A simple method for estimating frequency response corrections for eddy covariance systems,

Abstract A simple analytical formula is developed for estimating the frequency attenuation of eddy covariance fluxes due to sensor response, path-length averaging, sensor separation, signal processing, and flux averaging periods. Although it is an approximation based on flat terrain cospectra, this analytical formula should have broader applicability than just flat-terrain providing the peak frequencies of the logarithmic cospectra are known. Comparing the integral and analytical formulations for momentum flux, heat flux, vapor flux, and closed-path and open-path CO 2 eddy covariance systems demonstrates that, except for a relatively uncommon atmospheric condition, the absolute difference between the integral and approximate correction factors is less than ±0.06 for both stable and unstable atmospheric conditions (0≤z/L≤2). Because closed-path systems can have the tube entrance separated longitudinally from the sonic anemometer, a cospectral transfer function is developed for the phase shift caused by the intrinsic time constant of a first-order scalar instrument and the longitudinal separation of the mouth of the tube and the sonic anemometer. The related issues of tube lag time and other spectral transfer functions are also discussed. In general, it is suggested that the simple formula should be quite useful for experimental design and numerical correction of eddy covariance systems for frequency attenuation. Published by Elsevier Science B.V

The fundamental equation of eddy covariance and its application in flux measurements

A fundamental equation of eddy covariance (FQEC) is derived that allows the net ecosystem exchange (NEE) N̅s of a specified atmospheric constituent s to be measured with the constraint of conservation of any other atmospheric constituent (e.g. N2, argon, or dry air). It is shown that if the condition │N̅s│ ˃˃ │X̅s│ │N̅co2│is true, the conservation of mass can be applied with the assumption of no net ecosystem source or sink of dry air and the FQEC is reduced to the following equation and its approximation for horizontally homogeneous mass fluxes: N̅s = c̅dw’X’s│h + ∫h0 c̅d(z) ∂Xs/∂t dz + ∫h0 [X̅s (z)- X̅s (h)] ∂̅c̅d̅/∂t dz = c̅d̅(h) {w̅’X̅’s│h + ∫h0 ∂Xs/∂t dz}. Here w is vertical velocity, c molar density, t time, h eddy flux measurement height, z vertical distance and Xs= cs/cd molar mixing ratio relative to dry air. Subscripts s, d and CO2 are for the specified constituent, dry air and carbon dioxide, respectively. Primes and overbars refer to turbulent fluctuations and time averages, respectively. This equation and its approximation are derived for non-steady state conditions that build on the steady-state theory of Webb, Pearman and Leuning (WPL; Webb et al., 1980. Quart. J. R. Meteorol. Soc. 106, 85–100), theory that is widely used to calculate the eddy fluxes of CO2 and other trace gases. The original WPL constraint of no vertical flux of dry air across the EC measurement plane, which is valid only for steady-state conditions, is replaced with the requirement of no net ecosystem source or sink of dry air for non-steady state conditions. This replacement does not affect the ‘eddy flux’ term c̅d̅w̅’X̅’s s but requires the change in storage to be calculated as the ‘effective change in storage’ as follows: ∫h0 ∂̅c̅s̅/ ∂̅t̅ dz – X̅s(h) ∫h0 ∂̅c̅d̅/∂t dz = ∫h0 c̅d̅ (z) - ∂Xs/∂t dz + ∫h0 [X̅s (z)- X̅s (h)] ∂̅c̅d̅/∂t dz= c̅d (h) ∫h0 ∂Xs/∂t dz. Without doing so, significant diurnal and seasonal biases may occur. We demonstrate that the effective change in storage can be estimated accurately with a properly designed profile of mixing ratio measurements made at multiple heights. However further simplification by using a single measurement at the EC instrumentation height is shown to produce substantial biases. It is emphasized that an adequately designed profile system for measuring the effective change in storage in proper units is as important as the eddy flux term for determining NEE

The fundamental equation of eddy covariance and its application in flux measurements

