Cloud thermodynamic phase inferred from merged POLDER and MODIS data

International audienceThe global spatial and diurnal distribution of cloud properties is a key issue for understanding the hydrological cycle, and critical for advancing efforts to improve numerical weather models and general circulation models. Satellite data provides the best way of gaining insight into global cloud properties. In particular, the determination of cloud thermodynamic phase is a critical first step in the process of inferring cloud optical and microphysical properties from satellite measurements. It is important that cloud phase be derived together with an estimate of the confidence of this determination, so that this information can be included with subsequent retrievals (optical thickness, effective particle radius, and ice/liquid water content). In this study, we combine three different and well documented approaches for inferring cloud phase into a single algorithm. The algorithm is applied to data obtained by the MODIS (MODerate resolution Imaging Spectroradiometer) and POLDER3 (Polarization and Directionality of the Earth Reflectance) instruments. It is shown that this synergistic algorithm can be used routinely to derive cloud phase along with an index that helps to discriminate ambiguous phase from confident phase cases. The resulting product provides a semi-continuous confidence index ranging from confident liquid to confident ice instead of the usual discrete classification of liquid phase, ice phase, mixed phase (potential combination of ice and liquid particles), or simply unknown phase clouds. This approach is expected to be useful for cloud assimilation and modeling efforts while providing more insight into the global cloud properties derived from satellite data

Cloud information content analysis of multi-angular measurements in the oxygen A-band: application to 3MI and MSPI

The vertical distribution of cloud cover has a significant impact on a large number of meteorological and climatic processes. Cloud top altitude and cloud geometrical thickness are then essential. Previous studies established the possibility of retrieving those parameters from multi-angular oxygen A-band measurements. Here we perform a study and comparison of the performances of future instruments. The 3MI (Multi-angle, Multi-channel and Multi-polarization Imager) instrument developed by EUMETSAT, which is an extension of the POLDER/PARASOL instrument, and MSPI (Multi-angles Spectro-Polarimetric Imager) develoloped by NASA's Jet Propulsion Laboratory will measure total and polarized light reflected by the Earth's atmosphere–surface system in several spectral bands (from UV to SWIR) and several viewing geometries. Those instruments should provide opportunities to observe the links between the cloud structures and the anisotropy of the reflected solar radiation into space. Specific algorithms will need be developed in order to take advantage of the new capabilities of this instrument. However, prior to this effort, we need to understand, through a theoretical Shannon information content analysis, the limits and advantages of these new instruments for retrieving liquid and ice cloud properties, and especially, in this study, the amount of information coming from the A-Band channel on the cloud top altitude (CTOP) and geometrical thickness (CGT). We compare the information content of 3MI A-Band in two configurations and that of MSPI. Quantitative information content estimates show that the retrieval of CTOP with a high accuracy is possible in almost all cases investigated. The retrieval of CGT seems less easy but possible for optically thick clouds above a black surface, at least when CGT > 1–2 km

The structure of the PapD-PapGII pilin complex reveals an open and flexible P5 pocket

P pili are hairlike polymeric structures that mediate binding of uropathogenic Escherichia coli to the surface of the kidney via the PapG adhesin at their tips. PapG is composed of two domains: a lectin domain at the tip of the pilus followed by a pilin domain that comprises the initial polymerizing subunit of the 1,000-plus-subunit heteropolymeric pilus fiber. Prior to assembly, periplasmic pilin domains bind to a chaperone, PapD. PapD mediates donor strand complementation, in which a beta strand of PapD temporarily completes the pilin domain's fold, preventing premature, nonproductive interactions with other pilin subunits and facilitating subunit folding. Chaperone-subunit complexes are delivered to the outer membrane usher where donor strand exchange (DSE) replaces PapD's donated beta strand with an amino-terminal extension on the next incoming pilin subunit. This occurs via a zip-in-zip-out mechanism that initiates at a relatively accessible hydrophobic space termed the P5 pocket on the terminally incorporated pilus subunit. Here, we solve the structure of PapD in complex with the pilin domain of isoform II of PapG (PapGIIp). Our data revealed that PapGIIp adopts an immunoglobulin fold with a missing seventh strand, complemented in parallel by the G1 PapD strand, typical of pilin subunits. Comparisons with other chaperone-pilin complexes indicated that the interactive surfaces are highly conserved. Interestingly, the PapGIIp P5 pocket was in an open conformation, which, as molecular dynamics simulations revealed, switches between an open and a closed conformation due to the flexibility of the surrounding loops. Our study reveals the structural details of the DSE mechanism

