The vertical structure of oceanic Rossby waves: a comparison of high-resolution model data to theoretical vertical structures

Tests of the new Rossby wave theories that have been developed over the past decade to account for discrepancies between theoretical wave speeds and those observed by satellite altimeters have focused primarily on the surface signature of such waves. It appears, however, that the surface signature of the waves acts only as a rather weak constraint, and that information on the vertical structure of the waves is required to better discriminate between competing theories. Due to the lack of 3-D observations, this paper uses high-resolution model data to construct realistic vertical structures of Rossby waves and compares these to structures predicted by theory. The meridional velocity of a section at 24° S in the Atlantic Ocean is pre-processed using the Radon transform to select the dominant westward signal. Normalized profiles are then constructed using three complementary methods based respectively on: (1) averaging vertical profiles of velocity, (2) diagnosing the amplitude of the Radon transform of the westward propagating signal at different depths, and (3) EOF analysis. These profiles are compared to profiles calculated using four different Rossby wave theories: standard linear theory (SLT), SLT plus mean flow, SLT plus topographic effects, and theory including mean flow and topographic effects. Our results support the classical theoretical assumption that westward propagating signals have a well-defined vertical modal structure associated with a phase speed independent of depth, in contrast with the conclusions of a recent study using the same model but for different locations in the North Atlantic. The model structures are in general surface intensified, with a sign reversal at depth in some regions, notably occurring at shallower depths in the East Atlantic. SLT provides a good fit to the model structures in the top 300 m, but grossly overestimates the sign reversal at depth. The addition of mean flow slightly improves the latter issue, but is too surface intensified. SLT plus topography rectifies the overestimation of the sign reversal, but overestimates the amplitude of the structure for much of the layer above the sign reversal. Combining the effects of mean flow and topography provided the best fit for the mean model profiles, although small errors at the surface and mid-depths are carried over from the individual effects of mean flow and topography respectively. Across the section the best fitting theory varies between SLT plus topography and topography with mean flow, with, in general, SLT plus topography performing better in the east where the sign reversal is less pronounced. None of the theories could accurately reproduce the deeper sign reversals in the west. All theories performed badly at the boundaries. The generalization of this method to other latitudes, oceans, models and baroclinic modes would provide greater insight into the variability in the ocean, while better observational data would allow verification of the model findings.

Simulation of the global ENSO–Tropical cyclone teleconnection by a high-resolution coupled general circulation model

This study assesses the influence of the El Niño–Southern Oscillation (ENSO) on global tropical cyclone activity using a 150-yr-long integration with a high-resolution coupled atmosphere–ocean general circulation model [High-Resolution Global Environmental Model (HiGEM); with N144 resolution: ~90 km in the atmosphere and ~40 km in the ocean]. Tropical cyclone activity is compared to an atmosphere-only simulation using the atmospheric component of HiGEM (HiGAM). Observations of tropical cyclones in the International Best Track Archive for Climate Stewardship (IBTrACS) and tropical cyclones identified in the Interim ECMWF Re-Analysis (ERA-Interim) are used to validate the models. Composite anomalies of tropical cyclone activity in El Niño and La Niña years are used. HiGEM is able to capture the shift in tropical cyclone locations to ENSO in the Pacific and Indian Oceans. However, HiGEM does not capture the expected ENSO–tropical cyclone teleconnection in the North Atlantic. HiGAM shows more skill in simulating the global ENSO–tropical cyclone teleconnection; however, variability in the Pacific is overpronounced. HiGAM is able to capture the ENSO–tropical cyclone teleconnection in the North Atlantic more accurately than HiGEM. An investigation into the large-scale environmental conditions, known to influence tropical cyclone activity, is used to further understand the response of tropical cyclone activity to ENSO in the North Atlantic and western North Pacific. The vertical wind shear response over the Caribbean is not captured in HiGEM compared to HiGAM and ERA-Interim. Biases in the mean ascent at 500 hPa in HiGEM remain in HiGAM over the western North Pacific; however, a more realistic low-level vorticity in HiGAM results in a more accurate ENSO–tropical cyclone teleconnection.

Propagation of the Madden–Julian Oscillation and scale interaction with the diurnal cycle in a high-resolution GCM

