer
    BioMetals 13 (2000), S. 65-72 
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    ISSN: 1572-8773
    Keywords: major facilitator superfamily ; iron transport ; siderophores ; enterobactin ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract While in fungi iron transport via hydroxamate siderophores has been amply proven, iron transport via enterobactin is largely unknown. Enterobactin is a catecholate-type siderophore produced by several enterobacterial genera grown in severe iron deprivation. By using the KanMX disruption module in vector pUG6 in a fet3Δ background of Saccharomyces cerevisiae we were able to disrupt the gene YOL158c Sce of the major facilitator super family (MFS) which has been previously described as a gene encoding a membrane transporter of unknown function. Contrary to the parental strain, the disruptant was unable to utilize ferric enterobactin in growth promotion tests and in transport assays using 55Fe-enterobactin. All other siderophore transport properties remained unaffected. The results are evidence that in S. cerevisiae the YOL158c Sce gene of the major facilitator super family, now designated ENB1, encodes a transporter protein (Enb1p), which specifically recognizes and transports enterobactin.
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    URL: http://dx.doi.org/10.1023/A:1009250017785
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    Manganese accumulation in yeast cells (1989)
    Springer
    BioMetals 2 (1989), S. 6-10 
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    ISSN: 1572-8773
    Keywords: Manganese ; Electron spin resonance ; Superoxide dismutase ; Saccharomyces cerevisiae ; Yeast
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary Manganese accumulation was studied by room-temperature electron spin resonance (ESR) spectroscopy inSaccharomyces cerevisiae grown in the presence of increasing amounts of MnSO4. Mn2+ retention was nearly linear in intact cells for fractions related to both low-molecular-mass and macromolecular complexes (‘free’ and ‘bound’ Mn2+, respectively). A deviation from linearity was observed in cell extracts between the control value and 0.1 mM Mn2+, indicating more efficient accumulation at low Mn2+ concentrations. The difference in slopes between the two straight lines describing Mn2+ retention at concentrations lower and higher than 0.1 mM, respectively, was quite large for the free Mn2+ fraction. Furthermore it was unaffected by subsequent dialyses of the extracts, showing stable retention in the form of low-molecular-mass complexes. In contrast, the slope of the line describing retention of ‘bound’ Mn2+ at concentrations higher than 0.1 mM became less steep after subsequent dialyses of the cell extracts. This result indicates that the macromolecule-bound Mn2+ was essentially associated with particulate structures. In contrast to Cu2+, Mn2+ had no effect on the major enzyme activities involved in oxygen metabolism except for a slight increase of cyanide-resistant Mn-superoxide dismutase activity, due to dialyzable Mn2+ complexes.
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    URL: http://dx.doi.org/10.1007/BF01116194
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    Adaptation of a Saccharomyces cerevisiae strain to high copper concentrations (1994)
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    BioMetals 7 (1994), S. 221-226 
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    ISSN: 1572-8773
    Keywords: catalase ; copper resistance ; pH-dependent growth ; Saccharomyces cerevisiae ; superoxide dismutase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract A strain of Saccharomyces cerevisiae has been adapted to increasing concentrations of copper at two different pH values. The growth curve at pH 5.5 is characterized by a time generation increasing with the amount of added copper. A significant decrease of cell volume as compared with the control is also observed. At pH 3 the cells grow faster than at pH 5.5 and resist higher copper concentrations (3.8 against 1.2 mm). Experimental evidence indicates that, after copper treatment, the metal is not bound to the cell wall, but is localized intracellularly. A significant precipitation of copper salts in the medium was observed only at pH 5.5. Increased levels of superoxide dismutase (SOD) activity were observed in copper-treated cells and which persisted after 20 subsequent inocula in a medium without added metal. On the contrary, catalase activity was not stimulated by copper treatment and, hence, not correlated with SOD levels. The mechanism of copper resistance, therefore, probably involves a persistent induction of SOD, but not of catalase, and it is strongly pH-dependent.
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    Electron paramagnetic resonance studies and effects of vanadium in Saccharomyces cerevisiae (1996)
    Springer
    BioMetals 9 (1996), S. 91-97 
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    ISSN: 1572-8773
    Keywords: EPR ; Saccharomyces cerevisiae ; uptake ; vanadate ; vanadyl
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract Vanadium uptake by whole cells and isolated cell walls of the yeast Saccharomyces cerevisiae was studied. When orthovanadate was added to wild-type S. cerevisiae cells growing in rich medium, growth was inhibited as a function of the VO4 3- concentration and the growth was completely arrested at a concentration of 20 mM of VO4 3- in YEPD. Electron paramagnetic resonance (EPR) spectroscopy was used to obtain structural and dynamic information about the cell-associated paramagnetic vanadyl ion. The presence of EPR signals indicated that vanadate was reduced by whole cells to the vanadyl ion. On the contrary, no EPR signals were detected after interaction of vanadate with isolated cell walls. A ‘mobile’ and an ‘immobile’ species associated in cells with small chelates and with macromolecular sites, respectively, were identified. The value of rotational correlation time τ r indicated the relative motional freedom at the macromolecular site. A strongly ‘immobilized’ vanadyl species bound to polar sites mainly through coulombic attractions was detected after interaction of VO2+ ions with isolated cell walls.
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    Inhibition ofSaccharomyces cerevisiae division by 5-trifluoro-methyl-6-azauracil (1984)
    Springer
    Cellular and molecular life sciences 40 (1984), S. 1159-1161 
    Details
    ISSN: 1420-9071
    Keywords: Saccharomyces cerevisiae ; 5-trifluoromethyl-6-àzauracil ; yeast cell cultures ; cell division ; inhibition of
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary Cell division, as studied in asynchronous cultures of yeast cells, is sensitive to 5-trifluoromethyl-6-azauracil (F3CAzU). Under defined conditions (10 mmoles l−1 F3CAzU) this compound blocks immediately and completely the process of cell division. Using synchronized cells, the time-point at which division process of yeast cell can be inhibited by F3CAzU has been determined. The inhibitor effect of this compound is completely reversed by thymine, thymidine and uracil.
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    Protective effect of vitamins against trichothecene toxicity towardsSaccharomyces cerevisiae (1987)
    Springer
    Cellular and molecular life sciences 43 (1987), S. 886-888 
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    ISSN: 1420-9071
    Keywords: Saccharomyces cerevisiae ; trichothecenes ; mycotoxins ; vitamins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary Several trichothecene mycotoxins were shown to inhibit the growth ofSaccharomyces cerevisiae. This effect was most pronounced with the macrocyclic trichothecenes, especially verrucarin A. Much less growth inhibition was observed with T-2 toxin. Verrucarol, diacetoxyscirpenol, acetyl T-2 toxin, HT-2 toxin, T-2 tetraol and neosolaniol were inactive at a concentration of 75 μg of toxin per disc. Incubation ofS. cerevisiae with verrucarin A together with vitamins resulted in a decrease in toxicity. Pyridoxine-HCl, Ca-pantothenate, thiamine-HCl and α-tocopheryl acetate were amongst the most potent of the vitamins tested which reversed growth inhibition, overcoming the inhibitory potential of the toxins.
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    Occurrence of thiaminase II inSaccharomyces cerevisiae (1987)
    Springer
    Cellular and molecular life sciences 43 (1987), S. 888-890 
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    ISSN: 1420-9071
    Keywords: Thiaminase ; thiamine ; thiamine antagonist ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary It was found that cell-free extracts ofSaccharomyces cerevisiae contain thiaminase II which hydrolyzes thiamine and thiamine analogs. The possible involvement of this enzyme and thiamine-synthesizing enzymes in thiamine production from thiamine antagonists is discussed.