Governments, grassroots, and the struggle for local food systems:Containing, coopting, contesting and collaborating

Local sustainable food systems have captured the popular imagination as a progressive, if not radical, pillar of a sustainable food future. Yet these grassroots innovations are embedded in a dominant food regime that reflects productivist, industrial, and neoliberal policies and institutions. Understanding the relationship between these emerging grassroots efforts and the dominant food regime is of central importance in any transition to a more sustainable food system. In this study, we examine the encounters of direct farm marketers with food safety regulations and other government policies and the role of this interface in shaping the potential of local food in a wider transition to sustainable agri-food systems. This mixed methods research involved interview and survey data with farmers and ranchers in both the USA and Canada and an in-depth case study in the province of Manitoba. We identified four distinct types of interactions between government and farmers: containing, coopting, contesting, and collaborating. The inconsistent enforcement of food safety regulations is found to contain progressive efforts to change food systems. While government support programs for local food were helpful in some regards, they were often considered to be inadequate or inappropriate and thus served to coopt discourse and practice by primarily supporting initiatives that conform to more mainstream approaches. Farmers and other grassroots actors contested these food safety regulations and inadequate government support programs through both individual and collective action. Finally, farmers found ways to collaborate with governments to work towards mutually defined solutions. While containing and coopting reflect technologies of governmentality that reinforce the status quo, both collaborating and contesting reflect opportunities to affect or even transform the dominant regime by engaging in alternative economic activities as part of the 'politics of possibility'. Developing a better understanding of the nature of these interactions will help grassroots movements to create effective strategies for achieving more sustainable and just food systems

Effects of N-Glycosylation Site Removal in Archaellins on the Assembly and Function of Archaella in Methanococcus maripaludis

In Methanococcus maripaludis S2, the swimming organelle, the archaellum, is composed of three archaellins, FlaB1S2, FlaB2S2 and FlaB3S2. All three are modified with an N-linked tetrasaccharide at multiple sites. Disruption of the N-linked glycosylation pathway is known to cause defects in archaella assembly or function. Here, we explored the potential requirement of N-glycosylation of archaellins on archaellation by investigating the effects of eliminating the 4 N-glycosylation sites in the wildtype FlaB2S2 protein in all possible combinations either by Asn to Glu (N to Q) substitution or Asn to Asp (N to D) substitutions of the N-glycosylation sequon asparagine. The ability of these mutant derivatives to complement a non-archaellated ΔflaB2S2 strain was examined by electron microscopy (for archaella assembly) and swarm plates (for analysis of swimming). Western blot results showed that all mutated FlaB2S2 proteins were expressed and of smaller apparent molecular mass compared to wildtype FlaB2S2, consistent with the loss of glycosylation sites. In the 8 single-site mutant complements, archaella were observed on the surface of Q2, D2 and D4 (numbers after N or Q refer to the 1st to 4th glycosylation site). Of the 6 double-site mutation complementations all were archaellated except D1,3. Of the 4 triple-site mutation complements, only D2,3,4 was archaellated. Elimination of all 4 N-glycosylation sites resulted in non-archaellated cells, indicating some minimum amount of archaellin glycosylation was necessary for their incorporation into stable archaella. All complementations that led to a return of archaella also resulted in motile cells with the exception of the D4 version. In addition, a series of FlaB2S2 scanning deletions each missing 10 amino acids was also generated and tested for their ability to complement the ΔflaB2S2 strain. While most variants were expressed, none of them restored archaellation, although FlaB2S2 harbouring a smaller 3-amino acid deletion was able to partially restore archaellation

Effect of Environmental and Spatial Factors on the Phylogenetic and Functional Diversity of the Mediterranean Tree Communities of Europe

The tree flora of the Mediterranean Basin contains an outstanding taxonomic richness and a high proportion of endemic taxa. Contrary to other regions of the Mediterranean biome, a comprehensive phylogenetic analysis of the relationship between phylogenetic diversity, trait diversity and environmental factors in a spatial ecological context is lacking. We inferred the first calibrated phylogeny of 203 native tree species occurring in the European Mediterranean Basin based on 12 DNA regions. Using a set of four functional traits, we computed phylogenetic diversity for all 10,042 grid cells of 10 × 10 km spatial resolution to completely cover Mediterranean Europe. Then, we tested the spatial influence of environmental factors on tree diversity. Our results suggest that the nature of the relationship between traits and phylogeny varies among the different studied traits and according to the evolutionary distance considered. Phylogenetic diversity and functional diversity of European Mediterranean trees correlated strongly with species richness. High values of these diversity indices were located in the north of the study area, at high altitude, and minimum temperature of the coldest month. In contrast, the two phylogenetic indices that were not correlated with species richness (Mean Phylogenetic Distance, Phylogenetic Species Variability) were located in the south of the study area and were positively correlated with high altitude, soil organic carbon stock and sand soil texture. Our study provides support for the use of phylogenies in conservation biology to assess ecosystem functioning, and provides insights for the implementation of sustainable forest ecosystem management

