Measurements of internal wave band eddy fluxes above a sloping bottom

The boundary layer near a sloping bottom may have a major influence on the ocean\u27s interior density structure (due to “boundary mixing”) and on its circulation (because of the arrest of the Ekman layer by buoyancy forces). As a first attempt to measure eddy fluxes of momentum and buoyancy, in order to quantify the mixing in this region, we have carried out a 5-day pilot experiment on a sloping side of Emerald Basin on the Scotian Shelf. A moored upward-looking 1.2 MHz ADCP and a thermistor chain mounted along its vertical axis returned analyzable data between 8 and 17 m above the bottom at one-minute intervals. An extensive set of microstructure profiles was also obtained. The predominantly tidal flow regime causes the bottom boundary layer thickness to vary between 3 \u3c z \u3c 30 m, with most high frequency activity during the upslope phase. A bottom-normal momentum flux significantly different from zero is found in the cross-isobath direction only. The main contribution comes from a band near the buoyancy frequency N, possibly indicative of advective or Kelvin-Helmholtz instability. When cast in terms of mean-flow shear, the stress yields an eddy viscosity A ≈ 9 × 10−3 m2 s−1 within the boundary layer and twice this value at z = 15 m, the average height of the pycnocline that caps the boundary layer. The buoyancy flux also seems to be dominated by fluctuating signals near N, but is countergradient and only significantly different from zero at a height of about 15 m. The associated restratification occurs in short periods of approximately one hour when isotherms rise rapidly. Indirect evidence for the importance of the tertiary circulation within the boundary layer is found from the gradient of stress divergence and the mean bottom-normal velocity. An approximate turbulent kinetic energy balance has been investigated, with the currents split into three parts (mean, tidal, and the high frequency part of the internal waveband (“turbulence”)). Production balances viscous dissipation within a factor of 2. Turbulent kinetic energy production by interaction between the turbulent Reynolds stress and the mean flow shear and tidal shear are of the same order of magnitude, but the buoyancy term appears to be of equal importance at the pycnocline

Measuring lateral heat flux across a thermohaline front: A model and observational test

We develop and test a method to observationally estimate lateral intrusive heat flux across a front. The model combines that of Joyce (1977), in which lateral cross-frontal advection by intrusions creates vertical temperature gradients, and Osborn and Cox (1972) in which vertical mixing of those gradients creates thermal microstructure that is dissipated by molecular conduction of heat. Observations of thermal microstructure dissipation χT are then used to estimate the production by intrusions, and hence the lateral heat flux and diffusivity. This method does not depend on the precise mechanism(s) of mixing, or on the dynamical mechanisms driving the frontal intrusions. It relies on several assumptions: (1) lateral cross-frontal advection produces diapycnal temperature gradients that are mixed locally, (2) thermal variance is dissipated locally and not exported, (3) intrusion scales are larger than turbulence scales, and (4) isotropy of temperature microstructure is assumed in order to estimate χT.The method is tested using microstructure observations in Meddy Sharon, where the erosion rate and associated lateral heat flux are known from successive mesoscale hydrographic observations (Hebert et al., 1990). An expression is developed for the production (lateral heat flux times lateral temperature gradient, expected to equal χT) in a front of steady shape that is eroding (detraining) at a steady rate; the production is proportional to the erosion speed and the square of the cross-frontal temperature contrast, both of which are well-known from observations. The qualitative structure and integrated value of the dissipation agree well with model assumptions and predictions: thermal variance produced by lateral intrusive heat flux is dissipated locally, dissipation in intrusive regions dominates total dissipation, and the total dissipation agrees with the observed erosion rate, all of which suggests that microstructure observations can be used to estimate intrusive heat flux. A direct comparison was made between lateral heat flux estimated from mesoscale Meddy structure plus the known rate of erosion, and lateral flux based on microscale temperature dissipation, with excellent agreement in the frontal zone and poorer agreement where lateral temperature gradient is too small to accurately measure