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    Translational control of endogenous and recoded nuclear genes in yeast mitochondria: Regulation and membrane targeting (1996)
    Springer
    Cellular and molecular life sciences 52 (1996), S. 1130-1135 
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    ISSN: 1420-9071
    Keywords: Saccharomyces cerevisiae ; mitochondria ; mRNA-specific translational activation ; synthetic genes ; gene regulation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Mitochondrial gene expression in yeast,Saccharomyces cerevisiae, depends on translational activation of individual mRNAs by distinct proteins encoded in the nucleus. These nuclearly coded mRNA-specific translational activators are bound to the inner membrane and function to mediate the interaction between mRNAs and mitochondrial ribosomes. This complex system, found to date only in organelles, appears to be an adaptation for targeting the synthesis of mitochondrially coded integral membrane proteins to the membrane. In addition, mRNA-specific translational activation is a rate-limiting step used to modulate expression of at least one mitochondrial gene in response to environmental conditions. Direct study of mitochondrial gene regulation and the targeting of mitochondrially coded proteins in vivo will now be possible using synthetic genes inserted into mtDNA that encode soluble reporter/passenger proteins.
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    Potentiation of antifungal activity of sesquiterpene dialdehydes againstCandida albicans and two other fungi (1992)
    Springer
    Cellular and molecular life sciences 48 (1992), S. 1162-1164 
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    ISSN: 1420-9071
    Keywords: Polygodial ; warburganal ; antifungal activity ; Candida albicans ; Saccharomyces cerevisiae ; Pityrosporum ovale ; enhancing effect ; antioxidants ; vitamin C ; BHA ; anethole
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract The antifungal activity of two drimane sesquiterpene dialdehydes, polygodial (1) and warburganal (2), alone and in combination with several other substances, was examined against three fungi,Candida albicans, Saccharomyces cerevisiae andPityrosporum ovale employing a broth dilution method. Anethole significantly synergized the activity of the two sesquiterpenoids againstC. albicans andS. cerevisiae however, it had only an, additive effect againstP. ovale. By contrast, two antioxidants, ascorbic acid (vitamin C) and BHA (butylated hydroxyanisole), noticeably enhanced the activity of the sesquiterpenoids againstP. ovale, but had no, effect againstC. albicans andS. cerevisiae.
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    Actin-, myosin- and ubiquitin-dependent endocytosis (1996)
    Springer
    Cellular and molecular life sciences 52 (1996), S. 1033-1041 
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    ISSN: 1420-9071
    Keywords: Ubiquitin ; yeast ; Saccharomyces cerevisiae ; Dictyostelium discoideum ; cytoskeleton ; mutants ; endocytosis ; actin ; myosin ; calmodulin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Endocytosis is a general term that is used to describe the internalization of external and plasma membrane molecules into the cell interior. In fact, several different mechanisms exist for the internalization step of this process. In this review we emphasize the work on the actin-dependent pathways, in particular in the yeastSaccharomyces cerevisiae, because several components of the molecular machinery are identified. In this yeast, the analysis of endocytosis in various mutants reveals a requirement for actin, calmodulin, a type I myosin, as well as a number of other proteins that affect actin dynamics. Some of these proteins have homology to proteins in animal cells that are believed to be involved in endocytosis. In addition, the demonstration that ubiquitination of some cell surface molecules is required for their efficient internalization is described. We compare the actin, myosin and ubiquitin requirements for endocytosis with recent results found studying these processes usingDictyostelium discoideum and animal cells.
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    Mitochondrial distribution and inheritance (1996)
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    Cellular and molecular life sciences 52 (1996), S. 1111-1116 
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    ISSN: 1420-9071
    Keywords: Mitochondria ; mitochondrial inheritance ; cytoskeleton ; Saccharomyces cerevisiae ; Schizosaccharomyces pombe ; membrane proteins ; organelle movement ; mitochondrial morphology
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Mechanisms mediating the inheritance of mitochondria are poorly understood, but recent studies with the yeastsSaccharomyces cerevisiae andSchizosaccharomyces pombe have begun to identify components that facilitate this essential process. These components have been identified through the analysis of conditional yeast mutants that display aberrant mitochondrial distribution at restrictive conditions. The analysis of these mutants has uncovered several novel proteins that are localized either to cytoskeletal structures or to the mitochondria themselves. Many mitochondrial inheritance mutants also show altered mitochondrial morphology and defects in maintenance of the mitochondrial genome. Although some inheritance components and mechanisms appear to function specifically in certain types of cells, other conserved proteins are likely to mediate mitochondrial behavior in all eukaryotic cells.
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    Molecular genetics of the peptidyl transferase center and the unusual Var1 protein in yeast mitochondrial ribosomes (1996)
    Springer
    Cellular and molecular life sciences 52 (1996), S. 1148-1157 
    Details
    ISSN: 1420-9071
    Keywords: Saccharomyces cerevisiae ; mitochondrial ribosomes ; peptidyl transferase ; Varl ribosomal protein ; gene relocation ; posttranscriptional rRNA modification
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Mitochondria posses their own ribosomes responsible for the synthesis of a small number of proteins encoded by the mitochondrial genome. In yeast,Saccharomyces cerevisiae, the two ribosomal RNAs and a single ribosomal protein, Varl, are products of mitochondrial genes, and the remaining approximately 80 ribosomal proteins are encoded in the nucleus. The mitochondrial translation system is dispensable in yeast, providing an excellent experimental model for the molecular genetic analysis of the fundamental properties of ribosomes in general as well as adaptations required for the specialized role of ribosomes in mitochondria. Recent studies of the peptidyl transferase center, one of the most highly conserved functional centers of the ribosome, and the Varl protein, an unusual yet essential protein in the small ribosomal subunit, have provided new insight into conserved and divergent features of the mitochondrial ribosome.
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    Interaction of Saccharomyces cerevisiae with gold: toxicity and accumulation (1999)
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    BioMetals 12 (1999), S. 289-294 
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    ISSN: 1572-8773
    Keywords: accumulation ; gold ; proton efflux ; Saccharomyces cerevisiae ; toxicity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract This paper examines the effects of ionic gold on Saccharomyces cerevisiae, as determined by long-term (growth in gold-containing media) and short-term interactions (H+ efflux activity). An increasing gold concentration inhibited growth and at 〈0.2 mM Au, growth was not observed. Transmission electron microscopy revealed no differences in ultrastructure but fine electron dense particles were observed in unstained preparations from gold-containing medium. After glucose addition (to 10mM) to starved suspensions of S. cerevisiae, glucose-dependent reduction of external pH occurred as the cells extruded protons. In the presence of increasing gold concentrations, the lag time before proton extrusion did not change but the rate and duration decreased significantly with a marked influence on proton efflux rate being observed at ≤ 10 μM. Extension of preincubation time of yeast cells in gold-containing medium resulted in a decreasing proton efflux rate and colloidal phase formation in the cell suspensions, the time between gold addition and the beginning of colloidal phase formation depending on the gold concentration used. Both Ca and Mg enhanced the inhibitory effect of gold on the yeast cells with Ca showing a stronger inhibitory effect than Mg.
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    Continuous production of fructose syrup and ethanol from hydrolysed Jerusalem artichoke juice (1991)
    Springer
    Journal of industrial microbiology and biotechnology 7 (1991), S. 131-135 
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    ISSN: 1476-5535
    Keywords: Saccharomyces cerevisiae ; Jerusalem artichoke ; High-fructose syrup ; Ethanol ; Immobilized yeast cells
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary The results from this study showed that Jerusalem artichoke juice can be used for the production of very enriched fructose syrup by selective conversion of glucose to ethanol in a continuous process using immobilized cells ofSaccharomyces cerevisiae ATCC 36859. The product contained up to 99% of the total carbohydrates as fructose compared to 76% in the feed. Using Jerusalem artichoke juice supplemented with some glucose a product was obtained with 7.5% w/v ethanol which made ethanol recovery economically favourable. It was found that some fructose was consumed in these continuous processes; the glucose/fructose conversion rate ratio was regulated by the glucose concentration in the product stream.