A fundamental equation of eddy covariance (FQEC) is derived that allows the net ecosystem exchange (NEE) N̅s of a specified atmospheric constituent s to be measured with the constraint of conservation of any other atmospheric constituent (e.g. N2, argon, or dry air). It is shown that if the condition │N̅s│ ˃˃ │X̅s│ │N̅co2│is true, the conservation of mass can be applied with the assumption of no net ecosystem source or sink of dry air and the FQEC is reduced to the following equation and its approximation for horizontally homogeneous mass fluxes: N̅s = c̅dw’X’s│h + ∫h0 c̅d(z) ∂Xs/∂t dz + ∫h0 [X̅s (z)- X̅s (h)] ∂̅c̅d̅/∂t dz = c̅d̅(h) {w̅’X̅’s│h + ∫h0 ∂Xs/∂t dz}. Here w is vertical velocity, c molar density, t time, h eddy flux measurement height, z vertical distance and Xs= cs/cd molar mixing ratio relative to dry air. Subscripts s, d and CO2 are for the specified constituent, dry air and carbon dioxide, respectively. Primes and overbars refer to turbulent fluctuations and time averages, respectively. This equation and its approximation are derived for non-steady state conditions that build on the steady-state theory of Webb, Pearman and Leuning (WPL; Webb et al., 1980. Quart. J. R. Meteorol. Soc. 106, 85–100), theory that is widely used to calculate the eddy fluxes of CO2 and other trace gases. The original WPL constraint of no vertical flux of dry air across the EC measurement plane, which is valid only for steady-state conditions, is replaced with the requirement of no net ecosystem source or sink of dry air for non-steady state conditions. This replacement does not affect the ‘eddy flux’ term c̅d̅w̅’X̅’s s but requires the change in storage to be calculated as the ‘effective change in storage’ as follows: ∫h0 ∂̅c̅s̅/ ∂̅t̅ dz – X̅s(h) ∫h0 ∂̅c̅d̅/∂t dz = ∫h0 c̅d̅ (z) - ∂Xs/∂t dz + ∫h0 [X̅s (z)- X̅s (h)] ∂̅c̅d̅/∂t dz= c̅d (h) ∫h0 ∂Xs/∂t dz. Without doing so, significant diurnal and seasonal biases may occur. We demonstrate that the effective change in storage can be estimated accurately with a properly designed profile of mixing ratio measurements made at multiple heights. However further simplification by using a single measurement at the EC instrumentation height is shown to produce substantial biases. It is emphasized that an adequately designed profile system for measuring the effective change in storage in proper units is as important as the eddy flux term for determining NEE

Functional interactions between NADPH oxidase 5 and actin

NADPH oxidase 5 (NOX5) is a transmembrane oxidative signaling enzyme which produces superoxide in response to intracellular calcium flux. Increasing evidence indicates that NOX5 is involved in a variety of physiological processes as well as human disease, however, details of NOX5 signaling pathways and targets of NOX5 mediated oxidative modifications remain poorly resolved. Actin dynamics have previously been shown to be modulated by oxidative modification, however, a direct connection to NOX5 expression and activity has not been fully explored. Here we show that NOX5 and actin interact in the cell, and each modulate the activity of the other. Using actin effector molecules jasplakinolide, cytochalasin D and latrunculin A, we show that changes in actin dynamics affect NOX5 superoxide production. In tandem, NOX5 oxidatively modifies actin, and shifts the ratio of filamentous to monomeric actin. Finally, we show that knockdown of NOX5 in the pancreatic cancer cell line PSN-1 impairs cell migration. Together our findings indicate an important link between actin dynamics and oxidative signaling through NOX5

High-frequency pressure variations in the vicinity of a surface CO2 flux chamber

We report measurements of 2 Hz pressure fluctuations at and below the soil surface in the vicinity of a surface-based CO2 flux chamber. These measurements were part of a field experiment to examine the possible role of pressure pumping due to atmospheric pressure fluctuations on measurements of surface fluxes of CO2. Under the moderate wind speeds, warm temperatures, and dry soil conditions present at the time of our observations, the chamber had no effect on the pressure field in its near vicinity that could be detected above the level of natural pressure fluctuations in the vicinity. At frequencies at or \u3c2 Hz, pressure fluctuations easily penetrated the soil to depths of several cm with little attenuation. We conclude that the presence of the chamber does not introduce pressure perturbations that lead to biases in measurements of surface fluxes of CO2