Stirring by small-scale vortices caused by patchy mixing

Author Posting. © American Meteorological Society, 2005. 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 35 (2005): 1245-1262, doi:10.1175/JPO2713.1.Evidence is presented that lateral dispersion on scales of 1–10 km in the stratified waters of the continental shelf may be significantly enhanced by stirring by small-scale geostrophic motions caused by patches of mixed fluid adjusting in the aftermath of diapycnal mixing events. Dye-release experiments conducted during the recent Coastal Mixing and Optics (CMO) experiment provide estimates of diapycnal and lateral dispersion. Microstructure observations made during these experiments showed patchy turbulence on vertical scales of 1–10 m and horizontal scales of a few hundred meters to a few kilometers. Momentum scaling and a simple random walk formulation were used to estimate the effective lateral dispersion caused by motions resulting from lateral adjustment following episodic mixing events. It is predicted that lateral dispersion is largest when the scale of mixed patches is on the order of the internal Rossby radius of deformation, which seems to have been the case for CMO. For parameter values relevant to CMO, lower-bound estimates of the effective lateral diffusivity by this mechanism ranged from 0.1 to 1 m2s−1. Revised estimates after accounting for the possibility of long-lived motions were an order of magnitude larger and ranged from 1 to 10 m2s−1. The predicted dispersion is large enough to explain the observed lateral dispersion in all four CMO dye-release experiments examined.The Coastal Mixing and Optics dye studies were funded by the Office of Naval Research under Grants N00014-95-1-0633 (tracer experiments) and N00014-95-1-1063 (AASERT fellowship). Additional analysis was also performed under ONR Grant N00014-01-1-0984

A genome wide association scan for (1,3;1,4)-β-glucan content in the grain of contemporary 2-row Spring and Winter barleys

Published: 17 October 2014BACKGROUND: (1,3;1,4)-β-Glucan is an important component of the cell walls of barley grain as it affects processability during the production of alcoholic beverages and has significant human health benefits when consumed above recommended threshold levels. This leads to diametrically opposed quality requirements for different applications as low levels of (1,3;1,4)-β-glucan are required for brewing and distilling and high levels for positive impacts on human health. RESULTS: We quantified grain (1,3;1,4)-β-glucan content in a collection of 399 2-row Spring-type, and 204 2-row Winter-type elite barley cultivars originating mainly from north western Europe. We combined these data with genotypic information derived using a 9 K Illumina iSelect SNP platform and subsequently carried out a Genome Wide Association Scan (GWAS). Statistical analysis accounting for residual genetic structure within the germplasm collection allowed us to identify significant associations between molecular markers and the phenotypic data. By anchoring the regions that contain these associations to the barley genome assembly we catalogued genes underlying the associations. Based on gene annotations and transcript abundance data we identified candidate genes. CONCLUSIONS: We show that a region of the genome on chromosome 2 containing a cluster of CELLULOSE SYNTHASE-LIKE (Csl) genes, including CslF3, CslF4, CslF8, CslF10, CslF12 and CslH, as well as a region on chromosome 1H containing CslF9, are associated with the phenotype in this germplasm. We also observed that several regions identified by GWAS contain glycoside hydrolases that are possibly involved in (1,3;1,4)-β-glucan breakdown, together with other genes that might participate in (1,3;1,4)-β-glucan synthesis, re-modelling or regulation. This analysis provides new opportunities for understanding the genes related to the regulation of (1,3;1,4)-β-glucan content in cereal grains.Kelly Houston, Joanne Russell, Miriam Schreiber, Claire Halpin, Helena Oakey, Jennifer M Washington, Allan Booth, Neil Shirley, Rachel A Burton, Geoffrey B Fincher and Robbie Waug

Layered mixing on the New England Shelf in summer

The article of record as published may be located at http://dx.doi.org/10.1002/2014JC009947The layered structure of stratification and mixing on the New England Shelf (NES) in summer is examined by analyzing a comprehensive set of observations of hydrography, currents and turbulence. A clear distinction in mixing characteristics between the midcolumn water (consisting of subsurface stratification, middepth weak stratification and lower-layer stratification) and a well-mixed bottom boundary layer (BBL) is revealed. The combination of subtidal Ekman onshore bottom transport and cross-shore density gradient created a lower-layer stratification that inhibited the upward extension of the BBL turbulence. The BBL mixing was related to strong shear generated by bottom stress, and the magnitude and periodic variation of BBL mixing was determined by both the tidal and subtidal flows. Mixing in the midcolumn water occurred under stably stratified conditions and showed correspondence with the occurrence of near-inertial and semidiurnal internal waves. Positive correlations between buoyancy frequency squared (N2) and shear variance (S2), S2 and dissipation rate (e), N2 and e are established in the midcolumn, but not in the BBL. The midcolumn e was reasonably described by a slightly modified MacKinnon-Gregg (MG) model.The field component of this program was jointly supported by the US Office of Naval Research (grants N00014-95-1-1030, N00014-95-1-0373, and N00014-96-1- 0953) and Fisheries and Oceans of Canada

