Physics of the atmosphere: Response of the water vapor channel of the Meteosat satellite

An accurate model of the atmospheric transmission function is used to obtain the relationship between the cloudless radiances measured by the 6-7 microns Meteosat radiometer (water vapor channel) and the numerical parameters associated to each point of an image. This relationship is compared to the temporary calibration curve published by the European Space Agency

The tropospheric gas composition of Jupiter's north equatorial belt (NH3, PH3, CH3D, GeH4, H2O) and the Jovian D/H isotropic ratio

The gas composition of the troposphere of Jupiter in the clearest regions of the North Equatorial Belt (NEB) was derived from the Voyager 1 IRIS data. The infrared spectrum for this homogeneous cloud free region was modeled to infer altitude profiles for NH3, PH3, GeH4 and H2O. The Profiles for NH3 and PH3 were found to be depleted in the upper troposphere but otherwise in agreement with their solar values at the 1 bar level. The mole fraction for CH3D was determined to be 3.5(+1.0 or -1.3) x 10 to the minus 7th power. The GeH4 mole fraction of 7+ or -2 x 10 to the minus 10th power at the 2 to 3 bar level is a factor of 10 lower than the solar value. The H2O mole fraction is approximately 1 x 0.00001 at the 2.5 bar level and is increasing to approximately 3 x 0.00001 at 4 bars where it is a factor of 30 lower than solar. Using IRIS infrared values for the mole fractions of CH3D and CH4 a value of D/H = 3.6(+1.0 or -1.4)x 0.00001 is derived. Assuming this Jovian D/H ratio is representative of the protosolar nebula, and correcting for chemical galactic evolution, yields a value of 5.5 - 9.0 x 0.00001 for the primordial D/H ratio and an upper limit of 1.8 to 2.4 x 10 to the minus 31st power cu cm for the present day baryon density

EURL-FA Control Proficiency test report: Determination of authorised coccidiostats in compound feed

The European Union Reference Laboratory for Feed Additives (EURL-FA), hosted by the Joint Research Centre (JRC), a Directorate General of the European Commission, has been mandated by the Directorate General for Health and Food Safety (DG SANTE) to organise a proficiency test (PT) among appointed National Reference Laboratories (NRLs) in the frame of its control activities (according to the Regulation (EC) No 882/2004 [1]). The aim of this PT was to assess the capacity of the NRLs to correctly determine selected authorised coccidiostats added to feed matrices at realistic authorised levels and at cross-contamination levels. Thirty-six European National and Official Control laboratories were invited and twenty-nine laboratories registered to the 2017 PT exercise. Twenty-five of the registered laboratories reported results for the analyses. The test items used in this exercise were produced by the JRC. Purchased commercial poultry compound feed, tested by the EURL-FA Control as being blank for the target analytes, was milled and ground and then spiked with the required coccidiostat standard solution or with the relevant authorised feed additive. The first item was spiked with a standard solution containing monensin, narasin and diclazuril, at cross-contamination level (MAT 1). The second test item (MAT 2) was spiked with an authorised feed additive Maxiban®, containing narasin (narasin AL) and nicarbazin, at additive level. MAT 1 and MAT 2 were subsequently homogenised and distributed in glass bottles. All bottles were labelled ensuring a random number encoding and dispatched to all registered participants on 27 June 2017. Laboratories were informed of the composition of the test material regarding the composition in coccidiostats for MAT 2 and had therefore only to quantify the content. For MAT 1 the laboratories had to screen for the presence of all 11 authorised coccidiostats and to quantify the detected ones. The assigned values (xpt) for the mass content of monensin, diclazuril and narasin in MAT 1 were calculated from the formulation as recommended by the IUPAC harmonized protocol [2]. The uncertainties for the assigned values (u(xpt)) were calculated according to the ISO Guide for the Expression of Uncertainty in Measurement (GUM) [3]. For narasin and nicarbazin in MAT 2, no assigned value was set since the criterion for sufficient homogeneity could not be met. Participants were invited to report their measurement uncertainties. This was done by twenty-three out of twenty-five reporting participants for monensin and narasin, seventeen for diclazuril, and twenty for narasin AL and nicarbazin. Laboratory results were rated using z and ζ (zeta) scores in accordance with ISO 13528:2015 [4]. The relative standard deviation for proficiency assessment (σpt) for each assigned value was calculated using the relevant Horwitz [5] or modified Horwitz equation [6]. The z scores obtained were considered satisfactory if their absolute values were equal to or below 2. The outcome of this PT exercise is mixed; the percentage of satisfactory results reported by the laboratories for MAT 1 is 88%, 80% and 57% for monensin, narasin and diclazuril respectively. For narasin AL and nicarbazin in MAT 2, no scoring was computed but the data reported by the laboratories were examined. In general, there was good agreement among the values of mass content of narasin and nicarbazin reported results. The laboratories also reported qualitative results as regards the presence of one or more of the other authorised coccidiostats. On the whole, the rate of false positive results was of 4% for robenidine, lasalocid, salinomycin and maduramicin; 5% for nicarbazin; 8% for decoquinate; and 0% for all the others. Two laboratories did not quantify diclazuril in MAT 1 while stating a limit of quantification of the method used lower than the assigned value, leading to a false negative rate of 9% for this analyte. One laboratory could not quantify diclazuril in MAT 1 due to the lack of sensitivity of the method used.JRC.F.5-Food and Feed Complianc

