Analytic and algorithmic solution of random satisfiability problems

We study the satisfiability of random Boolean expressions built from many clauses with K variables per clause (K-satisfiability). Expressions with a ratio alpha of clauses to variables less than a threshold alphac are almost always satisfiable, whereas those with a ratio above this threshold are almost always unsatisfiable. We show the existence of an intermediate phase below alphac, where the proliferation of metastable states is responsible for the onset of complexity in search algorithms. We introduce a class of optimization algorithms that can deal with these metastable states; one such algorithm has been tested successfully on the largest existing benchmark of K-satisfiability.     

The crystal structure of the signal recognition particle in complex with its receptor

Cotranslational targeting of membrane and secretory proteins is mediated by the universally conserved signal recognition particle (SRP). Together with its receptor (SR), SRP mediates the guanine triphosphate (GTP)-dependent delivery of translating ribosomes bearing signal sequences to translocons on the target membrane. Here, we present the crystal structure of the SRP:SR complex at 3.9 angstrom resolution and biochemical data revealing that the activated SRP:SR guanine triphosphatase (GTPase) complex binds the distal end of the SRP hairpin RNA where GTP hydrolysis is stimulated. Combined with previous findings, these results suggest that the SRP:SR GTPase complex initially assembles at the tetraloop end of the SRP RNA and then relocalizes to the opposite end of the RNA. This rearrangement provides a mechanism for coupling GTP hydrolysis to the handover of cargo to the translocon.     

Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1

Eukaryotic ribosomes are substantially larger and more complex than their bacterial counterparts. Although their core function is conserved, bacterial and eukaryotic protein synthesis differ considerably at the level of initiation. The eukaryotic small ribosomal subunit (40S) plays a central role in this process; it binds initiation factors that facilitate scanning of messenger RNAs and initiation of protein synthesis. We have determined the crystal structure of the Tetrahymena thermophila 40S ribosomal subunit in complex with eukaryotic initiation factor 1 (eIF1) at a resolution of 3.9 angstroms. The structure reveals the fold of the entire 18S ribosomal RNA and of all ribosomal proteins of the 40S subunit, and defines the interactions with eIF1. It provides insights into the eukaryotic-specific aspects of protein synthesis, including the function of eIF1 as well as signaling and regulation mediated by the ribosomal proteins RACK1 and rpS6e.     

Paucity of genes on the Drosophila X chromosome showing male-biased expression

Sex chromosomes are primary determinants of sexual dimorphism in many organisms. These chromosomes are thought to arise via the divergence of an ancestral autosome pair and are almost certainly influenced by differing selection in males and females. Exploring how sex chromosomes differ from autosomes is highly amenable to genomic analysis. We examined global gene expression in Drosophila melanogaster and report a dramatic underrepresentation of X-chromosome genes showing high relative expression in males. Using comparative genomics, we find that these same X-chromosome genes are exceptionally poorly conserved in the mosquito Anopheles gambiae. These data indicate that the X chromosome is a disfavored location for genes selectively expressed in males.     

The vertical distribution of the Cs-137 derived from Chernobyl fall-out in the uppermostSphagnum layer of two peatlands in the southern Alps (Italy)

The patterns of concentration of the Cs-137 derived from the Chernobyl accident were analysed in a series of vertical profiles ofSphagnum collected at two peatlands in the southern Alps. The peak concentrations of the Chernobyl radiocesium were found in segments ofSphagnum located at different distances from the growing apex, probably corresponding to the plant tissues produced in the 1986 vegetation season. This indicated that the growth rates ofSphagnum are subject to considerable variations not only between species, but also between years and even between individuals of the same species when growing in different microhabitats at the same site. However, the concentrations of the Chernobyl-derived radiocesium are high also in theSphagnum segments produced after 1986. This was due to a continuous translocation of Cs-137 towards the capitulum, probably determined by the chemical similarity between cesium and potassium. Although the two sites investigated received nearly the same amounts of rainfall in the two-week period following the arrival of the Chernobyl plume, the average concentrations of radiocesium in allSphagnum species were significantly higher at one of them, presumably because the fall-out deposition was conditioned by a number of meteorological factors besides precipitation.     

Extractable iron and organic matter in the suspended insoluble material of fog droplets

In this work the formation and composition of aggregates between metals and organic material is studied in real fog samples. In a preliminary experiment it has been found that concentrated cloud samples form a yellow-brown precipitate in the presence of Fe(III). Standards of humic acids and fulvic acids co-precipitate with Fe(III), forming similar aggregates i.e. iron-humates (Fe-HA) and iron-fulvates (Fe-FA). By comparing the solubility properties of aggregates by extracting organic carbon (OC) in different pH conditions, it has been observed that fog droplet particulate samples are characterised by solubility properties more similar to those of Fe-HA than Fe-FA. Dilute alkaline solutions can also easily extract organic refractory substances that form aggregates with metals. The recoveries of the total extractable organic matter (accounting for 12% of total insoluble carbon and 15% of particulate mass) are similar to those of humic-like substances (HULIS) from particulate samples. The chromatographic behaviour and functional group characteristics measured in the alkali-extract fraction of precipitated aggregates with iron and in the insoluble particulate of fog samples, are those of humic-like material. Thus, soluble HULIS are able to interact with iron to form particulate, but the composition of a large fraction of insoluble organic carbon is still unknown. These findings have implications on the solubility and surface tension properties of fog droplets and can therefore potentially influence droplet formation, as well as cloud chemical and photochemical processes.     

Isolation and biochemical characterization of a basic myrosinase from ripe Crambe abyssinica seeds,highly specific for epi-progoitrin

On the basis of previous studies on the mechanism-based inhibition, activation, and active site structure of myrosinase(s) isolated from Sinapis alba and other cruciferous seeds, crambe myrosinase shows uncommon properties and behavior. For this reason homogeneous crambe myrosinase was isolated and investigated to establish the most important physicochemical features, including kinetic properties determined with the epimers progoitrin (R) and epi-progoitrin (S) as substrates, with and without ascorbate as an activator. The results of this study demonstrate that crambe myrosinase is highly specific for epi-progoitrin due to a better stabilization of the enzyme-substrate complex. This stabilization is caused by additional hydrogen bonding that only epi-progoitrin can set up between its hydroxyl group and a suitable residue in the hydrophobic pocket where the "docking" of the glucosinolates side chain takes place.     

Iron chelation by the powerful antioxidant flavonoid quercetin

Chelation of the bare and hydrated iron(II) cation by quercetin has been investigated at the DF/B3LYP level in the gas phase. Several complexed species arising from neutral and anionic forms of the ligand have been taken into account. Both 1:1 and 1:2 metal/flavonoid stoichiometries have been considered. Results indicate that among the potential sites of chelation present on quercetin, the oxygen atoms belonging to the 3-hydroxy and 4-oxo, and to the 5-hydroxy and 4-oxo groups, are the preferred ones. Time-dependent density functional theory (TDDFT) calculations, used to reproduce the electronic UV-vis spectra of isolated quercetin and its complexes with Fe2+, were also performed in methanol and dimethylsulfoxide.