Astronomical site testing in the era of the extremely large telescopes

The quality of astronomical sites is the first step to be considered to have the best performances from the telescopes. In particular, the efficiency of large telescopes in UV, IR, radio etc. is critically dependent on atmospheric transparency. It is well known that the random optical effects induced on the light propagation by turbulent atmosphere also limit telescope’s performances. Nowadays, clear appears the importance to correlate the main atmospheric physical parameters with the optical quality reachable by large aperture telescopes. The sky quality evaluation improved with the introduction of new techniques, new instrumentations and with the understanding of the link between the meteorological (or synoptical parameters and the observational conditions thanks to the application of the theories of electromagnetic waves propagation in turbulent medias: what we actually call astroclimatology. At the present the site campaigns are evolved and are performed using the classical scheme of optical seeing properties, meteorological parameters, sky transparency, sky darkness and cloudiness. New concept are added and are related to the geophysical properties such as seismicity, microseismicity, local variability of the climate, atmospheric conditions related to the ground optical turbulence and ground wind regimes, aerosol presence, use of satellite data. The purpose of this project is to provide reliable methods to analyze the atmospheric properties that affect ground-based optical astronomical observations and to correlate them with the main atmospheric parameters generating turbulence and affecting the photometric accuracy. The first part of the research concerns the analysis and interpretation of longand short-time scale meteorological data at two of the most important astronomical sites located in very different environments: the Paranal Observatory in the Atacama Desert (Chile), and the Observatorio del Roque de Los Muchachos(ORM) located in La Palma (Canary Islands, Spain). The optical properties of airborne dust at ORM have been investigated collecting outdoor data using a ground-based dust monitor. Because of its dryness, Paranal is a suitable observatory for near-IR observations, thus the extinction properties in the spectral range 1.00-2.30 um have been investigated using an empirical method. Furthermore, this PhD research has been developed using several turbulence profilers in the selection of the site for the European Extremely Large Telescope(E-ELT). During the campaigns the properties of the turbulence at different heights at Paranal and in the sites located in northern Chile and Argentina have been studied. This given the possibility to characterize the surface layer turbulence at Paranal and its connection with local meteorological conditions.

Pollen and macroremains from profiles from site Osterholz and Elm

The biostratigraphic classification of the Pleistocene in north-western and central Europe is still insufficiently known, in spite of numerous geological and vegetation-history investigations. The question is not even clear, for example, how often a warm-period vegetation with thermophilous trees such as Quercus, Ulmus, Tilia, Carpinus etc could develop here. In past years, on the basis of several geological and vegetation-history findings, suspicion has often been expressed that some of the classical stages of the Pleistocene could include more warm periods than heretofore assumed, and as a result of recent investigations the period between the Waal and Holstein interglacials seems to include at least two warm periods, of which the Cromer is one. This paper contributes to this problem. The interglacial sediments coming from the Elm-Mountains near Brunswick and from the Osterholz near Elze - both within the limits of the German Mittelgebirge - were investigated by pollen analysis. In both cases a Pinus-Betula zone and a QM zone were found. The vegetation development of the Pinus-Betula zone is characterized in both sequences by the early appearance of Picea. Because of strong local influence at the Osterholz a detailed correlation is difficult. However, vegetation development at the time of the QM zone at both sites was similar; it is especially characterized by the facts that Ulmus clearly migrated to the site earlier than Quercus and was very abundant throughout this time. Furthermore, both diagrams show very low amounts of Corylus. The interglacial of the Osterholz shows in addition to the above; a Carpinus-QM-Picea-zone in which Eucommia reaches a relative high value and in the upper of which Azolla filiculoides was also found. The similarity of vegetation development justifies acceptance of the same age for the occurrences. A comparison of the vegetation development at the Elm and the Osterholz with those of the Eem, Holstein, Waal, and Tegelen warm periods as well as with all the Cromer sites so far investigated shows that only a correlation with the Cromer Complex is possible. This correlation is supported by the geologic relations in the Osterholz (the deposit is overlain by Elster till). Therefore the till-like material with Scandinavian rock fragments underlying the deposit at Elm is of particular interest. The 'Rhume' interglacial beds at Bilshausen, only 60 km south of Osterholz, is also assigned to the Cromer complex, but the two deposits cannot be of the same age because the vegetation development differs. Therefore the Cromer complex must include at least two warm periods. Further conclusions about the relative stratigraphic position of these two occurrences and correlations of other Cromer sites are at this time not possible, however.

