The E-site story: the importance of maintaining two tRNAs on the ribosome during protein synthesis

In the sixties James Watson suggested a twosite model for the ribosome comprising the P site for the peptidyl transfer RNA (tRNA) before peptide-bond formation and the A site, where decoding takes place according to the codon exposed there. In the eighties a third tRNA binding site was detected, the E site, which was specific for deacylated tRNA and turned out to be a universal feature of ribosomes. However, despite having three tRNA binding sites, only two tRNAs occupy the ribosome at a time during protein synthesis: at the A and P sites before translocation (PRE state) and at the P and E sites after translocation (POST state). The importance of having two tRNAs in the POST state has been revealed during the last 25 years, showing that the E site contributes two fundamental features: (i) the fact that incorporation of a wrong amino acid is not harmful for the cell (only 1 in about 400 misincorporations destroys the function of a protein) stems from the presence of an E-tRNA; (ii) maintenance of the reading frame is one of the most remarkable achievements of the ribosome, essential for faithful translation of the genetic information. The presence of the POST state E-tRNA prevents loss of the reading frame. Received 14 March 2006; received after revision 8 June 2006; accepted 4 August 2006     

Observation of the dynamical Casimir effect in a superconducting circuit

One of the most surprising predictions of modern quantum theory is that the vacuum of space is not empty. In fact, quantum theory predicts that it teems with virtual particles flitting in and out of existence. Although initially a curiosity, it was quickly realized that these vacuum fluctuations had measurable consequences--for instance, producing the Lamb shift of atomic spectra and modifying the magnetic moment of the electron. This type of renormalization due to vacuum fluctuations is now central to our understanding of nature. However, these effects provide indirect evidence for the existence of vacuum fluctuations. From early on, it was discussed whether it might be possible to more directly observe the virtual particles that compose the quantum vacuum. Forty years ago, it was suggested that a mirror undergoing relativistic motion could convert virtual photons into directly observable real photons. The phenomenon, later termed the dynamical Casimir effect, has not been demonstrated previously. Here we observe the dynamical Casimir effect in a superconducting circuit consisting of a coplanar transmission line with a tunable electrical length. The rate of change of the electrical length can be made very fast (a substantial fraction of the speed of light) by modulating the inductance of a superconducting quantum interference device at high frequencies (>10 gigahertz). In addition to observing the creation of real photons, we detect two-mode squeezing in the emitted radiation, which is a signature of the quantum character of the generation process.     

Flying in a flock comes at a cost in pigeons

Flying birds often form flocks, with social, navigational and anti-predator implications. Further, flying in a flock can result in aerodynamic benefits, thus reducing power requirements, as demonstrated by a reduction in heart rate and wingbeat frequency in pelicans flying in a V-formation. But how general is an aerodynamic power reduction due to group-flight? V-formation flocks are limited to moderately steady flight in relatively large birds, and may represent a special case. What are the aerodynamic consequences of flying in the more usual 'cluster' flock? Here we use data from innovative back-mounted Global Positioning System (GPS) and 6-degrees-of-freedom inertial sensors to show that pigeons (1) maintain powered, banked turns like aircraft, imposing dorsal accelerations of up to 2g, effectively doubling body weight and quadrupling induced power requirements; (2) increase flap frequency with increases in all conventional aerodynamic power requirements; and (3) increase flap frequency when flying near, particularly behind, other birds. Therefore, unlike V-formation pelicans, pigeons do not gain an aerodynamic advantage from flying in a flock. Indeed, the increased flap frequency, whether due to direct aerodynamic interactions or requirements for increased stability or control, suggests a considerable energetic cost to flight in a tight cluster flock.     

