Accurate localization and excision of genomic islands in four strains of <Emphasis Type=Italic>Pseudomonas aeruginosa</Emphasis> and <Emphasis Type=Italic>Pseudomonas fluorescens</Emphasis>

Mobile genomic islands (GIs) can be excised from the chromosome, then form a circular intermediate and be reintegrated into the chromosome by the GI internal integrase. Some mobile GIs can also be transferred into a new receptor cell by transformation, conjugation, or transduction. The action sites of the integrase are usually flanked direct repeats (DRs) of the GIs. Accurate localization of the flanking sequences is a precondition for determining the mobility of the GI. Mobile GIs are generally associated with transfer RNAs (tRNAs). Based on the correlation between flanking sequences and tRNA sequences, the flanking sequences of 11 putative mobile GIs in Pseudomonas aeruginosa PAO1, P. aeruginosa PA14, P. fluorescens Pf-5 and P. fluorescens Pf0-1 were identified. Among the 11 GIs, Pf0-1GI-1 is responsible for benzoate degradation. PAO1GI-1, Pf5GI-2, Pf5GI-3, and Pf5GI-4 were confirmed experimentally to be excised from a chromosome to form a circular intermediate. The action sites of the integrases are these GIs direct repeats. Due to distinct DRs, cutting sites for the internal integrase of PAO1GI-1, Pf5GI-2, Pf5GI-3 and Pf5GI-4 were determined outside the T-loop of the tRNA^Gly gene, outside the anticodon loop of the tRNA^Ser gene and tRNA^Lys gene, and at the asymmetric 3′-end of the tRNA^Leu gene, respectively. PAO1GI-1 and other mobile GIs may be transferred into many different strains that belong to different phyla because of the clear flanking sequences. This study describes basic information about the action sites of the integrases, assesses the mobility of GIs, and can help design and transfer mobile GIs to candidate strains.     

Highlights of recent advances in functional coordination polymers made in China

Coordination polymers (or metal-organic frameworks, MOFs), as one of the essences of crystal engineering and coordination chemistry, have attracted considerable atten-tion from chemists,     

Superfluid density of two-dimensional weakly interacting boson system at zero temperature

We compute the superfluid density of a two-dimensional boson system with weak two-body repulsive interactions at zero temperature using one-loop perturbation theory in the weak coupling region. The boson fields are taken to be in continuum form in real space, and the interactions are approximated by a δ function of the distance between the bosons. We find that the one-loop fluctuations slightly decrease the superfluid density of a classical level. The superfluid density is approximated by the condensate density multiplied by the mass of the boson particle.     

Prediction of sites under adaptive evolution in flavin-containing monooxygenases: Selection pattern revisited

Flavin-containing monooxygenase (FMO), like cytochrome P450 (CYP), is a monooxygenase that uses the reducing equivalents of NADPH to reduce one atom of molecular oxygen to water, while the other atom is used to oxidize the substrate. Recently, it was shown that some CYP isoforms have been subject to positive selection. However, it is unknown whether the highly conserved phase I detoxification enzyme, FMO, has undergone similar positive Darwinian selection. We used maximum-likelihood models of codon substitution, evolutionary fingerprinting, and cross species comparison to investigate the occurrence of adaptive evolution in FMO sequences. We used recent genomic data from a range of species, including vertebrates and invertebrates. We present the evidence for the occurrence of adaptive evolution in mammalian FMO 3, 4, 5, and fugu FMOs but not in mammalian FMO 1, FMO 2, frog FMOs, other fish FMOs and invertebrate FMOs. The sites under adaptive evolution were significantly associated with the insertion domain in mammalian FMO 5. We identified specific amino acid sites in FMOs 3–5 that are likely targets for selection based on the patterns of parallel amino acid change. The most likely role of adaptive evolution is the repair of mutations that permitted optimal NADP+ binding and improved catalytic efficiency. The occurrence of positive selection during the evolution of phase I detoxification enzymes such as FMOs 3–5 and fugu FMO suggests the occurrence of both high selection pressure acting on species within their unique habitats and significant changes in intensity and direction (forms of xenobiotics and drugs) resulting from changes in microhabitat and food.     

