Influence of calcium and calcium and calmodulin antagonists on the cytokinin-induced amaranthin accumulation in Amaranthus tricolor

The concentration of kinetin and kinetinriboside plays an essential role in the induction of amaranthin accumulation in cotyledons of Amaranthus tricolor during germination. The dose/effect ratio shows that kinetin induced 3- to 3.5-fold more amaranthin than kinetinriboside at the same molecular concentration. Various concentrations of exogenous Ca2+ did not influence the effects of kinetin on the betacyanin synthesis. However, when Ca2+ was applied together with kinetinriboside, the amaranthin production was stimulated. Time-course experiments show a lag phase of 16 h starting from the incubation with kinetin and a distinct increase of amaranthin thereafter. If the seedlings were treated simultaneously with kinetin and Ca2+, the increase of amaranthin started after 12 h. At 16 h of incubation in kinetin/Ca2+, the amount of amaranthin increased significantly compared to controls incubated with kinetin alone. If Ca2+ ions (16 h kinetin/Ca2+ incubation) were removed from the medium after 2 h, 4 h, and up to 14 h, the amaranthin content was enhanced compared to controls without Ca2+. The stimulating effect was highest in the presence of Ca2+ for 8 h. These data show that exogenous Ca2+ stimulated the amaranthin synthesis mainly during the first 12 h of incubation. The Ca2+ antagonists EGTA, chlorotetracycline, and CoCl2 reduced the amaranthin content up to 80%. The calmodulin antagonists chloropromazine and trifluoperazine inhibited the betacyanin accumulation up to 97% when applied at the beginning of the incubation. Neither Co2+ nor trifluoperazine after 12 h of preincubation in kinetin had inhibiting effects on the amaranthin production. Therefore, we presume that a specific period of competence is required for calmodulin-mediated Ca2+ effects on the accumulation of amaranthin induced by cytokinins in the seedlings of Amaranthus tricolor

The Chlamydomonas genome project: A decade on

The green alga Chlamydomonas reinhardtii is a popular unicellular organism for studying photosynthesis, cilia biogenesis, and micronutrient homeostasis. Ten years since its genome project was initiated an iterative process of improvements to the genome and gene predictions has propelled this organism to the forefront of the omics era. Housed at Phytozome, the plant genomics portal of the Joint Genome Institute (JGI), the most up-to-date genomic data include a genome arranged on chromosomes and high-quality gene models with alternative splice forms supported by an abundance of whole transcriptome sequencing (RNA-Seq) data. We present here the past, present, and future of Chlamydomonas genomics. Specifically, we detail progress on genome assembly and gene model refinement, discuss resources for gene annotations, functional predictions, and locus ID mapping between versions and, importantly, outline a standardized framework for naming genes

Technical Note: Intercomparison of ILAS-II version 2 and 1.4 trace species with MIPAS-B measurements

The Improved Limb Atmospheric Spectrometer (ILAS)-II sensor aboard the Japanese ADEOS-II satellite was launched into its sun-synchronous orbit on 14 December 2002 and performed solar occultation measurements of trace species, aerosols, temperature, and pressure in the polar stratosphere until 25 October 2003. Vertical trace gas profiles obtained with the balloon version of the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS-B) provide one of the sparse data sets for validating ILAS-II version 2 and 1.4 data. The MIPAS-B limb emission spectra were collected on 20 March 2003 over Kiruna (Sweden, 68° N) at virtually the same location that has been sounded by ILAS-II about 5.5 h prior to the sampling of MIPAS-B. The intercomparison of the new ILAS-II version 2 (Northern Hemispheric sunrise) data to MIPAS-B vertical trace gas profiles shows a good to excellent agreement within the combined error limits for the species O<sub>3</sub>, N<sub>2</sub>O, CH<sub>4</sub>, H<sub>2</sub>O (above 21 km), HNO<sub>3</sub>, ClONO<sub>2</sub>, and CFC-11 (CCl<sub>3</sub>F) in the compared altitude range between 16 and 31 km such that these data appear to be very useful for scientific analysis. With regard to the previous version 1.4 ILAS-II data, significant improvements in the consistency with MIPAS-B are obvious especially for the species CH<sub>4</sub> and H<sub>2</sub>O, but also for O<sub>3</sub>, HNO<sub>3</sub>, ClONO<sub>2</sub>, NO<sub>2</sub>, and N<sub>2</sub>O<sub>5</sub>. However, comparing gases like NO<sub>2</sub>, N<sub>2</sub>O<sub>5</sub>, and CFC-12 (CCl<sub>2</sub>F<sub>2</sub>) exhibits only poor agreement with MIPAS-B such that these species cannot be assumed to be validated at the present time