Depth tie points and ages of IODP Site 306-U1314

Integrated Ocean Drilling Program (IODP) Site U1314 of the North Atlantic is a critical sedimentary archive record of subpolar deep water from the southern Gardar Drift for which we derived an age model of orbital resolution for the last 1.8 Ma. This chronology combined with high-resolution (cm scale) X-ray fluorescence core scanning measurements of major elements allows tracking changes in terrigenous provenance during the last 1.1 Ma. Low Potassium to Titanium (K/Ti) ratios reflect enhanced transport of basalt-derived titanomagnetites during warm climate intervals, while high K/Ti ratios indicate a dominance of acidic sediment sources typical for glacial and stadial events. Changes in K/Ti and magnetic concentration at Site 1314 are coeval with fluctuations in smectite content and grain size data from nearby piston cores, suggesting that the provenance changes are mainly controlled by variable flow of the Iceland-Scotland Overflow Water, an important branch of North Atlantic Deep Water. Furthermore, K/Ti variations on orbital time scales show a striking similarity to the deep sea d13C record from ODP Site 607. Pervasive features of the K/Ti time series during and after the Mid-Pleistocene Transition are suborbital changes similar to Dansgaard/Oeschger and Bond oscillations that appear to be strongly amplified during ice growth phases when global benthic d18O was within the range of ~4.1-4.6 per mil. The strong increase in variability of sediment provenance and subsequently deep hydrography at benthic d18O values below ~4.1 suggests that the extent of glaciations and, therefore, sea level corresponding to this value constitutes an important physical threshold that was persistent at least for the last 1.1 Ma.

Iodine and boron concentrations in pore fluids, ultramafic clasts and interstitial serpentinite mud of ODP Hole 125-779A and Site 195-1200

Iodine and boron were analyzed in pore fluids, serpentinized ultramafic clasts, and the serpentinized mud matrix of the South Chamorro Seamount mud volcano (Ocean Drilling Program Leg 195 Site 1200) to determine the distribution of these elements in deep forearc settings. Similar analyses of clasts and muds from the Conical Seamount mud volcano (Leg 125 Site 779) were also carried out. Interstitial pore fluids are enriched in boron and iodine without appreciable change in chloride concentration relative to seawater. Both the ultramafic clasts and the associated serpentinized mud present the highest documented iodine concentrations for all types of nonsedimentary rocks (6.3-101.7 µmol/kg). Such high iodine concentrations, if commonplace in marine forearc settings, may constitute a significant, previously unknown reservoir of iodine. This serpentinized forearc mantle reservoir may potentially contribute to the total crustal iodine budget and provide a mechanism for its recycling at convergent plate margins. Both clasts and mud show concurrent enrichments in boron and iodine, and the similarity in pore fluid profiles also suggests that these two incompatible, fluid-mobile elements behave similarly at convergent plate margins.

Mid-Pleistocene (800-400 ka) records of benthic and planktic foraminfer d18O and d13C, planktic foraminifer based SST, and IRD of IODP Site 306-U1314

Stable carbon and oxygen isotopes from benthic and planktic foraminifers, planktic foraminifer assemblages and ice rafted debris from the North Atlantic Site U1314 (Integrated Ocean Drilling Program Expedition 306) were examined to investigate orbital and millennial-scale climate variability in the North Atlantic and its impact on global circulation focusing on the development of glacial periods during the mid-Pleistocene (ca 800-400 ka). Glacial initiations were characterized by a rapid cooling (6-10 °C in less than 7 kyr) in the mean annual sea surface temperature (SST), increasing benthic d18O values and high benthic d13C values. The continuous increase in benthic d18O suggests a continuous ice sheet growth whereas the positive benthic d13C values indicate that the flow of the Iceland Scotland Overflow water (ISOW) was vigorous. Strong deep water formation in the Norwegian Greenland Sea promoted a high transfer of freshwater from the ocean to the continents. However, low SSTs at Site U1314 suggest a subpolar gyre cooling and freshening that may have reduced deep water formation in the Labrador Sea during glacial initiations. Once the 3.5 per mil threshold in the benthic d18O record was exceeded, ice rafting started and ice sheet growth was punctuated by millennial-scale waning events which returned to the ocean part of the freshwater accumulated on the continents. Ice-rafting events were associated with a rapid reduction in the ISOW (benthic d13C values dropped 0.5-1 per mil) and followed by millennial-scale warmings. The first two millennial-scale warm intervals of each glacial period reached interglacial temperatures and were particularly abrupt (6-10 °C in ~3 kyr). Subsequent millennial-scale warm events were cooler probably because the AMOC was rather reduced as suggested by the low benthic d13C values. These two abrupt warming events that occurred at early glacial periods were also observed in the Antarctic temperature and CO2 records, suggesting a close correlation between both Hemispheres. The comparison of the sea surface proxies with the benthic d18O record (as the Southern sign) indicates the presence of a millennial-scale seesaw pattern similar to that seen during the Last Glacial period.