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    Analytical differentiation of wine fermentations using pure and mixed yeast cultures (1991)
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    Journal of industrial microbiology and biotechnology 7 (1991), S. 181-189 
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    ISSN: 1476-5535
    Keywords: Saccharomyces cerevisiae ; Torulaspora delbrueckii ; Aroma
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary Thirty-three fermentations of Pedro Ximénez grapes, collected in three degrees of ripeness, were carried out by inoculation with three types of inoculum: pure cultures ofSaccharomyces cerevisiae races and ofTorulaspora delbrueckii, indigenous yeasts, and mixed cultures of indigenous yeasts enriched with the pure cultures. By means of variance analysis 21 compounds were determined whose final concentrations in the wines significantly depended on the musts, the inocula or both. Eleven products that depended significantly on the inocula were subjected to a discriminant analysis in which most of the pure cultures gathered in a discriminant space area different from that occupied by the indigenous yeasts. The centroids corresponding to most of the mixed cultures were shifted to the central area of the discriminant space, moved away from their corresponding pure cultures and approached the indigenous yeasts. The results show a high similarity between the fermentations carried out with mixed cultures with the addedS. cerevisiae races and those fermentations carried out with the indigenous yeasts, with regard to those compounds which were significantly dependent on the inocula.
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    Control of the G1-G0 transition and G0 protein synthesis by cyclic AMP in Saccharomyces cerevisiae (1987)
    Springer
    Current genetics 12 (1987), S. 577-582 
    Details
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Cell cycle ; Cyclic AMP ; G0 protein
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary When the cyr1-1 cells of Saccharomyces cerevisiae, which require cyclic AMP (cAMP) for growth, were starved for cAMP, cell division was arrested at the G1 state of the mitotic cell cycle and the cells entered the resting state (G0) also observed in wild-type cells transferred to sulfur-free medium. The level of cAMP in wild-type cells decreased rapidly when the cells were starved for sulfur and subsequently increased following its addition. The cyr1-1 cells starved for cAMP preferentially synthesized nine G0 proteins. The synthesis of these G0 proteins in the sulfur-starved cells was repressed by the addition of cAMP. The RAS2 val19 or bcy1 cells, which produced an elevated level of cAMP or cAMP-independent protein kinase, did not synthesize the G0 proteins under the sulfur-starved condition. The results suggest that cAMP plays a role in the transition between the proliferating state and G0 state.
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    The OGD1 gene, affecting 2-oxoglutarate dehydrogenase in S. cerevisiae, is closely linked to HIS5 on chromosome IX (1990)
    Springer
    Current genetics 17 (1990), S. 85-88 
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    ISSN: 1432-0983
    Keywords: 2-oxoglutarate dehydrogenase ; Saccharomyces cerevisiae ; rad52-mediated chromosome loss
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Ogd1 mutants of Saccharomyces cerevisiae are deficient in mitochondrial 2-oxoglutarate dehydrogenase activity; they cannot grow on glycerol and produce an increased amount of organic acids during growth on glucose as substrate. Using gamma ray-induced rad52-mediated chromosome loss the ogd1 mutation can be assigned to chromosome IX. Tetrad analysis of crosses between ogd1 and other markers on chromosome IX revealed that the OGD1 gene maps on the left arm of this chromosome 1.9 cM from his5.
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    Cloning and sequencing of URA10, a second gene encoding orotate phosphoribosyl transferase in Saccharomyces cerevisiae (1990)
    Springer
    Current genetics 17 (1990), S. 105-111 
    Details
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Orotate phosphoribosyl transferase ; Nucleotide sequence-5-phosphoribosyl 1-pyrophosphate (5PRPP)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Orotate phosphoribosyl transferase (OPRTase) catalyses the transformation of orotate to OMP in the pyrimidine pathway. In the yeast Saccharomyces cerevisiae, the URA5 gene is known to encode this enzyme activity. In this paper we present the cloning and sequencing of a yeast gene, named URA10, encoding a second OPRTase enzyme. Comparison of the predicted amino acid sequences between URA5 and URA10 genes shows more than 75% similarity. These sequences have also been compared to those of Escherichia coli, Podospora anserina, Sordaria macrospora and Dictyostelium discoideum. Remarkable similarities in the primary structure of these proteins have been found. Gene disruption experiments revealed that URA10 gene expression is responsible for the leaky phenotype of a ura5 mutant. Assays of OPRTase activity in extracts from ura5 and ura10 mutants indicate that the URA10 product contributes only 20% of the total activity found in wild type cells.
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    URL: http://dx.doi.org/10.1007/BF00312853
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    High frequency FLP-independent homologous DNA recombination of 2 μ plasmid in the yeast Saccharomyces cerevisiae (1988)
    Springer
    Current genetics 14 (1988), S. 191-199 
    Details
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Site specific recombination ; 2 μ DNA plasmid
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The purpose of this work is to identify and quantitate in vivo 2 μ plasmid FLP-independent recombination in yeast, using a nonselective assay system for rapid detection of phenotypic expression of the recombination events. A tester plasmid was constructed such that in vivo recombination between 2 μ direct repeat sequences produces the resolution of the plasmid into two circular DNA molecules. This recombinational event is detected as a phenotypic shift from red to white colonies, due to the mitotic loss of the plasmid portion containing the yeast ADE8 gene in a recipient ade1 ade2 ade8 genetic background. In the absence of the 2 μ FLP recombinase and/or its target DNA sequence, recombination is not abolished but rather continues at a high frequency of about 17%. This suggests that the FLP-independent events are mediated by the chromosomally-encoded general homologous recombination system. We therefore conclude that the totality of 2 μ DNA recombination events occurring in FLP+ cells is the contribution of both FLP-mediated and FLP-independent events.
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    URL: http://dx.doi.org/10.1007/BF00376739
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    Molecular cloning of the ARG7 gene of Schizosaccharomyces pombe encoding argininosuccinate lyase (1988)
    Springer
    Current genetics 14 (1988), S. 381-385 
    Details
    ISSN: 1432-0983
    Keywords: Schizosaccharomyces pombe ; Saccharomyces cerevisiae ; Argininosuccinate lyase ; Gene cloning
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A gene bank of Sau3A partially restricted Schizosaccharomyces pombe DNA in YEp13 was used to transform an arg4 mutant of Saccharomyces cerevisiae. One colony was recovered which contained the YEp13 plasmid bearing a large insert complementing the argininosuccinate lyase (ASL) mutation. As shown by restriction mapping and subcloning experiments, the DNA sequence required for complementation is localized on a 2 kb BamHI-BamHI fragment. The plasmid complemented several S. cerevisiae arg4 mutants of independent origin and a S. pombe arg7 mutant lacking ASL. Low but significant ASL activities were detected in crude extracts of these transformants. No complementation of the E. coli argH mutant was observed. Southern blot hybridizations showed that the insert originates from the S. pombe genome. No cross-hybridization was found between this sequence and S. cerevisiae DNA. It can be concluded that the cloned DNA fragment bears the S. pombe ARG7 gene coding for ASL.
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    URL: http://dx.doi.org/10.1007/BF00419996
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    Inheritance of chromosome length polymorphisms in Saccharomyces cerevisiae (1988)
    Springer
    Current genetics 14 (1988), S. 413-418 
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    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Chromosome length polymorphisms ; FIGE ; OFAGE
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Although Saccharomyces cerevisiae strains generally have similar chromosomal band patterns as revealed by pulsed field gel electrophoresis, individual bands often move slightly differently from one strain to the other. Surveying strains from our stock collection, we found that nearly all the bands of a certain pair of strains differed in their mobility. Some of these chromosome length polymorphisms segregated in a 2:2 ratio, indicating that they resulted from single structural alterations (i.e. additions or deletions). One of these was mapped on the right arm of chromosome 1. Others did not segrate in a simple 2:2 ratio. That is, there were progenies which had bands not present in either parent. We suggest that these new bands are the products of recombination between homologous chromosomes having two or more structural alterations.