Comparison of different stomatal conductance algorithms for ozone flux modelling

A multiplicative and a semi-mechanistic, BWB-type [Ball, J.T., Woodrow, I.E., Berry, J.A., 1987. A model predicting stomatalconductance and its contribution to the control of photosynthesis under different environmental conditions. In: Biggens, J. (Ed.), Progress in Photosynthesis Research, vol. IV. Martinus Nijhoff, Dordrecht, pp. 221–224.] algorithm for calculating stomatalconductance (gs) at the leaf level have been parameterised for two crop and two tree species to test their use in regional scale ozone deposition modelling. The algorithms were tested against measured, site-specific data for durum wheat, grapevine, beech and birch of different European provenances. A direct comparison of both algorithms showed a similar performance in predicting hourly means and daily time-courses of gs, whereas the multiplicative algorithm outperformed the BWB-type algorithm in modelling seasonal time-courses due to the inclusion of a phenology function. The re-parameterisation of the algorithms for local conditions in order to validate ozone deposition modelling on a European scale reveals the higher input requirements of the BWB-type algorithm as compared to the multiplicative algorithm because of the need of the former to model net photosynthesis (An

Spectral Characteristics and Correction of Long-Term Eddy-Covariance Measurements Over Two Mixed Hardwood Forests in Non-Flat Terrain

We present turbulence spectra and cospectra derived from long-term eddy-covariancemeasurements (nearly 40,000 hourly data over three to four years) and the transferfunctions of closed-path infrared gas analyzers over two mixed hardwood forests inthe mid-western U.S.A. The measurement heights ranged from 1.3 to 2.1 times themean tree height, and peak vegetation area index (VAI) was 3.5 to 4.7; the topographyat both sites deviates from ideal flat terrain. The analysis follows the approach ofKaimal et al. ( Quart. J. Roy. Meteorol. Soc. 98 , 563–589, 1972) whose results were based upon 15 hours of measurements atthree heights in the Kansas experiment over flatter and smoother terrain. Both thespectral and cospectral constants and stability functions for normalizing and collapsingspectra and cospectra in the inertial subrange were found to be different from those ofKaimal et al. In unstable conditions, we found that an appropriate stabilityfunction for the non-dimensional dissipation of turbulent kinetic energy is of the form Φ ε(ζ) = (1 - b - ζ) -1/4 - c - ζ, where ζ representsthe non-dimensional stability parameter. In stable conditions, a non-linear functionG xy (ζ) = 1 + b xy ζ c xy (c xy < 1) was found to benecessary to collapse cospectra in the inertial subrange. The empirical cospectralmodels of Kaimal et al. were modified to fit the somewhat more (neutraland unstable) or less (stable) sharply peaked scalar cospectra observed over forestsusing the appropriate cospectral constants and non-linear stability functions. Theempirical coefficients in the stability functions and in the cospectral models varywith measurement height and seasonal changes in VAI. The seasonal differencesare generally larger at the Morgan Monroe State Forest site (greater peak VAI) andcloser to the canopy.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/42506/1/10546_2004_Article_5127238.pd

The USDA Barley Core Collection:Genetic Diversity, Population Structure, and Potential for Genome-Wide Association Studies

New sources of genetic diversity must be incorporated into plant breeding programs if they are to continue increasing grain yield and quality, and tolerance to abiotic and biotic stresses. Germplasm collections provide a source of genetic and phenotypic diversity, but characterization of these resources is required to increase their utility for breeding programs. We used a barley SNP iSelect platform with 7,842 SNPs to genotype 2,417 barley accessions sampled from the USDA National Small Grains Collection of 33,176 accessions. Most of the accessions in this core collection are categorized as landraces or cultivars/breeding lines and were obtained from more than 100 countries. Both STRUCTURE and principal component analysis identified five major subpopulations within the core collection, mainly differentiated by geographical origin and spike row number (an inflorescence architecture trait). Different patterns of linkage disequilibrium (LD) were found across the barley genome and many regions of high LD contained traits involved in domestication and breeding selection. The genotype data were used to define 'mini-core' sets of accessions capturing the majority of the allelic diversity present in the core collection. These 'mini-core' sets can be used for evaluating traits that are difficult or expensive to score. Genome-wide association studies (GWAS) of 'hull cover', 'spike row number', and 'heading date' demonstrate the utility of the core collection for locating genetic factors determining important phenotypes. The GWAS results were referenced to a new barley consensus map containing 5,665 SNPs. Our results demonstrate that GWAS and high-density SNP genotyping are effective tools for plant breeders interested in accessing genetic diversity in large germplasm collections