Interplay between DNA sequence and negative superhelicity drives R-loop structures.

R-loops are abundant three-stranded nucleic-acid structures that form in cis during transcription. Experimental evidence suggests that R-loop formation is affected by DNA sequence and topology. However, the exact manner by which these factors interact to determine R-loop susceptibility is unclear. To investigate this, we developed a statistical mechanical equilibrium model of R-loop formation in superhelical DNA. In this model, the energy involved in forming an R-loop includes four terms-junctional and base-pairing energies and energies associated with superhelicity and with the torsional winding of the displaced DNA single strand around the RNA:DNA hybrid. This model shows that the significant energy barrier imposed by the formation of junctions can be overcome in two ways. First, base-pairing energy can favor RNA:DNA over DNA:DNA duplexes in favorable sequences. Second, R-loops, by absorbing negative superhelicity, partially or fully relax the rest of the DNA domain, thereby returning it to a lower energy state. In vitro transcription assays confirmed that R-loops cause plasmid relaxation and that negative superhelicity is required for R-loops to form, even in a favorable region. Single-molecule R-loop footprinting following in vitro transcription showed a strong agreement between theoretical predictions and experimental mapping of stable R-loop positions and further revealed the impact of DNA topology on the R-loop distribution landscape. Our results clarify the interplay between base sequence and DNA superhelicity in controlling R-loop stability. They also reveal R-loops as powerful and reversible topology sinks that cells may use to nonenzymatically relieve superhelical stress during transcription

EURL-FA Control Proficiency Test Report: Determination of the mass fraction of the total cobalt in compound feed for rabbits

The European Union Reference Laboratory for Feed Additive Control (EURL-FA Control) organised a proficiency test (EURL-FAC 2017-2) for the determination of the mass fraction of total cobalt in compound feed, to support the Commission Implementing Regulation (EU) No 131/2014 concerning the authorisation of various cobalt(II) compounds as feed additives. This proficiency test was open to National Reference Laboratories (NRLs) and official feed control laboratories (OCLs). The material used as test item was a commercially available compound feed for rabbits (containing the coated granulated cobalt (II) carbonate, 3b304 ) which, after appropriate processing, was bottled, labelled and dispatched to participants on June 21, 2017. The homogeneity and stability of the test item were evaluated and the assigned values were derived from the results reported by the selected expert laboratories. Twenty one NRLs and two OCLs from 21 countries - representing EU Member States and Norway - registered to the exercise and reported results at the end of August 2017. Laboratory results were rated using z' and zeta scores in accordance with ISO 13528:2015. A relative standard deviation for proficiency assessment (σpt) of 16 % of the assigned value was set according to the modified Horwitz equation. Twenty (out of 23) laboratories reported satisfactory results (according to the z' score). This confirms the ability of most NRLs in monitoring maximum levels set by the Commission Implementing Regulation (EU) No 131/2014 in this type of animal feed. The majority (74 %) of the participating laboratories provided realistic estimates of their measurement uncertainties.JRC.F.5-Food and Feed Complianc

Tropospheric methane in the tropics – first year from IASI hyperspectral infrared observations