A multiproxy analysis of late MIS 6 to early MIS 5d OSP Site 161-975 sediments

A multiproxy analysis based on planktic foraminiferal abundances, derived SSTs, and stable planktic isotopes measurements together with alkenone abundances and Uk'37 SSTs was performed on late MIS 6 to early MIS 5d sediment recovered from Site 975 (ODP Leg 161) in the South Balearic Islands basin (Western Mediterranean) with emphasis on reconstructing the climate progression of the last interglacial period. A number of abrupt climate changes related to alternative influence of nutrient rich northern and oligotrophic southern water masses were revealed. Heinrich event 11 and cooling events C27, C26, C25, C24, C23, which have been previously described in the North Atlantic, were recognized. However, in comparison to the eastern North Atlantic mid-latitude region, events C27 and C26 at Site 975 seem to be significantly more pronounced. Together with evidence of a two-phase climate optimum with maximum SSTs reached during its later phase, this implies a close similarity in climate dynamics between the Western Mediterranean and the Nordic seas. We propose that postglacial effects in the Nordic seas had an influence on the western Mediterranean climate via atmospheric circulation and that these effects competed with the insolation force.

Pliocene sediment and silicon isotope record of ODP Site 145-882

Increases in the low-field mass-specific magnetic susceptibility (chi), dropstones and the terrigenous sediment component from Ocean Drilling Program (ODP) Site 882 (~45°N) have been interpreted to indicate a major onset of ice-rafting to the sub-Arctic northwest Pacific Ocean during marine isotope stage (MIS) G6 (from ~2.75 Ma). In contrast, studies of the terrigenous content of sediments cored downwind of ODP Site 882 indicate that dust and disseminated volcanic ash deposition in the sub-Arctic Pacific increased markedly during MIS G6. To investigate the relative contribution of dust, volcanic ash and ice rafting to the Pliocene chi increase, we present new high-resolution environmental magnetic and ice-rafted debris records from ODP Sites 882 and 885. Our results demonstrate that the chi increase at both sites across MIS G6 is predominantly controlled by a previously overlooked mixture of aeolian dust and volcanic ash. Our findings call into question the reliability of chi as a proxy for ice-rafting to the North Pacific. They also highlight a previously undocumented link between iron fertilisation and biogeochemical cycling in the North Pacific at a key stage during intensification of late Pliocene northern hemisphere glaciation.

Organic matter and sediment properties of samples from site GeoB15105 from the Black Sea

Dissolved organic matter (DOM) in marine sediments is a complex mixture of thousands of individual constituents that participate in biogeochemical reactions and serve as substrates for benthic microbes. Knowledge of the molecular composition of DOM is a prerequisite for a comprehensive understanding of the biogeochemical processes in sediments. In this study, interstitial water DOM was extracted with Rhizon samplers from a sediment core from the Black Sea and compared to the corresponding water-extractable organic matter fraction (<0.4 µm) obtained by Soxhlet extraction, which mobilizes labile particulate organic matter and DOM. After solid phase extraction (SPE) of DOM, samples were analyzed for the molecular composition by Fourier Transform Ion-Cyclotron Resonance Mass Spectrometry (FT-ICR MS) with electrospray ionization in negative ion mode. The average SPE extraction yield of the dissolved organic carbon (DOC) in interstitial water was 63%, whereas less than 30% of the DOC in Soxhlet-extracted organic matter was recovered. Nevertheless, Soxhlet extraction yielded up to 4.35% of the total sedimentary organic carbon, which is more than 30-times the organic carbon content of the interstitial water. While interstitial water DOM consisted primarily of carbon-, hydrogen- and oxygen-bearing compounds, Soxhlet extracts yielded more complex FT-ICR mass spectra with more peaks and higher abundances of nitrogen- and sulfur-bearing compounds. The molecular composition of both sample types was affected by the geochemical conditions in the sediment; elevated concentrations of HS- promoted the early diagenetic sulfurization of organic matter. The Soxhlet extracts from shallow sediment contained specific three- and four-nitrogen-bearing molecular formulas that were also detected in bacterial cell extracts and presumably represent proteinaceous molecules. These compounds decreased with increasing sediment depth while one- and two-nitrogen-bearing molecules increased, resulting in a higher similarity of both sample types in the deep sediment. In summary, Soxhlet extraction of sediments accessed a larger and more complex pool of organic matter than present in interstitial water DOM.