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    Comparison of Tetrahymena ARS sequence function in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe (1988)
    Springer
    Current genetics 14 (1988), S. 225-233 
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    ISSN: 1432-0983
    Keywords: ARS ; Saccharomyces cerevisiae ; Schizosaccharomyces pombe ; Tetrahymena thermophila
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have isolated several Tetrahymena thermophila chromosomal DNA fragments which function as autonomously replicating sequences (ARS) in the heterologous Saccharomyces cerevisiae and Schizosaccharomyces pombe selection systems. The Tetrahymena ARS sequences were first isolated in S. cerevisiae and were derived from non-ribosomal micro- and macronuclear DNA. Sequence analysis of the ARS elements identified either perfect or close matches with the 11 by S. cerevisiae ARS core consensus sequence. Subcloning studies of two Tetrahymena ARS elements defined functional regions ranging in size from 50 to 300 bp. Testing of the ARS elements in S. pombe revealed that most of the T. thermophila inserts confer ARS function in both yeasts, at least in the sense of promoting a high transformation frequency to plasmids which contain them. However, the actual sequences responsible for ARS activity were not always identical in the two yeasts.
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    URL: http://dx.doi.org/10.1007/BF00376742
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    Construction and characterization of a haploid strain of Saccharomyces cerevisiae that completely lacks all genomic CYH2 sequences (1988)
    Springer
    Current genetics 14 (1988), S. 325-329 
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    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Ribosomal protein genes ; CYH2
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A diploid strain of the yeast Saccharomyces cerevisiae has been constructed that has one copy of the ribosomal protein gene CYH2 completely deleted and replaced with the TRP1 gene using the method of Rothstein (1983). There are only small differences in growth rate and no detectable difference in steady state level of CYH2 mRNA between the diploid that is heterozygous for the CYH2 deletion and the parent diploid with two normal copies of this gene. This suggests that the diploid must partially compensate for the loss of one CYH2 gene. Tetrad dissection shows that haploid spores lacking the CYH2 gene cannot germinate. The lethality of this deletion can be rescued by a CYH2 cDNA on a low copy vector. Haploids which lack the genomic copy of the CYH2 gene, but contain a plasmid copy of the CYH2 cDNA are able to grow normally. These CYH2 deleted yeast haploids should be useful to analyze mutationally altered CYH2 genes and genes homologous to CYH2 from other organisms without interference from a genomic copy.
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    URL: http://dx.doi.org/10.1007/BF00419989
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    The glucose- and ethanol-dependent regulation of PDC1 from Saccharomyces cerevisiae are controlled by two distinct promoter regions (1988)
    Springer
    Current genetics 14 (1988), S. 337-344 
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    ISSN: 1432-0983
    Keywords: Yeast ; Gene regulation ; Saccharomyces cerevisiae ; PDCI promoter
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A 870 by promoter fragment of the PDC1 gene that includes the carbon source dependent regulatory regions was investigated using 5′ and 3′ promoter deletions. The results indicate that glucose and ethanol regulation of PDC1 transcription are independently controlled by distinct cis-acting regions. The consensus sequence AAATCGATA may play a role in this regulation, while the sequence (ATCA)AACCT may be important in transcription initiation.
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    URL: http://dx.doi.org/10.1007/BF00419991
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    Isolation and properties of yeast mutants affected in farnesyl diphosphate synthetase (1990)
    Springer
    Current genetics 18 (1990), S. 41-46 
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    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Mutants ; Farnesyl diphosphate synthetase ; Ergosterol
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Two yeast mutant strains auxotrophic for ergosterol and blocked in farnesyl diphosphate synthetase (EC 2.5.1.1) were isolated. Genetic analysis has shown that these mutant strains carry additional mutations in the ergosterol pathway besides erg20-1 and erg20-2 which affect FPP synthetase. The novel feature of these mutants is their ability to excrete prenyl alcohols (farnesol and geraniol). As geraniol is toxic for yeast cells, the above leaky mutations in FPP synthetase have to be associated with others in the sterol pathway, in order to slow down geraniol synthesis.
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    Heterologous gene expression of the glyphosate resistance marker and its application in yeast transformation (1989)
    Springer
    Current genetics 15 (1989), S. 91-98 
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    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Vector ; Glyphosate resistance ; Transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The E. coli aroA gene was inserted between yeast promoter and terminator sequences in different shuttle expression plasmids and found to confer enhanced EPSP synthase activity as well as resistance to glyphosate toxicity. Subsequently, a transformation system using these newly constructed vectors in yeast was characterized. The efficiency of the glyphosate resistance marker for transformation and selection with plasmid pHR6/20-1 in S. cerevisiae laboratory strain SHY2 was found to be relatively high when compared with selection for LEU2 prototrophy. The fate of the recombinant plasmid pHR6/20-1 in the transformants, the preservation of the aroA E. coli DNA fragment in yeast, mitotic stability, EPSP synthase activity, and growth on glyphosate-containing medium have been investigated. As this plasmid also allows direct selection for glyphosate resistant transformants on rich media, the glyphosate resistance marker was used for transforming both S. cerevisiae laboratory strain SHY2 and brewer's yeast strains S. cerevisiae var. “uvarum” BHS5 and BHS2. In all cases, the vector pHR6/20-1 was maintained as an autonomously replicating plasmid. The resistance marker is, therefore, suitable for transforming genetically unlabeled S. cerevisiae laboratory, wild, and industrial yeast strains.
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    Expression of the Aspergillus niger glucose oxidase gene in A. niger, A. nidulans and Saccharomyces cerevisiae (1990)
    Springer
    Current genetics 18 (1990), S. 531-536 
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    ISSN: 1432-0983
    Keywords: Glucose oxidase ; Aspergillus ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We report the cloning of the Aspergillus niger glucose oxidase gene and its use to elevate glucose oxidase productivity in A. niger by increasing the gene dosage. In addition, the gene has been introduced into A. nidulans where it provides the novel capacity to produce glucose oxidase. A plasmid, in which DNA encoding the mature form of glucose oxidase was preceded by a Saccharomyces cerevisiae secretion signal, effected high-level production of extracellular glucose oxidase in this yeast.
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    Sequence analysis of the ARG7 gene of Schizosaccharomyces pombe coding for argininosuccinate lyase (1991)
    Springer
    Current genetics 19 (1991), S. 255-260 
    Details
    ISSN: 1432-0983
    Keywords: Schizosaccharomyces pombe ; Saccharomyces cerevisiae ; Argininosuccinate lyase ; Sequence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The complete nucleotide sequence of the ARG7 gene, coding for argininosuccinate lyase (EC 4.3.2.1), in the fission yeast (Schizosaccharomyces pombe) has been determined. It consists of an open reading frame of 461 codons. The deduced protein has a molecular weight of 51 200 Da. The gene is devoid of introns which is confirmed by the fact that it is expressed in Escherichia coli after spontaneous insertion of a bacterial sequence probably bearing a prokaryotic promoter. A perfect “TATA” box is found at-72 and the major transcription initiation site in Saccharomyces cerevisiae is located at-11 as shown by primer extension experiments. Comparison of the S. pombe lyase with related proteins from other organisms reveals an important degree of conservation except in the carboxyterminal part of the polypeptide. Additionally, a deletion removing 66 amino acids of the carboxy terminus yields an enzyme exhibiting some biological activity. A unique 1500 b transcript was found in S. cerevisiae when the intact gene was present, but the deleted version of the gene gave rise to at least three transcripts of 1800, 2800 and 3900 b.
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    A hot-spot for transposition of various Ty elements on chromosome V in Saccharomyces cerevisiae (1989)
    Springer
    Current genetics 16 (1989), S. 247-252 
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    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Chromosome V ; Ty elements ; tRNA genes ; Transposition hot-spots ; Yeast polymorphism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Ty4 is a novel transposable element in the yeast, Saccharomyces cerevisiae, which is present in only a few copies in the genome (Stucka et al. 1989). In strain C836 one of the three copies (Ty4-90) is contained in cosmid clone c90, where it resides on chromosome V. Analysis of this region reveals a “hot-spot” of transposition: in addition to Ty4-90, the locus contains a complete Ty3 element and seven singular delta, sigma and tau elements. Three tRNA genes (for His, Lys, and Ile) are located in this region, and these are closely associated with one or the other of the elements, a phenomenon commonly observed in yeast. A comparison of c90 with corresponding regions from other strains shows that the locus is highly polymorphic and that this polymorphism is explicitly associated with Ty transposition and recombination events.