RNA sequencing-based single sample predictors of molecular subtype and risk of recurrence for clinical assessment of early-stage breast cancer

BackgroundMultigene expression assays for molecular subtypes and biomarkers can aid clinical management of early invasive breast cancer. Based on RNA-sequencing we aimed to develop single-sample predictor (SSP) models for conventional clinical markers, molecular intrinsic subtype and risk of recurrence (ROR).MethodsA uniformly accrued breast cancer cohort of 7743 patients with RNA-sequencing data from fresh tissue was divided into a training set and a reserved test set. We trained SSPs for PAM50 molecular subtypes and ROR assigned by nearest-centroid (NC) and SSPs for conventional clinical markers from histopathology data. Additionally, SSP classifications were compared with Prosigna® in two external cohorts. Prognostic value was assessed using distant recurrence-free interval.ResultsIn the test set, agreement between SSP and NC classifications for PAM50 (five subtypes) and Subtype (four subtypes) was high (85%, Kappa=0.78) and very high (90%, Kappa=0.84) respectively. Accuracy for ROR risk category was high (84%, Kappa=0.75, weighted Kappa=0.90). The prognostic value for SSP and NC was assessed as equivalent. Agreement for SSP and histopathology was very high or high for receptor status, while moderate and poor for Ki67 status and Nottingham histological grade, respectively. SSP concordance with Prosigna® was high for subtype and moderate and high for ROR risk category. In pooled analysis, concordance between SSP and Prosigna® for emulated treatment recommendation for chemotherapy (yes vs. no) was high (85%, Kappa=0.66). In postmenopausal ER+/HER2-/N0 patients SSP application suggested changed treatment recommendations for up to 17% of patients, with nearly balanced escalation and de-escalation of chemotherapy.ConclusionsSSP models for histopathological variables, PAM50, and ROR classifications can be derived from RNA-sequencing that closely matches clinical tests. Agreement and outcome analyses suggest that NC and SSP models are interchangeable on a group-level and nearly so on a patient level. Retrospective evaluation in postmenopausal ER+/HER2-/N0 patients suggested that molecular testing could lead to a changed therapy recommendation for almost one-fifth of patients

HCl and ClO in activated Arctic air; first retrieved vertical profiles from TELIS submillimetre limb spectra

The first profile retrieval results of the Terahertz and submillimeter Limb Sounder (TELIS) balloon instrument are presented. The spectra are recorded during a 13-h balloon flight on 24 January 2010 from Kiruna, Sweden. The TELIS instrument was mounted on the MIPAS-B2 gondola and shared this platform with the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) and the mini- Differential Optical Absorption Spectroscopy (mini-DOAS) instruments. The flight took place within the Arctic vortex at an altitude of ≈34 km in chlorine activated air, and both active (ClO) and inactive chlorine (HCl) were measured over an altitude range of respectively ≈16–32 km and ≈10– 32 km. In this altitude range, the increase of ClO concentration levels during sunrise has been recorded with a temporal resolution of one minute. During the daytime equilibrium, a maximum ClO level of 2.1±0.3 ppbv has been observed at an altitude of 23.5 km. This equilibrium profile is validated against the ClO profile by the satellite instrument Microwave Limb Sounder (MLS) aboard EOS Aura. HCl profiles have been determined from two different isotopes – H35Cl and H37Cl – and are also validated againstMLS. The precision of all profiles is well below 0.01 ppbv and the overall accuracy is therefore governed by systematic effects. The total uncertainty of these effects is estimated to be maximal 0.3 ppbv for ClO around its peak value at 23.5 km during the daytime equilibrium, and for HCl it ranges from 0.05 to 0.4 ppbv, depending on altitude. In both cases the main uncertainty stems from a largely unknown non-linear response in the detector

