The prolyl isomerase Pin1 is a regulator of p53 in genotoxic response

p53 is activated in response to various genotoxic stresses resulting in cell cycle arrest or apoptosis. It is well documented that DNA damage leads to phosphorylation and activation of p53 (refs 1-3), yet how p53 is activated is still not fully understood. Here we report that DNA damage specifically induces p53 phosphorylation on Ser/Thr-Pro motifs, which facilitates its interaction with Pin1, a member of peptidyl-prolyl isomerase. Furthermore, the interaction of Pin1 with p53 is dependent on the phosphorylation that is induced by DNA damage. Consequently, Pin1 stimulates the DNA-binding activity and transactivation function of p53. The Pin1-mediated p53 activation requires the WW domain, a phosphorylated Ser/Thr-Pro motif interaction module, and the isomerase activity of Pin1. Moreover, Pin1-deficient cells are defective in p53 activation and timely accumulation of p53 protein, and exhibit an impaired checkpoint control in response to DNA damage. Together, these data suggest a mechanism for p53 regulation in cellular response to genotoxic stress.     

Sequence and analysis of rice chromosome 4

Rice is the principal food for over half of the population of the world. With its genome size of 430 megabase pairs (Mb), the cultivated rice species Oryza sativa is a model plant for genome research. Here we report the sequence analysis of chromosome 4 of O. sativa, one of the first two rice chromosomes to be sequenced completely. The finished sequence spans 34.6 Mb and represents 97.3% of the chromosome. In addition, we report the longest known sequence for a plant centromere, a completely sequenced contig of 1.16 Mb corresponding to the centromeric region of chromosome 4. We predict 4,658 protein coding genes and 70 transfer RNA genes. A total of 1,681 predicted genes match available unique rice expressed sequence tags. Transposable elements have a pronounced bias towards the euchromatic regions, indicating a close correlation of their distributions to genes along the chromosome. Comparative genome analysis between cultivated rice subspecies shows that there is an overall syntenic relationship between the chromosomes and divergence at the level of single-nucleotide polymorphisms and insertions and deletions. By contrast, there is little conservation in gene order between rice and Arabidopsis.     

Automated soil resources mapping based on decision tree and Bayesian predictive modeling

This article presents two approaches for automated building of knowledge bases of soil resources mapping. These methods used decision tree and Bayesian predictive modeling, respectively to generate knowledge from training data. With these methods, building a knowledge base for automated soil mapping is easier than using the conventional knowledge acquisition approach. The knowledge bases built by these two methods were used by the knowledge classifier for soil type classification of the Longyou area, Zhejiang Province, China using TM bi-temporal imageries and GIS data. To evaluate the performance of the resultant knowledge bases, the classification results were compared to existing soil map based on field survey. The accuracy assessment and analysis of the resultant soil maps suggested that the knowledge bases built by these two methods were of good quality for mapping distribution model of soil classes over the study area.     

Transposition of hAT elements links transposable elements and V(D)J recombination

Transposons are DNA sequences that encode functions that promote their movement to new locations in the genome. If unregulated, such movement could potentially insert additional DNA into genes, thereby disrupting gene expression and compromising an organism's viability. Transposable elements are classified by their transposition mechanisms and by the transposases that mediate their movement. The mechanism of movement of the eukaryotic hAT superfamily elements was previously unknown, but the divergent sequence of hAT transposases from other elements suggested that these elements might use a distinct mechanism. Here we have analysed transposition of the insect hAT element Hermes in vitro. Like other transposons, Hermes excises from DNA via double-strand breaks between the donor-site DNA and the transposon ends, and the newly exposed transposon ends join to the target DNA. Interestingly, the ends of the donor double-strand breaks form hairpin intermediates, as observed during V(D)J recombination, the process which underlies the combinatorial formation of antigen receptor genes. Significant similarities exist in the catalytic amino acids of Hermes transposase, the V(D)J recombinase RAG, and retroviral integrase superfamily transposases, thereby linking the movement of transposable elements and V(D)J recombination.     