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    Regulation of the pyrimidine salvage pathway by the FUR1 gene product of Saccharomyces cerevisiae (1991)
    Springer
    Current genetics 19 (1991), S. 333-337 
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    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Pyrimidine salvage pathway ; Semi-dominant mutants ; FUR1 ; Uracil phosphoribosyl transferase ; Regulation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary In Saccharomyces cerevisiae, the protein encoded by the FUR1 gene is absolutely required for the expression of uracil phosphoribosyl transferase activity. The occurrence of semi-dominant mutations for 5-fluorouracil-(5FU)-resistance at this locus led us to clone and sequence the semi-dominant fur 1–5 allele. A single point mutation, resulting in the substitution of arginine 134 for serine, is responsible for this mutant phenotype. The fur 1–5 allele is transcribed and expressed at the same level as the wild-type allele. But, in contrast with the wild-type, the UPR Tase activity of the fur 1–5 mutant strain is stimulated in vitro by UTP and does not, therefore, correspond to a loss of feedback of UPR Tase activity. We found that uracil, as a free base, induces a significative increase in transcription and UPR Tase activity in a wild-type strain as well as in uracil-overproducing mutants which principally explains the high efficiency of the pyrimidine salvage pathway in S. cerevisiae.
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    High frequency recombination and the expression of genes cloned on chimeric yeast plasmids: Identification of a fragment of 2-μm circle essential for transformation (1980)
    Springer
    Current genetics 2 (1980), S. 17-251 
    Details
    ISSN: 1432-0983
    Keywords: Gene cloning ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have carried out experiments aimed at explaining the observed variations in transformation frequencies when Saccharomyces cerevisiae or Saccharomyces carlbergensis are transformed with chimeric plasmids that contain one of 4 possible EcoRI fragments of the yeast 2-μm circle. These plasmids fall into 2 classes when used to transform 2 different yeast his3 auxotrophs, one (strain LL20) harbours indigenous 2-μm circle, and the other (strain YF233) is devoid of this plasmid. Hybrid plasmids containing either the 2.4 mega-dalton (mD) R-form EcoRI fragment (pYF88) or the l.4 mD L-form EcoRI fragment (pYF177) of 2-μm circle transform either of the two hosts at a high frequency (50,000 colonies per Mg in LL20 and 10,000 colonies per μg in YF233). Hybrid plasmids containing the 1.5 mD R-form EcoRI fragment (pYF87) or the 2.5 mD L-form EcoRI fragment (pYF178) of the 2-μm circle transform LL20 at a reduced frequency (6,000–16,000 colonies per μg) and YF233 at extremely low frequencies (1–5 colonies per μg). All plasmids retrieved from strain YF233 that had been transformed with pYF88 or pYF177 were identical to the original transforming plasmid. Of the plasmids retrieved from strain LL20 that had been transformed with pYF87 and pYF178, approximately half had acquired an extra copy of the 2-μm circle. Of the plasmids retrieved from strain LL20 that had been transformed with pYF88 and pYF177, an average of only approximately 13% had acquired an extra copy of 2-μm circle. Taken together, these observations indicate that the transformation of yeast by a plasmid lacking the ability to replicate (pYF87 and pYF1780) occurs by the recombinational acquisition of 1 copy of the host 2-μm circle, which serves to supply the incoming plasmid with missing essential sequences. A comparison of 2-μm circle DNA fragments carried by pYF88 and pYF177 indicates that the region of 2-μm circle required for high frequency transformation is a 1.2 mD segment that is common to the 2.4 mD R-form and 1.4 ml) L-form EcoRI fragments. This region extends from the EcoRI cut site adjacent to the PstI site, through to the end of the inverted repeat. However, the inverted repeat sequence alone is not sufficient to bestow high frequency transformation of yeast.
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    Effect of chromosome loss on the leavening ability of Saccharomyces cerevisiae in dough (1990)
    Springer
    Current genetics 18 (1990), S. 401-403 
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    ISSN: 1432-0983
    Keywords: Baking yeast ; Saccharomyces cerevisiae ; Dough leavening ; Benomyl
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary To investigate the leavening ability of yeast in dough, chromosome loss was induced by benomyl treatment in YOY1037, a diploid between a baking strain and a laboratory strain, and its effect on the leavening ability was studied. When benomyl-treated cells were spread on plates with a dye indicator for ploidy, about 20% of the visible colonies were stained dark blue or dark purple; the rest stained pale blue, similar to the diploid YOY1037. Strains showing the MATα phenotype, and non-galactose fermenting strains, apparently having lost particular chromosomes, were observed only in those with darkcoloured colonies. Strains with dark-coloured colonies showed a wider range of leavening ability than did those with pale-coloured colonies.
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    Isolation and characterization of the Pichia stipitis xylitol dehydrogenase gene, XYL2, and construction of a xylose-utilizing Saccharomyces cerevisiae transformant (1990)
    Springer
    Current genetics 18 (1990), S. 493-500 
    Details
    ISSN: 1432-0983
    Keywords: Xylitol dehydrogenase gene ; Pichia stipitis ; Saccharomyces cerevisiae ; Xylose utilization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A P. stipitis cDNA library in λgt11 was screened using antisera against P. stipitis xylose reductase and xylitol dehydrogenase, respectively. The resulting cDNA clones served as probes for screening a P. stipitis genomic library. The genomic XYL2 gene was isolated and the nucleotide sequence of the 1089 bp structural gene, and of adjacent non-coding regions, was determined. The XYL2 open-reading frame codes for a protein of 363 amino acids with a predicted molecular mass of 38.5 kDa. The XYL2 gene is actively expressed in S. cerevisiae transformants. S. cerevisiae cells transformed with a plasmid, pRD1, containing both the xylose reductase gene (XYL1) and the xylitol dehydrogenase gene (XYL2), were able to grow on xylose as a sole carbon source. In contrast to aerobic glucose metabolism, S. cerevisiae XYL1-XYL2 transformants utilize xylose almost entirely oxidatively.
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    A gene tightly linked to CEN6 is important for growth of Saccharomyces cerevisiae (1991)
    Springer
    Current genetics 19 (1991), S. 1-8 
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    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Centromere flanking sequences ; tRNA modification enzymes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Transcriptional analysis of the region flanking the left boundary of the centromere of chromosome VI revealed the presence of a gene immediately adjacent to CEN6. The transcription of the gene is directed toward the centromere, and nucleotide sequence analysis showed that the coding region terminates only 50 bp away from CEN6. Our results extend to chromosome VI the observation that centromere-flanking regions of S. cerevisiae are transcriptionally active. Disruption of the coding region of the gene showed that its product, whilst not essential for cell viability, is important for normal cell growth. The gene has been termed DEG1 (DEpressed Growth rate). Comparison of the deduced amino acid sequence of DEG1 with a protein sequence databank revealed homology with the enzyme tRNA pseudouridine synthase I of E. coli.
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    Altered patterns of protein synthesis induced by heat shock of yeast (1979)
    Springer
    Current genetics 1 (1979), S. 63-74 
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    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Translation ; Coordinate regulation ; Electrophoresis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The products of protein synthesis from exponential phase cultures of Saccharomyces cerevisiae grown at 23 °C or at 36 °C appear to be essentially identical. However, yeast cells respond to a shift in culture temperature from 23 °C to 36 °C with the rapid de novo synthesis of a polypeptide species of molecular weight 100,000. Within 60–90 min after the shift this polypeptide represents approximately 2.5% of the total cellular protein, a 5–10 fold increase over the preshift level. The level of this polypeptide then decreases with continued growth of the cells at 36 °C. Analyses by SDS-polyacrylamide gel electrophoresis of polypeptides obtained from cells pulse labeled with [35S]methionine demonstrate that following a temperature shift from 23 °C to 36 °C the synthetic rate of the 100,000 molecular weight polypeptide (as well as a number of other polypeptide species) increases to a level at least 10 fold higher than that observed prior to the shift. A concomittant decrease is observed in the synthesis of a large number of polypeptide species which were actively synthesized before the shift. Maximum changes in synthetic rates are observed 20–30 min after the shift and preshift synthetic patterns are regained within 60–90 min. Synthetic changes of the same magnitude and time course can be produced by short (20–30 min) exposures to 36 °C implicating a heat shock response. Several of the transiently induced polypeptides, including the 100,000 molecular weight species, show an affinity for DNA as determined by DNA-cellulose chromatography.
