Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array

Background A whole-genome genotyping array has previously been developed for Malus using SNP data from 28 Malus genotypes. This array offers the prospect of high throughput genotyping and linkage map development for any given Malus progeny. To test the applicability of the array for mapping in diverse Malus genotypes, we applied the array to the construction of a SNPbased linkage map of an apple rootstock progeny. Results Of the 7,867 Malus SNP markers on the array, 1,823 (23.2 %) were heterozygous in one of the two parents of the progeny, 1,007 (12.8 %) were heterozygous in both parental genotypes, whilst just 2.8 % of the 921 Pyrus SNPs were heterozygous. A linkage map spanning 1,282.2 cM was produced comprising 2,272 SNP markers, 306 SSR markers and the S-locus. The length of the M432 linkage map was increased by 52.7 cM with the addition of the SNP markers, whilst marker density increased from 3.8 cM/marker to 0.5 cM/marker. Just three regions in excess of 10 cM remain where no markers were mapped. We compared the positions of the mapped SNP markers on the M432 map with their predicted positions on the ‘Golden Delicious’ genome sequence. A total of 311 markers (13.7 % of all mapped markers) mapped to positions that conflicted with their predicted positions on the ‘Golden Delicious’ pseudo-chromosomes, indicating the presence of paralogous genomic regions or misassignments of genome sequence contigs during the assembly and anchoring of the genome sequence. Conclusions We incorporated data for the 2,272 SNP markers onto the map of the M432 progeny and have presented the most complete and saturated map of the full 17 linkage groups of M. pumila to date. The data were generated rapidly in a high-throughput semi-automated pipeline, permitting significant savings in time and cost over linkage map construction using microsatellites. The application of the array will permit linkage maps to be developed for QTL analyses in a cost-effective manner, and the identification of SNPs that have been assigned erroneous positions on the ‘Golden Delicious’ reference sequence will assist in the continued improvement of the genome sequence assembly for that variety.

A theoretical framework for energy and momentum consistency in subgrid-scale parameterization for climate models

A theoretical framework for the joint conservation of energy and momentum in the parameterization of subgrid-scale processes in climate models is presented. The framework couples a hydrostatic resolved (planetary scale) flow to a nonhydrostatic subgrid-scale (mesoscale) flow. The temporal and horizontal spatial scale separation between the planetary scale and mesoscale is imposed using multiple-scale asymptotics. Energy and momentum are exchanged through subgrid-scale flux convergences of heat, pressure, and momentum. The generation and dissipation of subgrid-scale energy and momentum is understood using wave-activity conservation laws that are derived by exploiting the (mesoscale) temporal and horizontal spatial homogeneities in the planetary-scale flow. The relations between these conservation laws and the planetary-scale dynamics represent generalized nonacceleration theorems. A derived relationship between the wave-activity fluxes-which represents a generalization of the second Eliassen-Palm theorem-is key to ensuring consistency between energy and momentum conservation. The framework includes a consistent formulation of heating and entropy production due to kinetic energy dissipation.

On the momentum fluxes associated with mountain waves in directionally sheared flows

The direct impact of mountain waves on the atmospheric circulation is due to the deposition of wave momentum at critical levels, or levels where the waves break. The first process is treated analytically in this study within the framework of linear theory. The variation of the momentum flux with height is investigated for relatively large shears, extending the authors’ previous calculations of the surface gravity wave drag to the whole atmosphere. A Wentzel–Kramers–Brillouin (WKB) approximation is used to treat inviscid, steady, nonrotating, hydrostatic flow with directional shear over a circular mesoscale mountain, for generic wind profiles. This approximation must be extended to third order to obtain momentum flux expressions that are accurate to second order. Since the momentum flux only varies because of wave filtering by critical levels, the application of contour integration techniques enables it to be expressed in terms of simple 1D integrals. On the other hand, the momentum flux divergence (which corresponds to the force on the atmosphere that must be represented in gravity wave drag parameterizations) is given in closed analytical form. The momentum flux expressions are tested for idealized wind profiles, where they become a function of the Richardson number (Ri). These expressions tend, for high Ri, to results by previous authors, where wind profile effects on the surface drag were neglected and critical levels acted as perfect absorbers. The linear results are compared with linear and nonlinear numerical simulations, showing a considerable improvement upon corresponding results derived for higher Ri.

