FLOWERING LOCUS C -dependent and -independent regulation of the circadian clock by the autonomous and vernalization pathways

Background The circadian system drives pervasive biological rhythms in plants. Circadian clocks integrate endogenous timing information with environmental signals, in order to match rhythmic outputs to the local day/night cycle. Multiple signaling pathways affect the circadian system, in ways that are likely to be adaptively significant. Our previous studies of natural genetic variation in Arabidopsis thaliana accessions implicated FLOWERING LOCUS C (FLC) as a circadian-clock regulator. The MADS-box transcription factor FLC is best known as a regulator of flowering time. Its activity is regulated by many regulatory genes in the "autonomous" and vernalization-dependent flowering pathways. We tested whether these same pathways affect the circadian system. Results Genes in the autonomous flowering pathway, including FLC, were found to regulate circadian period in Arabidopsis. The mechanisms involved are similar, but not identical, to the control of flowering time. By mutant analyses, we demonstrate a graded effect of FLC expression upon circadian period. Related MADS-box genes had less effect on clock function. We also reveal an unexpected vernalization-dependent alteration of periodicity. Conclusion This study has aided in the understanding of FLC's role in the clock, as it reveals that the network affecting circadian timing is partially overlapping with the floral-regulatory network. We also show a link between vernalization and circadian period. This finding may be of ecological relevance for developmental programing in other plant species

Proteomic identification of extracellular proteins regulated by the Gna1 Gα subunit in Stagonospora nodorum

The fungus Stagonospora nodorum is the causal agent of stagonospora nodorum blotch (syn.leaf and glume blotch) disease of wheat. The Gna1-encoded Ga protein is an important signaltransduction component in the fungus, which is required for full pathogenicity, sporulationand extracellular depolymerase production. In this study, we sought to gaina better understanding of defects associated with the gna1 mutant by using twodimensionalgel electrophoresis to analyse the extracellular proteome for differences tothe wildtype. Mass spectrometry analysis of altered abundant protein spots and peptidematching to the Stagonospora nodorum genome database have led to the identification ofgenes implicated in cell wall degradation, proteolysis, RNA hydrolysis and aromatic compoundmetabolism. In addition, quantitative RT-PCR has demonstrated that some of theencoding genes showed differential expression throughout host infection. Implicationsof these proteins and their corresponding genes in fungal virulence are discussed.The fungus Stagonospora nodorum is the causal agent of stagonospora nodorum blotch (syn. leaf and glume blotch) disease of wheat. The Gna1-encoded Gα protein is an important signal transduction component in the fungus, which is required for full pathogenicity, sporulation and extracellular depolymerase production. In this study, we sought to gain a better understanding of defects associated with the gna1 mutant by using two-dimensional gel electrophoresis to analyse the extracellular proteome for differences to the wildtype. Mass spectrometry analysis of altered abundant protein spots and peptide matching to the Stagonospora nodorum genome database have led to the identification of genes implicated in cell wall degradation, proteolysis, RNA hydrolysis and aromatic compound metabolism. In addition, quantitative RT-PCR has demonstrated that some of the encoding genes showed differential expression throughout host infection. Implications of these proteins and their corresponding genes in fungal virulence are discussed

Global temperature definition affects achievement of long-term climate goals

The Paris Agreement on climate change aims to limit 'global average temperature' rise to 'well below 2 °C' but reported temperature depends on choices about how to blend air and water temperature data, handle changes in sea ice and account for regions with missing data. Here we use CMIP5 climate model simulations to estimate how these choices affect reported warming and carbon budgets consistent with the Paris Agreement. By the 2090s, under a low-emissions scenario, modelled global near-surface air temperature rise is 15% higher (5%-95% range 6%-21%) than that estimated by an approach similar to the HadCRUT4 observational record. The difference reduces to 8% with global data coverage, or 4% with additional removal of a bias associated with changing sea-ice cover. Comparison of observational datasets with different data sources or infilling techniques supports our model results regarding incomplete coverage. From high-emission simulations, we find that a HadCRUT4 like definition means higher carbon budgets and later exceedance of temperature thresholds, relative to global near-surface air temperature. 2 °C warming is delayed by seven years on average, to 2048 (2035-2060), and CO2 emissions budget for a >50% chance of <2 °C warming increases by 67 GtC (246 GtCO2)

SBSI:an extensible distributed software infrastructure for parameter estimation in systems biology