Antibiotic resistance is ancient

The discovery of antibiotics more than 70 years ago initiated a period of drug innovation and implementation in human and animal health and agriculture. These discoveries were tempered in all cases by the emergence of resistant microbes. This history has been interpreted to mean that antibiotic resistance in pathogenic bacteria is a modern phenomenon; this view is reinforced by the fact that collections of microbes that predate the antibiotic era are highly susceptible to antibiotics. Here we report targeted metagenomic analyses of rigorously authenticated ancient DNA from 30,000-year-old Beringian permafrost sediments and the identification of a highly diverse collection of genes encoding resistance to β-lactam, tetracycline and glycopeptide antibiotics. Structure and function studies on the complete vancomycin resistance element VanA confirmed its similarity to modern variants. These results show conclusively that antibiotic resistance is a natural phenomenon that predates the modern selective pressure of clinical antibiotic use.     

New occurrence of Ba-REE fluorcarbonate minerals at Bayan Obo, Inner Mongolia, North China, and their mineralogical features

Ba-REE fluorcarbonate minerals from a carbonatite dyke at Bayan Obo, Inner Mongolia, North China, are first reported in this contribution, in which chemical composition, rare earth element (REE) patterns, and intergrowth relationships for these minerals have been investigated. Syntactic intergrowth or syntaxy between cebaite and cordylite, as well as cordylite and huanghoite were observed. This syntactic texture resulted from the variation of chemical composition of crystallizing agents for those minerals that crystallized directly from carbonatite magmas. It is worth noting that REE patterns of the Ba-REE fluorcarbonate minerals in the dyke are similar to those of the corresponding minerals from the ore hosted dolomite marble of the Bayan Obo giant REE-Nb-Fe mineral deposit, which implies their relation in origin.     

Cobalt doped ZrO2 decorated multiwalled carbon nanotube: A promising nanocatalyst for photodegradation of indigo carmine and eosin Y dyes

This paper reports the degradation of indigo carmine and eosin Y dyes in water, catalyzed by cobalt and multiwalled carbon nanotube modified zirconium oxide nanocomposite(Co-ZrO_2-MWCNTs) under simulated visible light. The bare ZrO_2,ZrO_2-MWCNTs, Co-ZrO_2 and Co-ZrO_2-MWCNTs with different percentage compositions of cobalt were synthesized by homogeneous co-precipitation method. Characterization of the prepared nanocomposites was carried out using X-Ray powder Diffraction(XRD), Fourier Transformer Infrared(FTIR) Spectroscopy, Transmission Electron Microscopy(TEM), Raman Spectroscopy,(UV–Vis)-Spectroscopy and Energy Dispersive Spectroscopy(EDS) for their structure, formation,morphology, size and elemental analysis. The experimental results indicated that all the cobalt and MWCNTs modified nanocomposites demonstrated higher photocatalytic activities compared to the bare ZrO_2. The most efficient catalyst(0.5% Co-ZrO_2-MWCNTs) with the band gap and Ka values of 5.21 e V and 16.86*10~(-3) min~(-1) respectively exhibited 98% degradation efficiency toward indigo carmine and 87% toward eosin Y in 180 min.     

Scaling laws of marine predator search behaviour

Many free-ranging predators have to make foraging decisions with little, if any, knowledge of present resource distribution and availability. The optimal search strategy they should use to maximize encounter rates with prey in heterogeneous natural environments remains a largely unresolved issue in ecology. Lévy walks are specialized random walks giving rise to fractal movement trajectories that may represent an optimal solution for searching complex landscapes. However, the adaptive significance of this putative strategy in response to natural prey distributions remains untested. Here we analyse over a million movement displacements recorded from animal-attached electronic tags to show that diverse marine predators-sharks, bony fishes, sea turtles and penguins-exhibit Lévy-walk-like behaviour close to a theoretical optimum. Prey density distributions also display Lévy-like fractal patterns, suggesting response movements by predators to prey distributions. Simulations show that predators have higher encounter rates when adopting Lévy-type foraging in natural-like prey fields compared with purely random landscapes. This is consistent with the hypothesis that observed search patterns are adapted to observed statistical patterns of the landscape. This may explain why Lévy-like behaviour seems to be widespread among diverse organisms, from microbes to humans, as a 'rule' that evolved in response to patchy resource distributions.     