The Madden–Julian Oscillation (MJO) is the chief source of tropical intra-seasonal variability, but is simulated poorly by most state-of-the-art GCMs. Common errors include a lack of eastward propagation at the correct frequency and zonal extent, and too small a ratio of eastward- to westward-propagating variability. Here it is shown that HiGEM, a high-resolution GCM, simulates a very realistic MJO with approximately the correct spatial and temporal scale. Many MJO studies in GCMs are limited to diagnostics which average over a latitude band around the equator, allowing an analysis of the MJO’s structure in time and longitude only. In this study a wider range of diagnostics is applied. It is argued that such an approach is necessary for a comprehensive analysis of a model’s MJO. The standard analysis of Wheeler and Hendon (Mon Wea Rev 132(8):1917–1932, 2004; WH04) is applied to produce composites, which show a realistic spatial structure in the MJO envelopes but for the timing of the peak precipitation in the inter-tropical convergence zone, which bifurcates the MJO signal. Further diagnostics are developed to analyse the MJO’s episodic nature and the “MJO inertia” (the tendency to remain in the same WH04 phase from one day to the next). HiGEM favours phases 2, 3, 6 and 7; has too much MJO inertia; and dies out too frequently in phase 3. Recent research has shown that a key feature of the MJO is its interaction with the diurnal cycle over the Maritime Continent. This interaction is present in HiGEM but is unrealistically weak.

High-resolution melt and morphological analyses of mealybugs (Hemiptera: Pseudococcidae) from cacao: tools for the control of Cacao Swollen Shoot Virus spread

BACKGROUND: Mealybugs (Hemiptera: Coccoidea: Pseudococcidae) are key vectors of badnaviruses, including Cacao Swollen Shoot Virus (CSSV) the most damaging virus affecting cacao (Theobroma cacao L.). The effectiveness of mealybugs as virus vectors is species dependent and it is therefore vital that CSSV resistance breeding programmes in cacao incorporate accurate mealybug identification. In this work the efficacy of a CO1-based DNA barcoding approach to species identification was evaluated by screening a range of mealybugs collected from cacao in seven countries. RESULTS: Morphologically similar adult females were characterised by scanning electron microscopy and then, following DNA extraction, were screened with CO1 barcoding markers. A high degree of CO1 sequence homology was observed for all 11 individual haplotypes including those accessions from distinct geographical regions. This has allowed for the design of a High Resolution Melt (HRM) assay capable of rapid identification of the commonly encountered mealybug pests of cacao. CONCLUSIONS: HRM Analysis (HRMA) readily differentiated between mealybug pests of cacao that can not necessarily be identified by conventional morphological analysis. This new approach, therefore, has potential to facilitate breeding for resistance to CSSV and other mealybug transmitted diseases.

Convective updraught evaluation in high-resolution NWP simulations using single-Doppler radar measurements

This study presents an evaluation of the size and strength of convective updraughts in high-resolution simulations by the UK Met Office Unified Model (UM). Updraught velocities have been estimated from range–height indicator (RHI) Doppler velocity measurements using the Chilbolton advanced meteorological radar, as part of the Dynamical and Microphysical Evolution of Convective Storms (DYMECS) project. Based on mass continuity and the vertical integration of the observed radial convergence, vertical velocities tend to be underestimated for convective clouds due to the undetected cross-radial convergence. Velocity fields from the UM at a resolution corresponding to the radar observations are used to scale such estimates to mitigate the inherent biases. The analysis of more than 100 observed and simulated storms indicates that the horizontal scale of updraughts in simulations tend to decrease with grid length; the 200 m grid length agreed most closely with the observations. Typical updraught mass fluxes in the 500 m grid length simulations were up to an order of magnitude greater than observed, and greater still in the 1.5 km grid length simulations. The effect of increasing the mixing length in the sub-grid turbulence scheme depends on the grid length. For the 1.5 km simulations, updraughts were weakened though their horizontal scale remained largely unchanged. Progressively more so for the sub-kilometre grid lengths, updraughts were broadened and intensified; horizontal scale was now determined by the mixing length rather than the grid length. In general, simulated updraughts were found to weaken too quickly with height. The findings were supported by the analysis of the widths of reflectivity patterns in both the simulations and observations.

Three-Dimensional Semiautomatic Road Extraction From a High-Resolution Aerial Image by Dynamic-Programming Optimization in the Object Space

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Plasmid-based controls to detect rpoB mutations in Mycobacterium tuberculosis by quantitative polymerase chain reaction-high-resolution melting

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Insights into metal ion binding in phospholipases A(2): ultra high-resolution crystal structures of an acidic phospholipase A(2) in the Ca2+ free and bound states

The electrophile Ca2+ is an essential multifunctional co-factor in the phospholipase A(2) mediated hydrolysis of phospholipids. Crystal structures of an acidic phospholipase A(2) from the venom of Bothrops jararacussu have been determined both in the Ca2+ free and bound states at 0.97 and 1.60 angstrom resolutions, respectively. In the Ca2+ bound state, the Ca2+ ion is penta-coordinated by a distorted pyramidal cage of oxygen and nitrogen atoms that is significantly different to that observed in structures of other Group I/II phospholipases A(2). In the absence of Ca2+, a water molecule occupies the position of the Ca2+ ion and the side chain of Asp49 and the calcium-binding loop adopts a different conformation. (c) 2005 Elsevier SAS. All rights reserved.