Real estate mutual funds: herding, momentum-trading and performance

This study jointly examines herding, momentum trading and performance in real estate mutual funds (REMFs). We do this using trading and performance data for 159 REMFs across the period 1998–2008. In support of the view that Real Estate Investment Trust (REIT) stocks are relatively more transparent, we find that stock herding by REMFs is lower in REIT stocks than other stock. Herding behavior in our data reveals a tendency for managers to sell winners, reflective of the “disposition effect.” We find low overall levels of REMF momentum trading, but further evidence of the disposition effect when momentum trading is segregated into buy–sell dimensions. We test the robustness of our analysis using style analysis, and by reference to the level of fund dividend distribution. Our results for this are consistent with our conjecture about the role of transparency in herding, but they provide no new insights in relation to the momentum-trading dimensions of our analysis. Summarizing what are complex interrelationships, we find that neither herding nor momentum trading are demonstrably superior investment strategies for REMFs.

The integration of proteomics and systems approaches to map regulatory mechanisms underpinning platelet function.

Platelets in the circulation are triggered by vascular damage to activate, aggregate and form a thrombus that prevents excessive blood loss. Platelet activation is stringently regulated by intracellular signalling cascades, which when activated inappropriately lead to myocardial infarction and stroke. Strategies to address platelet dysfunction have included proteomics approaches which have lead to the discovery of a number of novel regulatory proteins of potential therapeutic value. Global analysis of platelet proteomes may enhance the outcome of these studies by arranging this information in a contextual manner that recapitulates established signalling complexes and predicts novel regulatory processes. Platelet signalling networks have already begun to be exploited with interrogation of protein datasets using in silico methodologies that locate functionally feasible protein clusters for subsequent biochemical validation. Characterization of these biological systems through analysis of spatial and temporal organization of component proteins is developing alongside advances in the proteomics field. This focused review highlights advances in platelet proteomics data mining approaches that complement the emerging systems biology field. We have also highlighted nucleated cell types as key examples that can inform platelet research. Therapeutic translation of these modern approaches to understanding platelet regulatory mechanisms will enable the development of novel anti-thrombotic strategies.

A Web Map Service implementation for the visualization of multidimensional gridded environmental data

We describe ncWMS, an implementation of the Open Geospatial Consortium’s Web Map Service (WMS) specification for multidimensional gridded environmental data. ncWMS can read data in a large number of common scientific data formats – notably the NetCDF format with the Climate and Forecast conventions – then efficiently generate map imagery in thousands of different coordinate reference systems. It is designed to require minimal configuration from the system administrator and, when used in conjunction with a suitable client tool, provides end users with an interactive means for visualizing data without the need to download large files or interpret complex metadata. It is also used as a “bridging” tool providing interoperability between the environmental science community and users of geographic information systems. ncWMS implements a number of extensions to the WMS standard in order to fulfil some common scientific requirements, including the ability to generate plots representing timeseries and vertical sections. We discuss these extensions and their impact upon present and future interoperability. We discuss the conceptual mapping between the WMS data model and the data models used by gridded data formats, highlighting areas in which the mapping is incomplete or ambiguous. We discuss the architecture of the system and particular technical innovations of note, including the algorithms used for fast data reading and image generation. ncWMS has been widely adopted within the environmental data community and we discuss some of the ways in which the software is integrated within data infrastructures and portals.