Rapid cloning of high-affinity human monoclonal antibodies against influenza virus

Pre-existing neutralizing antibody provides the first line of defence against pathogens in general. For influenza virus, annual vaccinations are given to maintain protective levels of antibody against the currently circulating strains. Here we report that after booster vaccination there was a rapid and robust influenza-specific IgG+ antibody-secreting plasma cell (ASC) response that peaked at approximately day 7 and accounted for up to 6% of peripheral blood B cells. These ASCs could be distinguished from influenza-specific IgG+ memory B cells that peaked 14-21 days after vaccination and averaged 1% of all B cells. Importantly, as much as 80% of ASCs purified at the peak of the response were influenza specific. This ASC response was characterized by a highly restricted B-cell receptor (BCR) repertoire that in some donors was dominated by only a few B-cell clones. This pauci-clonal response, however, showed extensive intraclonal diversification from accumulated somatic mutations. We used the immunoglobulin variable regions isolated from sorted single ASCs to produce over 50 human monoclonal antibodies (mAbs) that bound to the three influenza vaccine strains with high affinity. This strategy demonstrates that we can generate multiple high-affinity mAbs from humans within a month after vaccination. The panel of influenza-virus-specific human mAbs allowed us to address the issue of original antigenic sin (OAS): the phenomenon where the induced antibody shows higher affinity to a previously encountered influenza virus strain compared with the virus strain present in the vaccine. However, we found that most of the influenza-virus-specific mAbs showed the highest affinity for the current vaccine strain. Thus, OAS does not seem to be a common occurrence in normal, healthy adults receiving influenza vaccination.     

Reduction and selective oxo group silylation of the uranyl dication

Uranium occurs in the environment predominantly as the uranyl dication [UO2]2+. Its solubility renders this species a problematic contaminant which is, moreover, chemically extraordinarily robust owing to strongly covalent U-O bonds. This feature manifests itself in the uranyl dication showing little propensity to partake in the many oxo group functionalizations and redox reactions typically seen with [CrO2]2+, [MoO2]2+ and other transition metal analogues. As a result, only a few examples of [UO2]2+ with functionalized oxo groups are known. Similarly, it is only very recently that the isolation and characterization of the singly reduced, pentavalent uranyl cation [UO2]+ has been reported. Here we show that placing the uranyl dication within a rigid and well-defined molecular framework while keeping the environment anaerobic allows simultaneous single-electron reduction and selective covalent bond formation at one of the two uranyl oxo groups. The product of this reaction is a pentavalent and monofunctionalized [O = U...OR]+ cation that can be isolated in the presence of transition metal cations. This finding demonstrates that under appropriate reaction conditions, the uranyl oxo group will readily undergo radical reactions commonly associated only with transition metal oxo groups. We expect that this work might also prove useful in probing the chemistry of the related but highly radioactive plutonyl and neptunyl analogues found in nuclear waste.     

Food web structure, energetics, and importance of allochthonous carbon in a desert cavernous limnocrene: Devils Hole, Nevada

We tested the hypothesis that allochthonous carbon is important in the diet of the endemic pupfish Cyprinodon diabolis over a 3-year period in Devils Hole, Nevada. Devils Hole is a cavernous limnocrene located in the Mojave Desert approximately 15 m below the land surface and receives direct solar radiation <7% of the total time during the year. The system is dominated by filamentous cyanobacteria in the summer and supports about 15 invertebrate species and the endemic pupfish C. diabolis . We examined food web structure and measured autochthonous carbon production and entry of allochthonous carbon with funnel traps. Stable isotopes were used to compare contributions of each carbon source. Allochthonous carbon contributed 2971 kj ⋅ yr -1 (60%) of the total available energy to the food web compared to only 2000 kj ⋅ yr -1 autochthonous production. A major stochastic rain event delivered more terrestrial carbon to Devils Hole in l hour than annual allochthonous carbon, estimated from data collected with funnel traps. Mixing models with δ 15 N, δ 13 C, and δ 34 S showed a seasonal shift in diet for C. diabolis from filamentous cyanobacteria in the summer to the collector/gathering insect Stenelmis calida in the winter. Stenelmis tissue had high proportions of allochthonous plant carbon in the winter.