Nonextensivity and the <Emphasis Type=Italic>q</Emphasis>-distribution of a relativistic gas under an external electromagnetic field

We investigate the nonextensivity and the q-distribution of a relativistic gas under an external electromagnetic field. We derive an expression for the nonextensive parameter q based on the relativistic generalized Boltzmann equation, the relativistic q-H theorem and the relativistic version of the q-power-law distribution function in the nonextensive q-kinetic theory. We thus provide the connection between the parameter q≠1 and the spatial-temporal derivatives of the temperature field of the gas as well as the four-potential, and thereby present a clearly physical meaning for the nonextensivity for the relativistic gas.     

A liquid helium temperature target with a 10 K vapor shield for shock compression experiment in the environment condition of 100 Pa

The shock compression experiment of liquid helium is an available way to gain properties of specimen at high temperatures and pressures.Based on Fluent,a thermal insulation analysis and design of a liquid helium temperature target in the environment condition of 100 Pa for shock compression experiment is performed.Then,a cryogenic target with a 10 K helium vapor shield and a separated vacuum interval is particularly developed.A lowest temperature of 3.63 K and a stable temperature of 3.70 K in the specimen cavity with an accuracy of 0.1 K are obtained by means of continuous flow and vacuum cooling.Both time-consuming and temperature stability are well-suited to the requirements of the shock compression experiment.The results show that the calculated and experimental data well-matched each other.The simulation method may be effective and feasible for the optimal design of the cryogenic target.     

Rapid reductive degradation of azo dyes by a unique structure of amorphous alloys

An Fe-based amorphous alloy was found to significantly enhance the reductive degradation of an azo dye in aqueous solution. The surface-area normalized rate constant was up to 2.0 L m-2 min-1 at room temperature,an order of magnitude larger than any previously reported value. The activation energy of the degradation process was calculated according to the Arrhenius equation,and a much lower value than those previously reported was obtained. Valence band measurement indicated that a depressed valence band maximum and a widened empty band were established in the amorphous ribbon. The unique structure of the amorphous alloy is important-it may reduce the activation energy of the degradation process and enhance the activity of the electrons,thus accelerating the degradation process.     

An important functional group,benzo[1,3]dioxole,of alkaloids induces the formation of the human telomeric DNA G-quadruplex

Over the past few decades, numerous molecules have been discovered or designed to interact efficiently and selectively with a peculiar DNA structure named G-quadruplex. Some of these molecules have been developed as anticancer agents. To aid the design of anticancer agents, the ability of alkaloids possessing Protoberberine and Benzophenanthridine groups to induce the formation of G-quadruplexes were studied using CD spectroscopy. By careful examination of their structures, we found that a benzo[1,3]dioxole group plays an important role in influencing their inductive properties. The more functional groups the alkaloids have, the stronger their G-quadruplex inductive ability.     

Identification of AtSM34, a novel tonoplast intrinsic protein-interacting polypeptide expressed in response to osmotic stress in germinating seedlings

Aquaporins are implicated in a wide variety of plant physiological processes, although the mechanisms involved in their regulation are not fully understood. To gain further insight into the regulatory factors involved in this process, we used a yeast two-hybrid system to screen for potential binding partners to the Arabidopsis tonoplast intrinsic protein (TIP) AtTIP1;1. This was the first protein identified to be associated with high water permeability in vacuolar membranes from Arabidopsis thaliana. Using ...     

Revisit the K-segment of the Southeast Indian Ridge for new evidence of hydrothermal plumes

During the first leg of a Chinese research cruise to the Southeast Indian Ridge (SEIR) in 2007, we revisited the K-segment of the SEIR and observed a water column turbidity anomaly at a CTD cast station. This station was located ~400 m from a dredge site on a plume anomaly detected in 1996 by US scientists. The characteristics of the turbidity anomaly detected in our survey are different from those observed 11 years previously, implying that either the detected anomalies have distinct and different plume sources or the robustness of the plume has changed in the intervening time. In addition, turbidity anomalies were observed at two localities on the K-segment in a deep tow-yo profile. If these two anomalies are not connected, the plume incidence calculated would be about 0.28, larger than the predicted value of 0.25 for a 65 mm/a spreading rate. This increase in plume incidence on the K-segment seems to be related to the influence of the St. Paul-Amsterdam hotspot, located about 300 km to the northwest.