Past and future of a century old Citrus tristeza virus collection: a California citrus germplasm tale.

Citrus tristeza virus (CTV) isolates collected from citrus germplasm, dooryard and field trees in California from 1914 have been maintained in planta under quarantine in the Citrus Clonal Protection Program (CCPP), Riverside, California. This collection, therefore, represents populations of CTV isolates obtained over time and space in California. To determine CTV genetic diversity in this context, genotypes of CTV isolates from the CCPP collection were characterized using multiple molecular markers (MMM). Genotypes T30, VT, and T36 were found at high frequencies with T30 and T30+VT genotypes being the most abundant. The MMM analysis did not identify T3 and B165/T68 genotypes; however, biological and phylogenetic analysis suggested some relationships of CCPP CTV isolates with these two genotypes. Phylogenetic analysis of the CTV coat protein (CP) gene sequences classified the tested isolates into seven distinct clades. Five clades were in association with the standard CTV genotypes T30, T36, T3, VT, and B165/T68. The remaining two identified clades were not related to any standard CTV genotypes. Spatiotemporal analysis indicated a trend of reduced genotype and phylogenetic diversity as well as virulence from southern California (SC) at early (1907-1957) in comparison to that of central California (CC) isolates collected from later (1957-2009) time periods. CTV biological characterization also indicated a reduced number and less virulent stem pitting (SP) CTV isolates compared to seedling yellows isolates introduced to California. This data provides a historical insight of the introduction, movement, and genetic diversity of CTV in California and provides genetic and biological information useful for CTV quarantine, eradication, and disease management strategies such as CTV-SP cross protection

AtCAP2 is crucial for lytic vacuole biogenesis during germination by positively regulating vacuolar protein trafficking

Protein trafficking is a fundamental mechanism of subcellular organization and contributes to organellar biogenesis. AtCAP2 is an Arabidopsis homolog of the Mesembryanthemum crystallinum calcium-dependent protein kinase 1 adaptor protein 2 (McCAP2), a member of the syntaxin superfamily. Here, we show that AtCAP2 plays an important role in the conversion to the lytic vacuole (LV) during early plant development. The AtCAP2 loss-of-function mutant atcap2-1 displayed delays in protein storage vacuole (PSV) protein degradation, PSV fusion, LV acidification, and biosynthesis of several vacuolar proteins during germination. At the mature stage, atcap2-1 plants accumulated vacuolar proteins in the pre-vacuolar compartment (PVC) instead of the LV. In wild-type plants, AtCAP2 localizes to the PVC as a peripheral membrane protein and in the PVC compartment recruits glyceraldehyde-3-phosphate dehydrogenase C2 (GAPC2) to the PVC. We propose that AtCAP2 contributes to LV biogenesis during early plant development by supporting the trafficking of specific proteins involved in the PSV-to-LV transition and LV acidification during early stages of plant development.11Ysciescopu

An observing system simulation experiment for the calibration and validation of the surface water ocean topography sea surface height measurement using in situ platforms

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 Atmospheric and Oceanic Technology 35 (2018): 281-297, doi:10.1175/JTECH-D-17-0076.1.The wavenumber spectrum of sea surface height (SSH) is an important indicator of the dynamics of the ocean interior. While the SSH wavenumber spectrum has been well studied at mesoscale wavelengths and longer, using both in situ oceanographic measurements and satellite altimetry, it remains largely unknown for wavelengths less than ~70 km. The Surface Water Ocean Topography (SWOT) satellite mission aims to resolve the SSH wavenumber spectrum at 15–150-km wavelengths, which is specified as one of the mission requirements. The mission calibration and validation (CalVal) requires the ground truth of a synoptic SSH field to resolve the targeted wavelengths, but no existing observational network is able to fulfill the task. A high-resolution global ocean simulation is used to conduct an observing system simulation experiment (OSSE) to identify the suitable oceanographic in situ measurements for SWOT SSH CalVal. After fixing 20 measuring locations (the minimum number for resolving 15–150-km wavelengths) along the SWOT swath, four instrument platforms were tested: pressure-sensor-equipped inverted echo sounders (PIES), underway conductivity–temperature–depth (UCTD) sensors, instrumented moorings, and underwater gliders. In the context of the OSSE, PIES was found to be an unsuitable tool for the target region and for SSH scales 15–70 km; the slowness of a single UCTD leads to significant aliasing by high-frequency motions at short wavelengths below ~30 km; an array of station-keeping gliders may meet the requirement; and an array of moorings is the most effective system among the four tested instruments for meeting the mission’s requirement. The results shown here warrant a prelaunch field campaign to further test the performance of station-keeping gliders.The authors would like to acknowledge the funding sources: the SWOT mission (JW, LF, DM); NASA Projects NNX13AE32G, NNX16AH76G, and NNX17AH54G (TF); and NNX16AH66G and NNX17AH33G (BQ). AF and MF were funded by the Keck Institute for Space Studies (which is generously supported by the W. M. Keck Foundation) through the project Science-driven Autonomous and Heterogeneous Robotic Networks: A Vision for Future Ocean Observations (http://kiss.caltech.edu/?techdev/seafloor/seafloor.html).2018-08-0

A two-graph guided multi-task lasso approach for eQTL mapping.