A site-specific recombinase is required for competitive root colonization by Pseudomonas fluorescens WCS365

A colonization mutant of the efficient root-colonizing biocontrol strain Pseudomonas fluorescens WCS365 is described that is impaired in competitive root-tip colonization of gnotobiotically grown potato, radish, wheat, and tomato, indicating a broad host range mutation. The colonization of the mutant is also impaired when studied in potting soil, suggesting that the defective gene also plays a role under more natural conditions. A DNA fragment that is able to complement the mutation for colonization revealed a multicistronic transcription unit composed of at least six ORFs with similarity to lppL, lysA, dapF, orf235/233, xerC/sss, and the largely incomplete orf238. The transposon insertion in PCL1233 appeared to be present in the orf235/233 homologue, designated orf240. Introduction of a mutation in the xerC/sss homologue revealed that the xerC/sss gene homologue rather than orf240 is crucial for colonization. xerC in Escherichia coli and sss in Pseudomonas aeruginosa encode proteins that belong to the λ integrase family of site-specific recombinases, which play a role in phase variation caused by DNA rearrangements. The function of the xerC/sss homologue in colonization is discussed in terms of genetic rearrangements involved in the generation of different phenotypes, thereby allowing a bacterial population to occupy various habitats. Mutant PCL1233 is assumed to be locked in a phenotype that is not well suited to compete for colonization in the rhizosphere. Thus we show the importance of phase variation in microbe–plant interactions.

Rational engineering of a miniprotein that reproduces the core of the CD4 site interacting with HIV-1 envelope glycoprotein

Protein–protein interacting surfaces are usually large and intricate, making the rational design of small mimetics of these interfaces a daunting problem. On the basis of a structural similarity between the CDR2-like loop of CD4 and the β-hairpin region of a short scorpion toxin, scyllatoxin, we transferred the side chains of nine residues of CD4, central in the binding to HIV-1 envelope glycoprotein (gp120), to a structurally homologous region of the scorpion toxin scaffold. In competition experiments, the resulting 27-amino acid miniprotein inhibited binding of CD4 to gp120 with a 40 μM IC50. Structural analysis by NMR showed that both the backbone of the chimeric β-hairpin and the introduced side chains adopted conformations similar to those of the parent CD4. Systematic single mutations suggested that most CD4 residues from the CDR2-like loop were reproduced in the miniprotein, including the critical Phe-43. The structural and functional analysis performed suggested five additional mutations that, once incorporated in the miniprotein, increased its affinity for gp120 by 100-fold to an IC50 of 0.1–1.0 μM, depending on viral strains. The resulting mini-CD4 inhibited infection of CD4+ cells by different virus isolates. Thus, core regions of large protein–protein interfaces can be reproduced in miniprotein scaffolds, offering possibilities for the development of inhibitors of protein–protein interactions that may represent useful tools in biology and in drug discovery.

Isolation of a superfamily of candidate disease-resistance genes in soybean based on a conserved nucleotide-binding site.

The tobacco N and Arabidopsis RPS2 genes, among several recently cloned disease-resistance genes, share highly conserved structure, a nucleotide-binding site (NBS). Using degenerate oligonucleotide primers for the NBS region of N and RPS2, we have amplified and cloned the NBS sequences from soybean. Each of these PCR-derived NBS clones detected low-or moderate-copy soybean DNA sequences and belongs to 1 of 11 different classes. Sequence analysis showed that all PCR clones encode three motifs (P-loop, kinase-2, and kinase-3a) of NBS nearly identical to those in N and RPS2. The intervening region between P-loop and kinase-3a of the 11 classes has high (26% average) amino acid sequence similarity to the N gene although not as high (19% average) to RPS2. These 11 classes represent a superfamily of NBS-containing soybean genes that are homologous to N and RPS2. Each class or subfamily was assessed for its positional association with known soybean disease-resistance genes through near-isogenic line assays, followed by linkage analysis in F2 populations using restriction fragment length polymorphisms. Five of the 11 subfamilies have thus far been mapped to the vicinity of known soybean genes for resistance to potyviruses (Rsv1 and Rpv), Phytophthora root rot (Rps1, Rps2, and Rps3), and powdery mildew (rmd). The conserved N- or RPS2-homologous NBS sequences and their positional associations with mapped soybean-resistance genes suggest that a number of the soybean disease-resistance genes may belong to this superfamily. The candidate subfamilies of NBS-containing genes identified by genetic mapping should greatly facilitate the molecular cloning of disease-resistance genes.