Crystal Structure Determination of Mebendazole Form A Using High-Resolution Synchrotron X-Ray Powder Diffraction Data

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Fast sequential multi-element determination of Ca, Mg, K, Cu, Fe, Mn and Zn for foliar diagnosis using high-resolution continuum source flame atomic absorption spectrometry: Feasibility of secondary lines, side pixel registration and least-squares background correction

The fast sequential multi-element determination of Ca, Mg, K, Cu, Fe, Mn and Zn in plant tissues by high-resolution continuum source flame atomic absorption spectrometry is proposed. For this, the main lines for Cu (324.754 nm), Fe (248.327 nm), Mn (279.482 nm) and Zn (213.857 nm) were selected, and the secondary lines for Ca (239.856 nm), Mg (202.582 nm) and K (404.414 nm) were evaluated. The side pixel registration approach was studied to reduce sensitivity and extend the linear working range for Mg by measuring at wings (202.576 nm; 202.577 nm; 202.578 nm; 202.580 nm: 202.585 nm; 202.586 nm: 202.587 nm; 202.588 nm) of the secondary line. The interference caused by NO bands on Zn at 213.857 nm was removed using the least-squares background correction. Using the main lines for Cu, Fe, Mn and Zn, secondary lines for Ca and K, and line wing at 202.588 nm for Mg, and 5 mL min(-1) sample flow-rate, calibration curves in the 0.1-0.5 mg L-1 Cu, 0.5-4.0 mg L-1 Fe, 0.5-4.0 mg L-1 Mn, 0.2-1.0 mg L-1 Zn, 10.0-100.0 mg L-1 Ca, 5.0-40.0 mg L-1 Mg and 50.0-250.0 mg L-1 K ranges were consistently obtained. Accuracy and precision were evaluated after analysis of five plant standard reference materials. Results were in agreement at a 95% confidence level (paired t-test) with certified values. The proposed method was applied to digests of sugar-cane leaves and results were close to those obtained by line-source flame atomic absorption spectrometry. Recoveries of Ca, Mg, K, Cu, Fe, Mn and Zn in the 89-103%, 84-107%, 87-103%, 85-105%, 92-106%, 91-114%, 96-114% intervals, respectively, were obtained. The limits of detection were 0.6 mg L-1 Ca, 0.4 mg L-1 Mg, 0.4 mg L-1 K, 7.7 mu g L-1 Cu, 7.7 mu g L-1 Fe, 1.5 mu g L-1 Mn and 5.9 mu g L-1 Zn. (C) 2009 Elsevier B.V. All rights reserved.

Determination of macro- and micronutrients in plant leaves by high-resolution continuum source flame atomic absorption spectrometry combining instrumental and sample preparation strategies

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Evaluation of solid sampling high-resolution continuum source graphite furnace atomic absorption spectrometry for direct determination of chromium in medicinal plants

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

OFF-LINE SUPERCRITICAL-FLUID EXTRACTION - HIGH-RESOLUTION GAS-CHROMATOGRAPHY APPLIED TO THE STUDY OF MORACEAE SPECIES

Supercritical fluid extraction with CO2, Performed in a home-made system, of rhizomes of Dorstenia bryoniifolia Mart. ex Miq. (Moraceae) and of bark roots of Brosimum gaudichaudii Trecul (Moraceae) afforded crude extracts that were analysed by high resolution gas chromatography (HRGC). The D. bryoniifolia extract contained, besides the previously reported pimpinelin and isobergapten, the furocoumarins psoralen, bergapten, isopimpinelin and the triterpenes alpha- and beta-amyrin and the acetate of the latter. The B. gaudichaudii extract contained a number of terpenoids as well as the previously reported psoralen and bergapten. Supercritical fluid extraction gave extracts qualitatively similar to those obtained by Soxhlet extraction with hexane and, together with off-line HRGC, was shown to be a fast and accurate technique to be used in rapid phytochemical examination.

Crytallization and high-resolution X-ray diffraction data collection of an Asp49 PLA(2) from Bothrops jararacussu venom both in the presence and absence of Ca2+ ions

Snake venom PLA(2)s have been extensively studied due to their role in mediating and disrupting physiological processes such as coagulation, platelet aggregation and myotoxicity. The Ca2+ ion bound to the putative calcium-binding loop is essential for hydrolytic activity. We report the crystallization in the presence and absence of Ca2+ and X-ray diffraction data collection at 1.60 Angstrom (with Ca2+) and 1.36 Angstrom (without Ca2+) of an Asp49 PLA(2) from Bothrops jararacussu venom. The crystals belong to orthorhombic space group C222(1). Initial refinement and electron density analysis indicate significant conformational. changes upon Ca2+ binding. (C) 2004 Elsevier B.V. All fights reserved.

High resolution ultra high pressure liquid chromatography-time-of-flight mass spectrometry dereplication strategy for the metabolite profiling of Brazilian Lippia species

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)