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    α-factor enhancement of hybrid formation by protoplast fusion in Saccharomyces cerevisiae II (1986)
    Springer
    Current genetics 10 (1986), S. 943-945 
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    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; α-factor ; Protoplasts
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary When Mat a cells are treated with α-factor prior to being protoplasted and fused, the frequency of karyogamy is higher than in unarrested controls.
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    Saccharomyces cerevisiae strains sensitive to inorganic mercury (1985)
    Springer
    Current genetics 10 (1985), S. 179-185 
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    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Resistance ; Mercury ; Tyrosine
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary From a cross of two strains ofSaccharomyces cerevisiae, both of which had the same (wild type or normal) level of resistance to inorganic mercury, segregants having three distinguishable resistance levels, normal, sensitive and semi-sensitive, were obtained. Genetic analyses of the parents and the progeny indicated that the levels of inorganic mercury sensitivity were determined by three distinct loci,HGS1, HGS2 andMSM1. The recessive allele of theHGS1 locus,hgsl-1, and the codominant allele of theHGS2 locus,HGS2-1, were necessary for the sensitive phenotypes, and alleles in theMSM1 locus,MSMI-1 andmsml-2, were responsible for the different sensitivity levels. In short, the strains of genotypeshgs1-1 HGS2-1 msml-2 andhgsl-1 HGS2-1 MSMI-1 were sensitive and semi-sensitive, respectively, while the strains of all other genotypes were normal. Although thehgs1-1 allele was identified as thearo7-1 mutation which confers deficiency of tyrosine and phenylalanine, mutations such asaro1B (deficiency of tyrosine, phenylalanine and tryptophan) andtyr1 (deficiency of tyrosine) had similar effects asaro7-1 on inorganic mercury sensitivity. From these results we conclude that theHGS2-1 allele causes inorganic mercury sensitivity when the cells are defective in the tyrosine biosynthesis. In fact, addition of tyrosine to the growth medium containing inorganic mercury resulted in increase of colony forming ability of the sensitive strains.
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    Genetic mapping of nuclear mucidin resistance mutations in Saccharomyces cerevisiae (1986)
    Springer
    Current genetics 10 (1986), S. 665-670 
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    ISSN: 1432-0983
    Keywords: Multiple drug resistance ; Genetic mapping ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary In the yeast Saccharomyces cerevisiae, two nuclear pleiotropic drug resistance mutations pdr3-1 (former designation muc PR) and pdr3-2 (former designation DRI9/T7) have been selected as resistant to mucidin and as resistant to chloramphenicol plus cycloheximide, respectively. The pdr3 mutations were found not to affect the plasma membrane ATPase activity measured in a crude membrane fraction. Meiotic mapping using strains with standard genetic markers revealed that mutation pdr3-1 is centromere linked on the left arm of chromosome II at a distance of 5.9 ± 3.3 cM from its centromere and 11.6 ± 3.1 cM from the marker pet9. The centromere linked pdr3-2 mutation exhibited also genetic linkage to pet9 with a map distance of 9.8 ± 3.2 cM. These results indicate that pdr3-1 and pdr3-2 are alleles of the same pleiotropic drug resistance locus PDR3 which is involved in the control of the plasma membrane permeability in yeast.
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    URL: http://dx.doi.org/10.1007/BF00410914
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    Identification and characterization of four new GCD genes in Saccharomyces cerevisiae (1986)
    Springer
    Current genetics 10 (1986), S. 657-664 
    Details
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Amino acid biosynthesis ; General control ; GCD-genes ; GCN-genes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Mutant strains, resistant against the amino acid analogues 5-methyltryptophan, 5-fluorotryptophan and canavanine were isolated, starting with a trp2 leaky auxotrophic strain. Of 10 such strains, only four turned out to be of the “general control derepressed” (gcd) mutant type. Three other isolates were shown to be defective in the general amino acid permease system, while the remaining three strains displayed low spore viability and were not further investigated. Complementation tests amongst the four new gcd-mutant strains, including strain RH558 gcd2-1 isolated earlier, yielded five complementation groups: GCD2, GCD3, GCD4, GCD5, and GCD6. All mutant strains showed a dual phenotype, which was not separable by wild type backcrosses: “constitutive derepression” and “slow growth”. Epistatis of all gcd mutations over gcn1-1, gcn2-1 and gcn3-1 was found with respect to both phenotypes, except for gcd5-1, which was lethal in these combinations. On the other hand gcn4-101 was found to be epistatic over all gcd mutations, but only with respect to the “constitutive derepression” phenotype, and not to “slow growth”; again the combination with gcd5-1 was lethal. Mutation gcd2-1 was mapped on chromosome VII, 50 cM from leu1 and 22 cM from ade6. A new model is discussed, in which GCD-genes are involved in the amino acid uptake into the vacuoles.
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    URL: http://dx.doi.org/10.1007/BF00410913
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    Induced cellular resistance to ultraviolet light in Saccharomyces cerevisiae is not accompanied by increased repair of plasmid DNA (1987)
    Springer
    Current genetics 11 (1987), S. 321-326 
    Details
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Inducible repair ; Plasmid transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Many reports show that resistance of Saccharomyces cerevisiae to a large UV dose can be enhanced by pre-induction with a smaller one given some hours before. This work tests if such increased cell survival is associated with increased DNA repair on UV damaged plasmid transformed into yeast. There was no change in transformation efficiency of UV-damaged plasmid DNA under conditions where RAD cell survival increased 5-fold, and where rad1-1 and rad6-1 survival increased 2-fold. It is concluded that DNA repair activity involving the RAD6 and RAD3 pathways is either not inducible or is unable to work on plasmid DNA. It is suggested that the enhancement of cellular survival detected may be based on changes in cell-cycle behaviour which permit cells generally proficient in repair a greater chance to recover.
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    URL: http://dx.doi.org/10.1007/BF00355407
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    Phenotypic differences between induced and spontaneous 2μ-plasmid-free segregants of Saccharomyces cerevisiae (1987)
    Springer
    Current genetics 11 (1987), S. 415-418 
    Details
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; 2 μ plasmids ; Plasmid free segregants
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The maximum specific growth rates (μmax) of 2 μ-plasmid-free ([cir°]) segregants of three haploid and one diploid strain of Saccharomyces cerevisiae have been determined and compared with the μmax of their 2 μ-plasmid-containing ([cir +]) progenitors. Two classes of [cir°] strains have been examined: those induced by transformation with a 2 μ-based recombinant plasmid according to the method of Dobson et al. (1980) and those isolated as spontaneous [cir°] segregants from glucose-limited continuous cultures. The μmax of the spontaneous [cir°] segregants was not found to differ significantly from that of their [cir +] parents. In all cases, however, the induced [cir°] strains had a μmax which was significantly less than that of their [cir +] counterparts. This effect was particularly marked in the case of the diploid strain where a 34% reduction in μmax was observed. The implications of these results are discussed in terms of the effect of the transformation process on host yeast cells.
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    URL: http://dx.doi.org/10.1007/BF00378186
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    One member of the tRNA(Glu) gene family in yeast codes for a minor GAGtRNA(Glu) species and is associated with several short transposable elements (1987)
    Springer
    Current genetics 12 (1987), S. 323-328 
    Details
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Minor tRNAs ; Codon usage ; Transposable elements ; Delta ; Tau
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary During characterization of the whole tRNA(Glu) family from the yeast, Saccharomyces cerevisiae, we isolated one cosmid clone bearing a tRNA(Glu) gene copy that is deviant from the major tRNA(Glu3) gene members in only five positions. This divergent tRNA(Glu) is a minor species and is represented by a single gene copy. One of the nucleotide exchanges concerns the anticodon which is modified from T-T-C in the tRNA(Glu3) gene to C-T-C which implies that this tRNA serves the codon triplet G-A-G. Two other minor yeast tRNA species have been reported which appear to be particularly designed for the translation of those codons that have a G in its third (Wobble) position. The low abundance of such minor tRNA species correlates positively to the low occurrence of most of the N-N-G codons in yeast. Furthermore, the GAGtRNA(Glu) locus represents another case of the general phenomenon in which the majority of the tRNA genes in yeast are associated with one or several transposable elements forming complex patterns. In this particular case, divergent segments of delta and tau are present in the 5′ flanking region of the tRNA gene and arranged in a novel configuration. The sequence data lend support to the view that tau is not an evolutionary young element as was earlier anticipated.