Simultaneous observations from the Infrared Atmospheric Sounding Interferometer (IASI) and from the Advanced Microwave Sounding Unit (AMSU), launched together onboard the European MetOp platform in October 2006, are used to retrieve a mid-to-upper tropospheric content of methane (CH4) in clear-sky conditions, in the tropics, over sea, for the first 16 months of operation of MetOp (July 2007–October 2008). With its high spectral resolution, IASI provides nine channels in the 7.7 μm band highly sensitive to CH4 with reduced sensitivities to other atmospheric variables. These channels, sensitive to both CH4 and temperature, are used in conjunction with AMSU channels, only sensitive to temperature, to decorrelate both signals through a non-linear inference scheme based on neural networks. A key point of this approach is that no use is made of prior information in terms of methane seasonality, trend, or geographical patterns. The precision of the retrieval is estimated to be about 16 ppbv (~0.9%). Features of the retrieved methane space-time distribution include: (1) a strong seasonal cycle of 30 ppbv in the northern tropics with a maximum in January–March and a minimum in July–September, and a flat seasonal cycle in the southern tropics, in agreement with in-situ measurements; (2) a latitudinal decrease of 30 ppbv from 20° N to 20° S, in boreal spring and summer, lower than what is observed at the surface but in excellent agreement with tropospheric aircraft measurements; (3) geographical patterns in good agreement with simulations from the atmospheric transport and chemistry model MOZART-2, but with a higher variability and a higher concentration in boreal winter; (4) signatures of CH4 emissions transported to the middle troposphere such as a large plume of elevated tropospheric methane south of the Asian continent, which might be due to Asian emissions from rice paddies uplifted by deep convection during the monsoon period and then transported towards Indonesia. In addition to bringing a greatly improved view of methane distribution, these results from IASI should provide a means to observe and understand atmospheric transport pathways of methane from the surface to the upper troposphere

Visualizing helicases unwinding DNA at the single molecule level

DNA helicases are motor proteins that catalyze the unwinding of double-stranded DNA into single-stranded DNA using the free energy from ATP hydrolysis. Single molecule approaches enable us to address detailed mechanistic questions about how such enzymes move processively along DNA. Here, an optical method has been developed to follow the unwinding of multiple DNA molecules simultaneously in real time. This was achieved by measuring the accumulation of fluorescent single-stranded DNA-binding protein on the single-stranded DNA product of the helicase, using total internal reflection fluorescence microscopy. By immobilizing either the DNA or helicase, localized increase in fluorescence provides information about the rate of unwinding and the processivity of individual enzymes. In addition, it reveals details of the unwinding process, such as pauses and bursts of activity. The generic and versatile nature of the assay makes it applicable to a variety of DNA helicases and DNA templates. The method is an important addition to the single-molecule toolbox available for studying DNA processing enzymes

Retrieval of tropospheric CO column from hyperspectral infrared sounders - application to four years of Aqua/AIRS and MetOp-A/IASI

International audienceFour years of tropospheric integrated content of CO were retrieved from infrared hyperspectral observations of AIRS onboard Aqua and IASI onboard MetOp-A, for the period July 2007-June 2011. The retrieval method is based on a double differential approach that relies on the difference between brightness temperatures observed by the sounder and BT simulated by the Automatised Atmospheric Absorption Atlas (4A) radiative transfer model on colocated ECMWF reanalyses, for several couples of channels located in the 4.67 mu m CO band. AIRS and IASI give access to similar integrated contents of CO with a maximum sensitivity near 450 hPa and a half-height width of the weighting function between 200 and 750 hPa depending on the thermal contrast (i.e., the difference between the surface temperature and the temperature of the first pressure level). However, differences in their spectral and radiometric characteristics yield differences in the retrieval characteristics with AIRS selected couples of channels being more sensitive to surface characteristics. Moreover, IASI covers the whole CO absorption band, with a 3 times better spectral resolution, giving access to channels presenting a 3 times higher signal to noise ratio. This results in a better precision and lower standard deviation of the IASI retrievals. Conservatively, comparisons with CARIBIC aircraft measurements yield an averaged relative difference of 3.4% for IASI and 4.9% for AIRS. On average, AIRS and IASI retrievals are in very good agreement, showing the same seasonality, seasonal amplitudes, interannual variability and spatial distribution. The analysis of the monthly evolution of CO particularly highlights the expected strong influence of biomass burning on the evolution of CO in several tropical regions. In particular, a sharp increase in CO in 2010 in the southern tropics, especially over South America and South Africa, is observed, and is shown to be related to El Nino and to the Atlantic Multidecadal Oscillation