The history and decay of a Mediterranean salt lens

Subsurface coherent vortices called Meddies1 are formed by the outflow of salty water from the Mediterranean Sea1,2 into the North Atlantic. In October 1984 we began a study to observe the life history and large-scale changes of a Meddy by identifying a specific Meddy, and carefully mapping it and seeding it with Sofar floats3. (These neutrally buoyant floats are tracked acoustically and can be located aboard ship.) As this Meddy moved southward across the Madeira Abyssal plain, it was resurveyed three more times during a span of two years. Being able to find this same lens (100km in diameter) on successive surveys was itself a unique achievement that allowed us to observe the Meddy evolution and to gain new insight into the importance of different mixing mechanisms that cause Meddy decay. We find evidence of mixing by at least three processes: (1) lateral mixing by the exchange of layers of water (\u27thermohaline intrusions\u27)4,5, (2) vertical mixing at the underside of the lens by salt fingers6 and (3) mixing by turbulence. Together these cause the net heat and salt anomalies to decay with an e-folding time of about one year. Despite the mixing, the relative vorticity at the core remained constant for the first year and the Meddy retained its coherent shape over a two-year period. © 1988 Nature Publishing Group

Observations and modelling of the tidal bottom boundary layer on the southern flank of Georges bank

We examine the vertical structure of the tidally driven bottom boundary layer during nearly homogeneous (N2 \u3c 10-5 s-2) and strongly stratified (N2 ∼ 10-4 s-2) conditions in a shallow coastal region dominated by semidiurnal tides. From moored array and shipboard measurements taken at a 76-m-deep study site on the southern flank of Georges Bank, we infer tidal velocity profiles, bottom stress estimates, Richardson numbers, and turbulent dissipation rates. On the basis of our measurements, we discuss changes in tidal boundary-layer dynamics in the presence of weak and strong stratification. We compare observations to results from two different one-dimensional numerical circulation models: a two-layer eddy viscosity model with linear eddy viscosity distribution in the lower layer and constant eddy viscosity in the upper layer (2LK), and a continuously varying eddy viscosity model (both in time and in the vertical) with Mellor-Yamada level 2.5 closure (MY2.5). Both models compare favorably with observations during nearly homogeneous conditions, but show disagreement with data when the water column is strongly stratified. In the case of 2LK, the model overestimates the bottom stress and does not reproduce the observed velocity maximum at mid-depth. This behavior is clearly related to the absence of buoyancy effects in the simplistic turbulence closure scheme. The advanced MY2.5 scheme, on the other hand, reproduces the observed velocity distribution and bottom stress well. However, the model also predicts an abrupt adjustment from the turbulent bottom boundary layer to a nearly nonturbulent region above which is not supported by our Richardson number estimates and observed turbulent dissipation rates. Potential reasons explaining the discrepancies between observations and MY2.5 include high-frequency internal-wave mixing and underestimation of the critical Richardson number used by the model to describe the transition from active to decaying turbulence. Copyright 2003 by the American Geophysical Union

Event logs from the U.S. GLOBEC Georges Bank project, from 10 vessels and 104 cruises in the Gulf of Maine and Georges Bank area from 1994-1999 (GB project)

Dataset: eventlogsEvent logs from the U.S. GLOBEC Georges Bank project, from 10 vessels and 104 cruises in the Gulf of Maine and Georges Bank area from 1994-1999. Event logs provide an overall summary of the sampling activities during a cruise. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/2321National Science Foundation (NSF) unknown GB NSF, National Oceanic and Atmospheric Administration (NOAA) unknown GB NOA

Linear assembly of a human centromere on the Y chromosome

The human genome reference sequence remains incomplete owing to the challenge of assembling long tracts of near-identical tandem repeats in centromeres. We implemented a nanopore sequencing strategy to generate high-quality reads that span hundreds of kilobases of highly repetitive DNA in a human Y chromosome centromere. Combining these data with short-read variant validation, we assembled and characterized the centromeric region of a human Y chromosome