A conformational switch controls hepatitis delta virus ribozyme catalysis

Ribozymes enhance chemical reaction rates using many of the same catalytic strategies as protein enzymes. In the hepatitis delta virus (HDV) ribozyme, site-specific self-cleavage of the viral RNA phosphodiester backbone requires both divalent cations and a cytidine nucleotide. General acid-base catalysis, substrate destabilization and global and local conformational changes have all been proposed to contribute to the ribozyme catalytic mechanism. Here we report ten crystal structures of the HDV ribozyme in its pre-cleaved state, showing that cytidine is positioned to activate the 2'-OH nucleophile in the precursor structure. This observation supports its proposed role as a general base in the reaction mechanism. Comparison of crystal structures of the ribozyme in the pre- and post-cleavage states reveals a significant conformational change in the RNA after cleavage and that a catalytically critical divalent metal ion from the active site is ejected. The HDV ribozyme has remarkable chemical similarity to protein ribonucleases and to zymogens for which conformational dynamics are integral to biological activity. This finding implies that RNA structural rearrangements control the reactivity of ribozymes and ribonucleoprotein enzymes.     

Palaeontology: leg feathers in an Early Cretaceous bird

Here we describe a fossil of an enantiornithine bird from the Early Cretaceous period in China that has substantial plumage feathers attached to its upper leg (tibiotarsus). The discovery could be important in view of the relative length and aerodynamic features of these leg feathers compared with those of the small 'four-winged' gliding dinosaur Microraptor and of the earliest known bird, Archaeopteryx. They may be remnants of earlier long, aerodynamic leg feathers, in keeping with the hypothesis that birds went through a four-winged stage during the evolution of flight.     

An unusual isotope effect in a high-transition-temperature superconductor

In conventional superconductors, the electron pairing that allows superconductivity is caused by exchange of virtual phonons, which are quanta of lattice vibration. For high-transition-temperature (high-T(c)) superconductors, it is far from clear that phonons are involved in the pairing at all. For example, the negligible change in T(c) of optimally doped Bi2Sr2CaCu2O8+delta (Bi2212; ref. 1) upon oxygen isotope substitution (16O --> 18O leads to T(c) decreasing from 92 to 91 K) has often been taken to mean that phonons play an insignificant role in this material. Here we provide a detailed comparison of the electron dynamics of Bi2212 samples containing different oxygen isotopes, using angle-resolved photoemission spectroscopy. Our data show definite and strong isotope effects. Surprisingly, the effects mainly appear in broad high-energy humps, commonly referred to as 'incoherent peaks'. As a function of temperature and electron momentum, the magnitude of the isotope effect closely correlates with the superconducting gap--that is, the pair binding energy. We suggest that these results can be explained in a dynamic spin-Peierls picture, where the singlet pairing of electrons and the electron-lattice coupling mutually enhance each other.     

Application of neural network in the study of combustion rate of natural gas／diesel dual fuel engine

In order to predict and improve the performance of matural gas/diesel dual fuel engine(DFE),a combustion rate model based on forward meural network was built to study the combustion process of the DFE.The effect of the operating parameters on combustion rate was also studied by means of this model.The study showed that the predicted results were good agreement with the experimental data.It was proved that the de-veloped combustion rate model could be used to successfully predict and optimize the combustion process of dual fuel engine.     

Four-winged dinosaurs from China

Although the dinosaurian hypothesis of bird origins is widely accepted, debate remains about how the ancestor of birds first learned to fly. Here we provide new evidence suggesting that basal dromaeosaurid dinosaurs were four-winged animals and probably could glide, representing an intermediate stage towards the active, flapping-flight stage. The new discovery conforms to the predictions of early hypotheses that proavians passed through a tetrapteryx stage.