3-D tomographic observations of Rossby wave breaking over the North Atlantic during the WISE aircraft campaign in 2017

This paper presents measurements of ozone, water vapour and nitric acid (HNO3) in the upper troposphere/lower stratosphere (UTLS) over North Atlantic and Europe. The measurements were acquired with the Gimballed Limb Observer for Radiance Imaging of the Atmosphere (GLORIA) during the Wave Driven Isentropic Exchange (WISE) campaign in October 2017. GLORIA is an airborne limb imager capable of acquiring both 2-D data sets (curtains along the flight path) and, when the carrier aircraft is flying around the observed air mass, spatially highly resolved 3-D tomographic data. Here, we present a case study of a Rossby wave (RW) breaking event observed during two subsequent flights 2 d apart. RW breaking is known to steepen tracer gradients and facilitate stratosphere–troposphere exchange (STE). Our measurements reveal complex spatial structures in stratospheric tracers (ozone and nitric acid) with multiple vertically stacked filaments. Backward-trajectory analysis is used to demonstrate that these features are related to several previous Rossby wave breaking events and that the small-scale structure of the UTLS in the Rossby wave breaking region, which is otherwise very hard to observe, can be understood as stirring and mixing of air masses of tropospheric and stratospheric origin. It is also shown that a strong nitric acid enhancement observed just above the tropopause is likely a result of NOx production by lightning activity. The measurements showed signatures of enhanced mixing between stratospheric and tropospheric air near the polar jet with some transport of water vapour into the stratosphere. Some of the air masses seen in 3-D data were encountered again 2 d later, stretched to very thin filament (horizontal thickness down to 30 km at some altitudes) rich in stratospheric tracers. This repeated measurement allowed us to directly observe and analyse the progress of mixing processes in a thin filament over 2 d. Our results provide direct insight into small-scale dynamics of the UTLS in the Rossby wave breaking region, which is of great importance to understanding STE and poleward transport in the UTLS

Geostationary Emission Explorer for Europe (G3E): mission concept and initial performance assessment

The Geostationary Emission Explorer for Europe (G3E) is a concept for a geostationary satellite sounder that targets at constraining the sources and sinks of the greenhouse gases carbon dioxide (CO2) and methane (CH4) for continental-scale regions. Thereby, its primary focus is on Central Europe. G3E carries a spectrometer system that collects sunlight backscattered from the Earth\u27s surface and atmosphere in the near-infrared (NIR) and shortwave-infrared (SWIR) spectral range. Solar absorption spectra allow for spatiotemporally dense observations of the column-average concentrations of carbon dioxide (XCO2), methane (XCH4), and carbon monoxide (XCO) including sampling of the diurnal variation with several measurements per day during summer. Here, we present the mission concept and carry out an initial performance assessment of the retrieval capabilities. The radiometric performance of the 4 grating spectrometers is tuned to reconcile small ground-pixel sizes (~ 2 km × 3 km at 50° latitude) with short single-shot exposures (∼ 2.9 s) that allow for sampling continental regions such as Central Europe within 2 h while providing sufficient signal-to-noise. The noise errors to be expected for XCO2, XCH4, and XCO are assessed through retrieval simulations for a European trial ensemble. Generally, single-shot precision for the targeted XCO2 and XCH4 is better than 0.5 % with some exception for scenes with low infrared surface albedo observed under low sun conditions in winter. For XCO, precision is generally better than 10 %. Performance for aerosol and cirrus loaded atmospheres is assessed by mimicking G3E\u27s slant view on Europe for an ensemble of atmospheric scattering properties used previously for evaluating nadir-viewing low-Earth-orbit (LEO) satellites. While retrieval concepts developed for LEO configurations generally succeed in mitigating aerosol and cirrus induced retrieval errors for G3E\u27s setup, residual errors are somewhat greater in geostationary orbit (GEO) than in LEO. G3E\u27s deployment in the vicinity of the Meteosat Third Generation (MTG) satellites suggests making synergistic use of MTG\u27s sounding capabilities e.g. with respect to characterization of aerosol and cloud properties or with respect to enhancing carbon monoxide retrievals by combining G3E\u27s solar and MTG\u27s thermal infrared spectra