Sensitivity of simulated climate to conservation of momentum in gravity wave drag parameterization

The Canadian Middle Atmosphere Model is used to examine the sensitivity of simulated climate to conservation of momentum in gravity wave drag parameterization. Momentum conservation requires that the parameterized gravity wave momentum flux at the top of the model be zero and corresponds to the physical boundary condition of no momentum flux at the top of the atmosphere. Allowing momentum flux to escape the model domain violates momentum conservation. Here the impact of momentum conservation in two sets of model simulations is investigated. In the first set, the simulation of present-day climate for two model-lid height configurations, 0.001 and 10 hPa, which are identical below 10 hPa, is considered. The impact of momentum conservation on the climate with the model lid at 0.001 hPa is minimal, which is expected because of the small amount of gravity wave momentum flux reaching 0.001 hPa. When the lid is lowered to 10 hPa and momentum is conserved, there is only a modest impact on the climate in the Northern Hemisphere; however, the Southern Hemisphere climate is more adversely affected by the deflection of resolved waves near the model lid. When momentum is not conserved in the 10-hPa model the climate is further degraded in both hemispheres, particularly in winter at high latitudes, and the impact of momentum conservation extends all the way to the surface. In the second set of simulations, the impact of momentum conservation and model-lid height on the modeled response to ozone depletion in the Southern Hemisphere is considered, and it is found that the response can display significant sensitivity to both factors. In particular, both the lower-stratospheric polar temperature and surface responses are significantly altered when the lid is lowered, with the effect being most severe when momentum is not conserved. The implications with regard to the current round of Intergovernmental Panel on Climate Change model projections are discussed.

Angular momentum conservation and gravity wave drag parameterization: implications for climate models

The robustness of the parameterized gravity wave response to an imposed radiative perturbation in the middle atmosphere is examined. When momentum is conserved and for reasonable gravity wave drag parameters, the response to a polar cooling induces polar downwelling above the region of the imposed cooling, with consequent adiabatic warming. This response is robust to changes in the gravity wave source spectrum, background flow, gravity wave breaking criterion, and model lid height. When momentum is not conserved, either in the formulation or in the implementation of the gravity wave drag parameterization, the response becomes sensitive to the above-mentioned factors—in particular to the model lid height. The spurious response resulting from nonconservation is found to be nonnegligible in terms of the total gravity wave drag–induced downwelling.

The angular momentum constraint on climate sensitivity and downward influence in the middle atmosphere

It is shown that under reasonable assumptions, conservation of angular momentum provides a strong constraint on gravity wave drag feedbacks to radiative perturbations in the middle atmosphere. In the time mean, radiatively induced temperature perturbations above a given altitude z cannot induce changes in zonal mean wind and temperature below z through feedbacks in gravity wave drag alone (assuming an unchanged gravity wave source spectrum). Thus, despite the many uncertainties in the parameterization of gravity wave drag, the role of gravity wave drag in middle-atmosphere climate perturbations may be much more limited than its role in climate itself. This constraint limits the possibilities for downward influence from the mesosphere. In order for a gravity wave drag parameterization to respect the momentum constraint and avoid spurious downward influence, any nonzero parameterized momentum flux at a model lid must be deposited within the model domain, and there must be no zonal mean sponge layer. Examples are provided of how violation of these conditions leads to spurious downward influence. For planetary waves, the momentum constraint does not prohibit downward influence, but it limits the mechanisms by which it can occur: in the time mean, downward influence from a radiative perturbation can only arise through changes in reflection and meridional propagation properties of planetary waves.

Energetics of a symmetric circulation including momentum constraints

A theory of available potential energy (APE) for symmetric circulations, which includes momentum constraints, is presented. The theory is a generalization of the classical theory of APE, which includes only thermal constraints on the circulation. Physically, centrifugal potential energy is included along with gravitational potential energy. The generalization relies on the Hamiltonian structure of the conservative dynamics, although (as with classical APE) it still defines the energetics in a nonconservative framework. It follows that the theory is exact at finite amplitude, has a local form, and can be applied to a variety of fluid models. It is applied here to the f -plane Boussinesq equations. It is shown that, by including momentum constraints, the APE of a symmetrically stable flow is zero, while the energetics of a mechanically driven symmetric circulation properly reflect its causality.