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    URL: http://dx.doi.org/10.1007/BF00405754
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    Mutations in ADE3 reduce the efficiency of the omnipotent suppressor sup45-2 (1989)
    Springer
    Current genetics 16 (1989), S. 315-321 
    Details
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Antisuppressor ; ADE3 ; Translation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Mutations in a known yeast gene, ADE3, were shown to act as an antisuppressor, reducing the efficiency of the omnipotent suppressor, sup45-2. The ADE3 locus encodes the trifunctional enzyme C1-tetrahydrofolate synthase, which is required for the biosynthesis of purines, thymidylate, methionine, histidine, pantothenic acid and formylmethionyl-tRNAfmet. The role of this enzyme in translational fidelity had not previously been suspected.
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    URL: http://dx.doi.org/10.1007/BF00340709
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    Two new loci that give rise to dominant omnipotent suppressors in Saccharomyces cerevisiae (1989)
    Springer
    Current genetics 16 (1989), S. 323-330 
    Details
    ISSN: 1432-0983
    Keywords: Yeast ; Saccharomyces cerevisiae ; Nonsense suppression ; Omnipotent suppressors ; Gene mapping
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Ten dominant omnipotent suppressors of Saccharomyces cerevisiae, which were previously shown to be different from SUP46, have been examined. Nine are mapped in a region between lys5 and cyh2 on the left arm of chromosome VII. These suppressors, like SUP46, manifest sensitivity to increased temperature and the antibiotics paromomycin and hygromycin B. In addition, they have an identical action spectrum. These results strongly suggest that they are allelic to each other and they are designated SUP138. The tenth is mapped to a position between his1 and arg6 on the right arm of chromosome V. This suppressor, named SUP139, does not manifest temperature sensitivity nor antibiotic sensitivity. SUP139 and SUP138, which are clearly distinguished by means of action spectrum, act on much fewer nonsense mutations than SUP46. It is now clear that dominant omnipotent suppressors arising at a single locus are homogeneous and that their efficiency is locus-dependent. The order of efficiency is SUP46〉SUP138〉SUP139.
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    URL: http://dx.doi.org/10.1007/BF00340710
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    A colony procedure for transformation of Saccharomyces cerevisiae (1988)
    Springer
    Current genetics 13 (1988), S. 21-23 
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    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Transformation ; Plasmid ; Colony ; Polyethylene glycol
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A rapid and simple yeast transformation procedure has been developed using colonies on agar plates. Saccharomyces cerevisiae SHY3 cells were picked up from colonies on YPD plates grown freshly or stored at 4 °C and incubated with M13RK9-T DNA at 30 °C for 1–2 h in a solution of Li+, Ca2+, Mg2+, triacetin and polyethylene glycol. About 3,500 transformants were obtained per µg of double stranded M13RK9-T DNA. Unlike the existing spheroplast techniques, single stranded M13RK9-T DNA transformed intact cells below one-hundredth frequency of the duplex form.
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    URL: http://dx.doi.org/10.1007/BF00365751
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    Cosmids carrying Aspergillus terreus DNA can integrate into Saccharomyces cerevisiae chromosome XII via recombination between yeast and foreign DNAs (1988)
    Springer
    Current genetics 14 (1988), S. 183-189 
    Details
    ISSN: 1432-0983
    Keywords: Aspergillus terreus clonotheque ; Saccharomyces cerevisiae ; Homologous integration ; 2 μ circledirected chromosome destabilization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A genome clonotheque consisting of 25- to 40-kb Sau3A1 fragments of Aspergillus terreus DNA was constructed in the episomal cosmid vector pES33 containing the yeastARG4 gene. From the 475 transformants of cir° yeast strain ESH-0, 23 stable Arg + transformants were independently selected. Genetic and Southern analysis of these stable transformants showed that 39% arose as a result of recombination between cloned A. terreus DNA sequences and yeast chromosome XII. The recombination events most likely occurred in the regions of homology within the rDNA clusters of A. terreus and Saccharomyces cerevisiae.
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    URL: http://dx.doi.org/10.1007/BF00376738
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    The Saccharomyces cerevisiae RAD2 gene complements a Schizosaccharomyces pombe repair mutation (1989)
    Springer
    Current genetics 15 (1989), S. 27-30 
    Details
    ISSN: 1432-0983
    Keywords: Yeast ; Repair ; Complementation ; Saccharomyces cerevisiae ; Schizosaccharomyces pombe ; Gene cloning
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Two Saccharomyces cerevisiae genes necessary for excision repair of UV damage in DNA, RAD1 and RAD2, were introduced individually, on a yeast shuttle vector, into seven Schizosaccharomyces pombe mutants — rads1, 2, 5, 13, 15,16 and 17. The presence of the cloned RAD1 gene did not affect survival of any of the S. pombe mutants. The RAD2 gene increased survival of S. pombe rad13 to near the wild-type level after UV irradiation and had no effect on any of the other mutants tested. S. pombe rad13 mutants are somewhat defective in removal of pyrimidine dimers so complementation by the S. cerevisiae RAD2 gene suggests that the genes may code for equivalent proteins in the two yeasts.
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    URL: http://dx.doi.org/10.1007/BF00445748
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    Introduction of nonselectible 2μ plasmid into [cir°] cells of the yeast S. cerevisiae by DNA transformation and in vivo site-specific resolution (1989)
    Springer
    Current genetics 15 (1989), S. 83-90 
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    ISSN: 1432-0983
    Keywords: DNA transformation ; Saccharomyces cerevisiae ; Site-specific recombination ; 2μ DNA plasmid
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The 2μ DNA plasmid of the yeast Saccharomyces cerevisiae does not confer any known selectable phenotype to the host cell carrying it. Selection of cells transformed with purified 2μ DNA therefore cannot be achieved, and the intracellular presence of 2μ can only be assessed by molecular analysis of the DNA complement. In addition, 2μ alone does not replicate in bacterial hosts, thus rendering its amplification by conventional methods impossible. We have isolated a shuttle plasmid, pBH-2L, generated by in vivo sites-pecific recombination between the endogenous 2μ DNA plasmid and pRL, a pBR322 derivative containing the yeast LEU2 gene and one 2μ repeat sequence associated with the origin of replication. This new shuttle plasmid has the property, when transformed into yeast, of undergoing site-specific recombinational resolution between its two direct repeat sequences. This releases 2μ plasmid and pRL as individual molecules. The latter can undergo progressive mitotic loss during growth in nonselective medium, ultimately leaving leucine auxotrophic transformants that contain only 2μ DNA plasmid. This system can be utilized to introduce 2μ DNA alone into cells lacking it, thereby providing a novel means to study the biology and the molecular genetics of the plasmid and its potential practical applications as a vector.
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    URL: http://dx.doi.org/10.1007/BF00435453
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    A galactose-dependent cmd1 mutant of Saccharomyces cerevisiae: involvement of calmodulin in nuclear division (1989)
    Springer
    Current genetics 15 (1989), S. 113-120 
    Details
    ISSN: 1432-0983
    Keywords: Calmodulin mutant ; Nuclear division ; Chromosome stability ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The coding region of a yeast calmodulin gene was fused to a galactose-inducible GAL1 promoter, and a conditional-lethal mutant of Saccharomyces cerevisiae, in which the expression of calmodulin was regulated by galactose, was constructed. The mutant grew normally in galactose medium, but in glucose medium, in which the promoter was repressed, it ceased growing after 12–15 h. The growth arrest was associated with a decrease in intracellular calmodulin levels: after 12h, no intracellular calmodulin protein was detectable. Analysis of the terminal phenotype showed that when the cell stopped growing, it had a bud, a nucleus after S-phase and a short mitotic spindle. Thus, the defect was mainly in nuclear division. Bud growth was partially inhibited in these cells: 27% of the cells stopped growing with a small bud. Furthermore, calmodulin-deficient cells showed elevated rates of chromosome loss, possibly as the result of a defect in the precise segregation of chromosomes.