Complex computational experiments in Systems Biology, such as fitting model parameters to experimental data, can be challenging to perform. Not only do they frequently require a high level of computational power, but the software needed to run the experiment needs to be usable by scientists with varying levels of computational expertise, and modellers need to be able to obtain up-to-date experimental data resources easily. We have developed a software suite, the Systems Biology Software Infrastructure (SBSI), to facilitate the parameter-fitting process. SBSI is a modular software suite composed of three major components: SBSINumerics, a high-performance library containing parallelized algorithms for performing parameter fitting; SBSIDispatcher, a middleware application to track experiments and submit jobs to back-end servers; and SBSIVisual, an extensible client application used to configure optimization experiments and view results. Furthermore, we have created a plugin infrastructure to enable project-specific modules to be easily installed. Plugin developers can take advantage of the existing user-interface and application framework to customize SBSI for their own uses, facilitated by SBSI’s use of standard data formats

Ge-on-Si Mid-Infrared Waveguide Platform for Molecular Fingerprint Sensing

The mid-infrared spectral region is key to several large market applications such as security, healthcare and environmental monitoring. This is due to how chemical compounds can be detected from unique vibrational modes that absorb in the molecular ‘fingerprint’ region ( 6.7−20 μm wavelength). There is significant interest in realizing cheaper and smaller spectrometers based on waveguide integrated photonics. Here we demonstrate Ge-on-Si waveguides operating up to 11 μm wavelength with low propagation loss (∼ 1 dB/cm). The performance of the waveguides is then demonstrated by measuring thin films that are used to calibrate the modal overlap for molecular sensing. Lastly, an ultra-broadband Ge-on-Si waveguide polarization rotator is presented. The fabricated polarization rotator devices demonstrate a polarization extinction ratio of ≥ 15 dB over a 2 μm bandwidth ( 9−11 μm wavelength) with an average insertion loss &lt; 1 dB

Direct Imaging in Reflected Light: Characterization of Older, Temperate Exoplanets With 30-m Telescopes

Direct detection, also known as direct imaging, is a method for discovering and characterizing the atmospheres of planets at intermediate and wide separations. It is the only means of obtaining spectra of non-transiting exoplanets. Characterizing the atmospheres of planets in the <5 AU regime, where RV surveys have revealed an abundance of other worlds, requires a 30-m-class aperture in combination with an advanced adaptive optics system, coronagraph, and suite of spectrometers and imagers - this concept underlies planned instruments for both TMT (the Planetary Systems Imager, or PSI) and the GMT (GMagAO-X). These instruments could provide astrometry, photometry, and spectroscopy of an unprecedented sample of rocky planets, ice giants, and gas giants. For the first time habitable zone exoplanets will become accessible to direct imaging, and these instruments have the potential to detect and characterize the innermost regions of nearby M-dwarf planetary systems in reflected light. High-resolution spectroscopy will not only illuminate the physics and chemistry of exo-atmospheres, but may also probe rocky, temperate worlds for signs of life in the form of atmospheric biomarkers (combinations of water, oxygen and other molecular species). By completing the census of non-transiting worlds at a range of separations from their host stars, these instruments will provide the final pieces to the puzzle of planetary demographics. This whitepaper explores the science goals of direct imaging on 30-m telescopes and the technology development needed to achieve them.Comment: (March 2018) Submitted to the Exoplanet Science Strategy committee of the NA

A mantle plume origin for the Palaeoproterozoic Circum-Superior Large Igneous Province

The Circum-Superior Large Igneous Province (LIP) consists predominantly of ultramafic-mafic lavas and sills with minor felsic components, distributed as various segments along the margins of the Superior Province craton. Ultramafic-mafic dykes and carbonatite complexes of the LIP also intrude the more central parts of the craton. Most of this magmatism occurred 1880 Ma. Previously a wide range of models have been proposed for the different segments of the CSLIP with the upper mantle as the source of magmatism. New major and trace element and Nd-Hf isotopic data reveal that the segments of the CSLIP can be treated as a single entity formed in a single tectonomagmatic environment. In contrast to most previous studies that have proposed a variety of geodynamic settings, the CSLIP is interpreted to have formed from a single mantle plume. Such an origin is consistent with the high MgO and Ni contents of the magmatic rocks, trace element signatures that similar to oceanic-plateaus and ocean island basalts and eNd-eHf isotopic signatures which are each more negative than those of the estimated depleted upper mantle at 1880 Ma. Further support for a mantle plume origin comes from calculated high degrees of partial melting, mantle potential temperatures significantly greater than estimated ambient Proterozoic mantle and the presence of a radiating dyke swarm. The location of most of the magmatic rocks along the Superior Province margins probably represents the deflection of plume material by the thick cratonic keel towards regions of thinner lithosphere at the craton margins. The primary magmas, generated by melting of the heterogeneous plume head, fractionated in magma chambers within the crust, and assimilated varying amounts of crustal material in the process