Integration of retrotransposons-based markers in a linkage map of barley

A deeper understanding of random markers is important if they are to be employed for a range of objectives. The sequence specific amplified polymorphism (S-SAP) technique is a powerful genetic analysis tool which exploits the high copy number of retrotransposon long terminal repeats (LTRs) in the plant genome. The distribution and inheritance of S-SAP bands in the barley genome was studied using the Steptoe × Morex (S × M) double haploid (DH) population. Six S-SAP primer combinations generated 98 polymorphic bands, and map positions were assigned to all but one band. Eight putative co-dominant loci were detected, representing 16 of the mapped markers. Thus at least 81 of the mapped S-SAP loci were dominant. The markers were distributed along all of the seven chromosomes and a tendency to cluster was observed. The distribution of S-SAP markers over the barley genome concurred with the knowledge of the high copy number of retrotransposons in plants. This experiment has demonstrated the potential for the S-SAP technique to be applied in a range of analyses such as genetic fingerprinting, marker assisted breeding, biodiversity assessment and phylogenetic analyses.

Construction of a Festuca pratensis BAC library for map-based cloning in Festulolium substitution lines

Introgression in Festulolium is a potentially powerful tool to isolate genes for a large number of traits which differ between Festuca pratensis Huds. and Lolium perenne L. Not only are hybrids between the two species fertile, but the two genomes can be distinguished by genomic in situ hybridisation and a high frequency of recombination occurs between homoeologous chromosomes and chromosome segments. By a programme of introgression and a series of backcrosses, L. perenne lines have been produced which contain small F. pratensis substitutions. This material is a rich source of polymorphic markers targeted towards any trait carried on the F. pratensis substitution not observed in the L. perenne background. We describe here the construction of an F. pratensis BAC library, which establishes the basis of a map-based cloning strategy in L. perenne. The library contains 49,152 clones, with an average insert size of 112 kbp, providing coverage of 2.5 haploid genome equivalents. We have screened the library for eight amplified fragment length polymorphism (AFLP) derived markers known to be linked to an F. pratensis gene introgressed into L. perenne and conferring a staygreen phenotype as a consequence of a mutation in primary chlorophyll catabolism. While for four of the markers it was possible to identify bacterial artificial chromosome (BAC) clones, the other four AFLPs were too repetitive to enable reliable identification of locus-specific BACs. Moreover, when the four BACs were partially sequenced, no obvious coding regions could be identified. This contrasted to BACs identified using cDNA sequences, when multiple genes were identified on the same BAC.

Tracking the momentum flux of a CME and quantifying its influence on geomagnetically induced currents at Earth

We investigate a coronal mass ejection (CME) propagating toward Earth on 29 March 2011. This event is specifically chosen for its predominately northward directed magnetic field, so that the influence from the momentum flux onto Earth can be isolated. We focus our study on understanding how a small Earth-directed segment propagates. Mass images are created from the white-light cameras onboard STEREO which are also converted into mass height-time maps (mass J-maps). The mass tracks on these J-maps correspond to the sheath region between the CME and its associated shock front as detected by in situ measurements at L1. A time series of mass measurements from the STEREO COR-2A instrument is made along the Earth propagation direction. Qualitatively, this mass time series shows a remarkable resemblance to the L1 in situ density series. The in situ measurements are used as inputs into a three-dimensional (3-D) magnetospheric space weather simulation from the Community Coordinated Modeling Center. These simulations display a sudden compression of the magnetosphere from the large momentum flux at the leading edge of the CME, and predictions are made for the time derivative of the magnetic field (dB/dt) on the ground. The predicted dB/dt values were then compared with the observations from specific equatorially located ground stations and showed notable similarity. This study of the momentum of a CME from the Sun down to its influence on magnetic ground stations on Earth is presented as a preliminary proof of concept, such that future attempts may try to use remote sensing to create density and velocity time series as inputs to magnetospheric simulations.

Simulations of angular momentum evolution in wind-fed CV precursors

It is thought that the secondary stars in cataclysmic variables (CVs) may undergo a period of mass loss in the form of a wind during the evolution of the system (Mullan et al. 1992). This wind is thought to magnetically brake the secondary star with a time-scale ~ 10^8 yr (e.g. van Paradijs 1986). When the secondary’s spin has been brought close to synchronism with the orbit it is possible for tidal torques to lock the secondary in synchronous rotation.