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    A rapid and simple method for extracting yeast mitochondrial DNA (1989)
    Springer
    Current genetics 15 (1989), S. 235-237 
    Details
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Mitochondrial DNA ; Method of extraction
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A rapid method for the extraction of yeast mitochondrial DNA (mtDNA) is described. In comparison with previous methods, it simplifies several steps, does not require either the isolation of mitochondria or phenol treatment and is less time consuming. This protocol gives a high yield of pure mtDNA (50–120 μg from a 100-ml culture), which can be directly used in various molecular applications: restriction enzyme digestion, electrophoresis, blotting, labeling, cloning and sequencing.
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    URL: http://dx.doi.org/10.1007/BF00435511
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    Molecular characterization of the two genes SNQ and SFA that confer Hyperresistance to 4-nitroquinoline-N-oxide and formaldehyde in Saccharomyces cerevisiae (1989)
    Springer
    Current genetics 16 (1989), S. 65-74 
    Details
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Mutagen hyperresistance ; Southern, Northern analysis ; Gene transplacement ; Transposon mapping
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The genes SNQ and SFA confer hyperresistance to 4-NQO and FA when present on a multi-copy plasmid in yeast. Both are non-essential genes since transplacement of SNQ by a disrupted snq-0::LEU2 yielded stable and viable haploid integrants. Southern analysis revealed that SNQ and SFA are single-loci genes, and OFAGE analysis showed that they are located on chromosome XIII and IV, respectively. Northern blot analysis of SNQ and SFA revealed poly(A)+ RNA transcripts of 2 kb and 1.7 kb, respectively. Nuclease S 1 mapping showed SNQ to have a coding region of 1.6 kb and SFA, one of 1.3 kb. The 5′ coding regions were determined for both genes, while the 3′ end could only be determined for gene SNQ. Both genes do not appear to contain introns. The SFA locus was also mapped by transposon mutagenesis. Tn10-LUK integrants disrupted the SFA gene function at sites that were determined by subcloning to lie within the SFA transcription unit.
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    URL: http://dx.doi.org/10.1007/BF00393397
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    Cloning and characterization of the SKI3 gene of Saccharomyces cerevisiae demonstrates allelism to SKI5 (1989)
    Springer
    Current genetics 16 (1989), S. 139-143 
    Details
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; SKI3 ; SKI5 ; M1 dsRNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have identified a mutant strain of the yeast Saccharomyces cerevisiae which overproduces killer toxin. This strain contains a single mutation which fails to complement defects in both the SKI3 and SKI5 genes, while a cloned copy of this gene complements both the ski3 and ski5 defects. The level of secreted toxin from a cDNA based plasmid is not increased in a ski3 strain, showing that the overproduction phenotype is dependent upon an increased level of M1 dsRNA.
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    Reassessing the genotoxic potential of 8-MOP + UVA-induced DNA damage in the yeast Saccharomyces cerevisiae (1989)
    Springer
    Current genetics 16 (1989), S. 75-80 
    Details
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Psoralen photoaddition ; Interstrand cross-link ; Repair deficiency ; Genotoxicity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Two different UVA irradiation systems were initially biologically calibrated with two haploid yeast strains proficient and deficient, respectively, in nucleotide excision repair. The number of DNA lesions introduced into the cell's genome by the photoactivated bifunctional furocoumarin 8-MOP was then calculated by means of the applied UVA exposure doses. At LD37 the repair-proficient wild type had about 14 ICL and 34 furan-side monoadducts in its DNA, while doubly blocked repair mutant rad3-12 pso1-1 had 2 ICL and 3 monoadducts. Locus-specific reversion of lys1-1 followed two-hit kinetics in the repair-proficient wild type and one-hit kinetics in an excision-deficient rad2-20 mutant, as would be expected if ICL was the main type of mutagenic lesion in the wild type and monoadducts the main mutagenic lesion type in the excision-deficient strain. Quantitative comparison of 8-MOP + UVA-induced ICL with those induced by bifunctional mustard revealed the former to have a much higher genotoxicity.
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    A recessive mutant allele of the HNM1 gene of Saccharomyces cerevisiae is responsible for hyper-resistance to nitrogen mustard (1990)
    Springer
    Current genetics 18 (1990), S. 187-192 
    Details
    ISSN: 1432-0983
    Keywords: Mutagen hyper-resistance ; Nitrogen mustard ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A screening of haploid yeast strains for enhanced resistance to nitrogen mustard (HN2) yielded a recessive mutant allele, hnm1, that conferred hyper-resistance (HYR) to HN2. Diploids, homo- or heterozygous for the HNM1 locus, exhibit normal wild-type like resistance while homozygosity for hnm1 leads to the phenotype HYR to HN2. The hnm1 mutation could be found in yeast strains proficient or deficient in different DNA repair systems. In these mostly HN2-sensitive haploid repair-deficient mutants, hnm1 acted as a partial suppressor of HN2 sensitivity. All isolated recessive mutations conferring hyper-resistance belonged to a single complementations group. The HYR to HN2 phenotype was maximally expressed in growing cells and was associated with reduced mutability by HN2. HNM1 most probably controls uptake of HN2 which would be impaired in the hnm1 mutants.
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    G418-resistance as a dominant marker and reporter for gene expression in Saccharomyces cerevisiae (1990)
    Springer
    Current genetics 18 (1990), S. 303-313 
    Details
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; G418 resistance ; Gene cartridges ; Heterologous Gene expression
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Coding sequence cartridges for aminoglycoside phosphotransferase (APT) were isolated from bacterial transposon Tn903. When incorporated into a heterologous gene construction utilising the PGK1 promoter and terminator, the heterologous APT gene provided a G418-resistance determinant that functioned efficiently as a dominant marker for yeast in both multiple- and single-copy. Transformant colonies on selective medium appeared rapidly, within 36–48 h, and growth rate of the transformed cells was normal. A simple and highly sensitive radiolabelling assay for APT enzyme activity was developed for use with crude cell protein extracts. Enzyme activity units were equated to the amount of APT protein present in the cells, and the APT protein was shown to be stable in yeast. Heterologous APT expression was 130-fold reduced compared with homologous PGK1. This resulted from an estimated two-fold decrease in mRNA level and a 65-fold decrease in translation efficiency. The latter was unaffected by AUG sequence context change, but corresponded with a high frequency of minor codons in the APT-coding sequence. APT can be used as a semi-quantitative reporter of gene expression, whose useful features are in vivo detection via the G418-resistance phenotype and powerful cell-free assay.
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    A novel mutation that affects utilization of galactose in Saccharomyces cerevisiae (1980)
    Springer
    Current genetics 2 (1980), S. 115-120 
    Details
    ISSN: 1432-0983
    Keywords: Galactose fermentation ; Saccharomyces cerevisiae ; Regulatory mutant
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A novel type of regulatory mutation for galactose metabolism in Saccharomyces cerevisiae is described. The mutation named gal11 was recessive, non-allelic to GAL4, GAL80, GAL2, or GAL3, and unlinked to the gene cluster of GAL1, GAL10, and GAL7. It caused a ‘coordinate’ reduction of galactokinase, galactose-1-P uridylyl transferase, and UDP-glucose 4-epimerase by a factor of more than 5, rendering the mutant cells galactose-nonfermenting. The effect of the mutation was manifested not only in cells grown on galactose but also in cells constitutively synthesizing the galactose-metabolizing enzymes.
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    URL: http://dx.doi.org/10.1007/BF00420623
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