Abstract Learning a small number of genetic variants associated with multiple complex genetic traits is of practical importance and remains challenging due to the highdimensional nature of data. In this paper, we proposed a two-graph guided multi-task Lasso to address this issue with an emphasis on estimating subnetwork-to-subnetwork associations in expression quantitative trait loci (eQTL) mapping. The proposed model can learn such subnetworkto-subnetwork associations and therefore can be seen as a generalization of several state-of-the-art multi-task feature selection methods. Additionally, this model has a nice property of allowing flexible structured sparsity on both feature and label domains. Simulation study shows the improved performance of our model and a human eQTL data set is analyzed to further demonstrate the applications of the model

Global Observations of Fine-Scale Ocean Surface Topography With the Surface Water and Ocean Topography (SWOT) Mission

The future international Surface Water and Ocean Topography (SWOT) Mission, planned for launch in 2021, will make high-resolution 2D observations of sea-surface height using SAR radar interferometric techniques. SWOT will map the global and coastal oceans up to 77.6 latitude every 21 days over a swath of 120 km (20 km nadir gap). Today’s 2D mapped altimeter data can resolve ocean scales of 150 km wavelength whereas the SWOT measurement will extend our 2D observations down to 15–30 km, depending on sea state. SWOT will offer new opportunities to observe the oceanic dynamic processes at scales that are important in the generation and dissipation of kinetic energy in the ocean, and that facilitate the exchange of energy between the ocean interior and the upper layer. The active vertical exchanges linked to these scales have impacts on the local and global budgets of heat and carbon, and on nutrients for biogeochemical cycles. This review paper highlights the issues being addressed by the SWOT science community to understand SWOT’s very precise sea surface height (SSH)/surface pressure observations, and it explores how SWOT data will be combined with other satellite and in situ data and models to better understand the upper ocean 4D circulation (x, y, z, t) over the next decade. SWOT will provide unprecedented 2D ocean SSH observations down to 15–30 km in wavelength, which encompasses the scales of “balanced” geostrophic eddy motions, high-frequency internal tides and internal waves. Frontiers in Marine Science | www.frontiersin.org 1 May 2019 | Volume 6 | Article 232 Morrow et al. SWOT Fine-Scale Global Ocean Topography This presents both a challenge in reconstructing the 4D upper ocean circulation, or in the assimilation of SSH in models, but also an opportunity to have global observations of the 2D structure of these phenomena, and to learn more about their interactions. At these small scales, ocean dynamics evolve rapidly, and combining SWOT 2D SSH data with other satellite or in situ data with different space-time coverage is also a challenge. SWOT’s new technology will be a forerunner for the future altimetric observing system, and so advancing on these issues today will pave the way for our future

Interfacial Dzyaloshinskii-Moriya interaction and chiral magnetic textures in a ferrimagnetic insulator

The interfacial Dzyaloshinskii-Moriya interaction (DMI) in multilayers of heavy metal and ferromagnetic metals enables the stabilization of novel chiral spin structures such as skyrmions. Magnetic insulators, on the other hand, can exhibit enhanced dynamics and properties such as lower magnetic damping and therefore it is of interest to combine the properties enabled by interfacial DMI with insulating systems. Here, we demonstrate the presence of interfacial DMI in heterostructures that include insulating magnetic layers. We use perpendicularly magnetized insulating thulium iron garnet (TmIG) films capped by the heavy metal platinum, grown on gadolinium gallium garnet (GGG) substrates, and find a surprisingly strong interfacial DMI that, combined with spin-orbit torque, results in efficient switching. The interfacial origin is confirmed through thickness-dependence measurements of the DMI, revealing the characteristic 1/thickness dependence. We combine chiral spin structures and spin-orbit torques for efficient switching and identify skyrmions that allow us to establish the GGG/TmIG interface as the possible origin of the DMI

Frontiers in Fine-Scale in situ Studies: Opportunities During the SWOT Fast Sampling Phase

Conceived as a major new tool for climate studies, the Surface Water and Ocean Topography (SWOT) satellite mission will launch in late 2021 and will retrieve the dynamics of the oceans upper layer at an unprecedented resolution of a few kilometers. During the calibration and validation (CalVal) phase in 2022, the satellite will be in a 1-day-repeat fast sampling orbit with enhanced temporal resolution, sacrificing the spatial coverage. This is an ideal opportunity – unique for many years to come – to coordinate in situ experiments during the same period for a focused study of fine scale dynamics and their broader roles in the Earth system. Key questions to be addressed include the role of fine scales on the ocean energy budget, the connection between their surface and internal dynamics, their impact on plankton diversity, and their biophysical dynamics at the ice margin