Genetic variability of hepatitis C virus before and after combined therapy of interferon plus ribavirin

We present an analysis of the selective forces acting on two hepatitis C virus genome regions previously postulated to be involved in the viral response to combined antiviral therapy. One includes the three hypervariable regions in the envelope E2 glycoprotein, and the other encompasses the PKR binding domain and the V3 domain in the NS5A region. We used a cohort of 22 non-responder patients to combined therapy (interferon alpha-2a plus ribavirin) for which samples were obtained before initiation of therapy and after 6 or/and 12 months of treatment. A range of 25-100 clones per patient, genome region and time sample were sequenced. These were used to detect general patterns of adaptation, to identify particular adaptation mechanisms and to analyze the patterns of evolutionary change in both genome regions. These analyses failed to detect a common adaptive mechanism for the lack of response to antiviral treatment in these patients. On the contrary, a wide range of situations were observed, from patients showing no positively selected sites to others with many, and with completely different topologies in the reconstructed phylogenetic trees. Altogether, these results suggest that viral strategies to evade selection pressure from the immune system and antiviral therapies do not result from a single mechanism and they are likely based on a range of different alternatives, in which several different changes, or their combination, along the HCV genome confer viruses the ability to overcome strong selective [email protected]; [email protected]; [email protected]; [email protected]; [email protected]; [email protected]; [email protected]; [email protected]

Alignment of the ALICE Inner Tracking System with cosmic-ray tracks

37 pages, 15 figures, revised version, accepted by JINSTALICE (A Large Ion Collider Experiment) is the LHC (Large Hadron Collider) experiment devoted to investigating the strongly interacting matter created in nucleus-nucleus collisions at the LHC energies. The ALICE ITS, Inner Tracking System, consists of six cylindrical layers of silicon detectors with three different technologies; in the outward direction: two layers of pixel detectors, two layers each of drift, and strip detectors. The number of parameters to be determined in the spatial alignment of the 2198 sensor modules of the ITS is about 13,000. The target alignment precision is well below 10 micron in some cases (pixels). The sources of alignment information include survey measurements, and the reconstructed tracks from cosmic rays and from proton-proton collisions. The main track-based alignment method uses the Millepede global approach. An iterative local method was developed and used as well. We present the results obtained for the ITS alignment using about 10^5 charged tracks from cosmic rays that have been collected during summer 2008, with the ALICE solenoidal magnet switched off.Peer reviewe

Cloud thermodynamic phase inferred from merged POLDER and MODIS data

The global spatial and diurnal distribution of cloud properties is a key issue for understanding the hydrological cycle, and critical for advancing efforts to improve numerical weather models and general circulation models. Satellite data provides the best way of gaining insight into global cloud properties. In particular, the determination of cloud thermodynamic phase is a critical first step in the process of inferring cloud optical and microphysical properties from satellite measurements. It is important that cloud phase be derived together with an estimate of the confidence of this determination, so that this information can be included with subsequent retrievals (optical thickness, effective particle radius, and ice/liquid water content). In this study, we combine three different and well documented approaches for inferring cloud phase into a single algorithm. The algorithm is applied to data obtained by the MODIS (MODerate resolution Imaging Spectroradiometer) and POLDER3 (Polarization and Directionality of the Earth Reflectance) instruments. It is shown that this synergistic algorithm can be used routinely to derive cloud phase along with an index that helps to discriminate ambiguous phase from confident phase cases. The resulting product provides a semi-continuous index ranging from confident liquid to confident ice instead of the usual discrete classification of liquid phase, ice phase, mixed phase (potential combination of ice and liquid particles), or simply unknown phase clouds. The index value provides simultaneously information on the phase and the associated confidence. This approach is expected to be useful for cloud assimilation and modeling efforts while providing more insight into the global cloud properties derived from satellite data