Crystal structure of D-amino acid oxidase: a case of active site mirror-image convergent evolution with flavocytochrome b2.

D-amino acid oxidase is the prototype of the FAD-dependent oxidases. It catalyses the oxidation of D-amino acids to the corresponding alpha-ketoacids. The reducing equivalents are transferred to molecular oxygen with production of hydrogen peroxide. We have solved the crystal structure of the complex of D-amino acid oxidase with benzoate, a competitive inhibitor of the substrate, by single isomorphous replacement and eightfold averaging. Each monomer is formed by two domains with an overall topology similar to that of p-hydroxybenzoate hydroxylase. The benzoate molecule lays parallel to the flavin ring and is held in position by a salt bridge with Arg-283. Analysis of the active site shows that no side chains are properly positioned to act as the postulated base required for the catalytic carboanion mechanism. On the contrary, the benzoate binding mode suggests a direct transfer of the substrate alpha-hydrogen to the flavin during the enzyme reductive half-reaction.The active site Of D-amino acid oxidase exhibits a striking similarity with that of flavocytochrome b2, a structurally unrelated FMN-dependent flavoenzyme. The active site groups (if these two enzymes are in fact superimposable once the mirror-image of the flavocytochrome b2 active site is generated with respect to the flavin plane. Therefore, the catalytic sites of D-amino acid oxidase and flavocytochrome b2 appear to have converged to a highly similar but enantiomeric architecture in order to catalvze similar reactions (oxidation of alpha-amino acids or alpha-hydroxy acids), although with opposite stereochemistry.

Nuclear protein import: Ran-GTP dissociates the karyopherin alphabeta heterodimer by displacing alpha from an overlapping binding site on beta.

The alpha subunit of the karyopherin heterodimer functions in recognition of the protein import substrate and the beta subunit serves to dock the trimeric complex to one of many sites on nuclear pore complex fibers. The small GTPase Ran and the Ran interactive protein, p10, function in the release of the docked complex. Repeated cycles of docking and release are thought to concentrate the transport substrate for subsequent diffusion into the nucleus. Ran-GTP dissociates the karyopherin heterodimer and forms a stoichiometric complex with Ran-GTP. Here we report the mapping of karyopherin beta's binding sites both for Ran-GTP and for karyopherin alpha. We discovered that karyopherin beta's binding site for Ran-GTP shows a striking sequence similarity to the cytoplasmic Ran-GTP binding protein, RanBP1. Moreover, we found that Ran-GTP and karyopherin alpha bind to overlapping sites on karyopherin beta. Having a higher affinity to the overlapping site, Ran-GTP displaces karyopherin alpha and binds to karyopherin beta. Competition for overlapping binding sites may be the mechanism by which GTP bound forms of other small GTPases function in corresponding dissociation-association reactions. We also mapped Ran's binding site for karyopherin beta to a cluster of basic residues analogous to those previously shown to constitute karyopherin alpha's binding site to karyopherin beta.

The glycine binding site of the N-methyl-D-aspartate receptor subunit NR1: identification of novel determinants of co-agonist potentiation in the extracellular M3-M4 loop region.

The N-methyl-D-aspartate (NMDA) subtype of ionotropic glutamate receptors is a heterooligomeric membrane protein composed of homologous subunits. Here, the contribution of the M3-M4 loop of the NR1 subunit to the binding of glutamate and the co-agonist glycine was investigated by site-directed mutagenesis. Substitution of the phenylalanine residues at positions 735 or 736 of the M3-M4 loop produced a 15- to 30-fold reduction in apparent glycine affinity without affecting the binding of glutamate and the competitive glycine antagonist 7-chlorokynurenic acid; mutation of both residues caused a >100-fold decrease in glycine affinity. These residues are found in a C-terminal region of the M3-M4 loop that shows significant sequence similarity to bacterial amino acid-binding proteins. Epitope tagging revealed both the N-terminus and the M3-M4 loop to be exposed extracellularly, whereas a C-terminal epitope was localized intracellularly. These results indicate that the M3-M4 loop is part of the ligand-binding pocket of the NR1 subunit and provide the basis for a refined model of the glycine-binding site of the NMDA receptor.