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

Occlusal adjustment using the bite plate-induced occlusal position as a reference position for temporomandibular disorders: a pilot study

<p>Abstract</p> <p>Background</p> <p>Many researchers have not accepted the use of occlusal treatments for temporomandibular disorders (TMDs). However, a recent report described a discrepancy between the habitual occlusal position (HOP) and the bite plate-induced occlusal position (BPOP) and discussed the relation of this discrepancy to TMD. Therefore, the treatment outcome of evidence-based occlusal adjustments using the bite plate-induced occlusal position (BPOP) as a muscular reference position should be evaluated in patients with TMD.</p> <p>Methods</p> <p>The BPOP was defined as the position at which a patient voluntarily closed his or her mouth while sitting in an upright posture after wearing an anterior flat bite plate for 5 minutes and then removing the plate. Twenty-one patients with TMDs underwent occlusal adjustment using the BPOP. The occlusal adjustments were continued until bilateral occlusal contacts were obtained in the BPOP. The treatment outcomes were evaluated using the subjective dysfunction index (SDI) and the Helkimo Clinical Dysfunction Index (CDI) before and after the occlusal adjustments; the changes in these two indices between the first examination and a one-year follow-up examination were then analyzed. In addition, the difference between the HOP and the BPOP was three-dimensionally measured before and after the treatment.</p> <p>Results</p> <p>The percentage of symptom-free patients after treatment was 86% according to the SDI and 76% according to the CDI. The changes in the two indices after treatment were significant (p < 0.001). The changes in the mean HOP-BPOP differences on the x-axis (mediolateral) and the y-axis (anteroposterior) were significant (p < 0.05), whereas the change on the z-axis (superoinferior) was not significant (p > 0.1).</p> <p>Conclusion</p> <p>Although the results of the present study should be confirmed in other studies, a randomized clinical trial examining occlusal adjustments using the BPOP as a reference position appears to be warranted.</p

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

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 aims to constrain the sources and sinks of greenhouse gases carbon dioxide (CO2) and methane (CH4) for continental-scale regions. 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). The mission concept in particular facilitates 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 a sufficient signal-to-noise ratio. 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 has the potential to make 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

The MIPAS balloon borne trace constitutent experiment

A novel cryogenic Fourier transform spectrometer (FTS) has been developed for limb emission measurements in the mid IR-region from balloon-borne platforms. The FTS is a rapid scanning interferometer using a modified Michelson arrangement which allows a spectral resolution of 0.04 cm(exp -1) to be achieved. Solid carbon-dioxide cooling of the spectrometer and liquid-helium cooling of the detectors provide adequate sensitivity. The line of sight can be stabilized in terms of azimuth and elevation. A three-mirror off-axis telescope provides good vertical resolution and straylight rejection. Calibration is performed by high elevation and internal blackbody measurements. Four balloon flights were performed, two of them during spring turn-around 1989 and 1990 over mid-latitudes (Aire sur L'Adour, France, 44 deg N) and two near the northern polar circle in winter 1992 (Esrange, Sweden, 68 deg N). Limb emission spectra were collected from 32 km to 39 km floating altitudes covering tangent heights between the lower troposphere and the floating altitude. The trace gases CO2, H2O, O3, CH4, N2O, HNO3, N2O5, ClONO2, CF2Cl2, CFCl3, CHF2Cl, CCl4, and C2H6 have been identified in the measured spectra. The 1989 data have been analyzed to retrieve profiles of O3, HNO3, CFCl3 and CF2Cl2. The flights over Kiruna have provided the first ever reported profile measurements of the key reservoir species ClONO2 and N2O5 inside the polar vortex

Variation in chemical composition and volatility of oxygenated organic aerosol in different rural, urban, and mountain environments

The apparent volatility of atmospheric organic aerosol (OA) particles is determined by their chemical composition and environmental conditions (e.g., ambient temperature). A quantitative, experimental assessment of volatility and the respective importance of these two factors remains challenging, especially in ambient measurements. We present molecular composition and volatility of oxygenated OA (OOA) particles in different rural, urban, and mountain environments (including Chacaltaya, Bolivia; Alabama, US; Hyytiälä, Finland; Stuttgart and Karlsruhe, Germany; and Delhi, India) based on deployments of a filter inlet for gases and aerosols coupled to a high-resolution time-of-flight chemical ionization mass spectrometer (FIGAERO-CIMS). We find on average larger carbon numbers (nC) and lower oxygen-to-carbon (O : C) ratios at the urban sites (nC: 9.8 ± 0.7; O : C: 0.76 ± 0.03; average ±1 standard deviation) compared to the rural (nC: 8.8 ± 0.6; O : C: 0.80 ± 0.05) and mountain stations (nC: 8.1 ± 0.8; O : C: 0.91 ± 0.07), indicative of different emission sources and chemistry