Differential selection on gene translation efficiency between the filamentous fungus Ashbya gossypii and yeasts

Background: The filamentous fungus Ashbya gossypii grows into a multicellular mycelium that is distinct from the unicellular morphology of its closely related yeast species. It has been proposed that genes important for cell cycle regulation play central

The topological configuration and conformational analysis of mRNA in translation

The theoretical model construction of mRNA hairpin structure and single-stranded structure as well as the simulation studies on RNA structure determined by the X-ray crystal diffraction and nuclear magnetic resonance revealed that in translation, after mRNA being unfolded into single-stranded structure, its topological configuration was closely correlative with the original hairpin structure. The conformational features of single-stranded mRNA appeared as helical regions alternating with curly regions to different extents, which might exert the influence on the folding of nascent polypeptide by various regulating effects including different translational rates.

The relation between translation speed and protein secondary structure

Based on the statistical analysis of 119 human and 92 E. coli proteins it was found that for both human and E. coli, the mRNA sequences consisting of tri-codon and tetra-codon with high translation speed preferably code for alpha helices more than for coils. For beta strand, the preference/ avoidance oscillates with the translation speed. Moreover, the non-homogeneous usages of tri-codon and tetra-codon with different translation speeds in a given secondary structure have also been found. These results cannot be simply explained by the effect of stochastic fluctuation.

The identification and quantification of highly stable 'common hairpin' in the dynamic process of co-transcriptional mRNA folding

In our studies, 88 human mRNA samples were collected from the Integrated Sequence-Structure database and then the dynamic process in co-transcriptional mRNA folding was simulated using the RNAstructure version 4.1 program. Through statistical analyses of the frequencies of occurrence of hairpins, a group of special folding structures-the 'common hairpins'-were identified. These 'common hairpins' have lower energies and occur in all the subsequent folding units that formed in the dynamic folding process. By applying the formulas (1)-(4) of the 'common hairpins' statistical model, 163 'common hairpins' were found, to make up about 7% of the total of 2286 hairpins. Classified studies further show that the 'common hairpins' that were studied may oscillate in the dynamic folding process. However, the hairpin loops of the 'common hairpins' and stems proximal to those 'common hairpins' loops maintain topologically stable structures, while other loops and stems distal to the 'common hairpins' loops are shown to be alterable structures. Strikingly, further studies indicate that the stable structures of these 'common hairpins' may have unbeknown effects on controlling the formation of protein structures in the translation process (unpublished results). (c) 2005 Elsevier B.V. All rights reserved.

QtUCP-A program for determining unit-cell parameters in electron diffraction experiments using double-tilt and rotation-tilt holders

A computer program, QtUCP, has been developed based on several well-established algorithms using GCC 4.0 and Qt (R) 4.0 (Open Source Edition) under Debian GNU/Linux 4.0r0. it can determine the unit-cell parameters from an electron diffraction tilt series obtained from both double-tilt and rotation-tilt holders. In this approach, two or more primitive cells of the reciprocal lattice are determined from experimental data, in the meantime, the measurement errors of the tilt angles are checked and minimized. Subsequently, the derived primitive cells are converted into the reduced form and then transformed into the reduced direct primitive cell. Finally all the patterns are indexed and the least-squares refinement is employed to obtain the optimized results of the lattice parameters. Finally, two examples are given to show the application of the program, one is based on the experiment, the other is from the simulation. (C) 2008 Elsevier B.V. All rights reserved.

A Structured Prediction Approach for Statistical Machine Translation

We propose a new formally syntax-based method for statistical machine translation. Transductions between parsing trees are transformed into a problem of sequence tagging, which is then tackled by a search- based structured prediction method. This allows us to automatically acquire transla- tion knowledge from a parallel corpus without the need of complex linguistic parsing. This method can achieve compa- rable results with phrase-based method (like Pharaoh), however, only about ten percent number of translation table is used. Experiments show that the structured pre- diction approach for SMT is promising for its strong ability at combining words.

Simulation of micromegas detector by garfield program

In this paper, a batch file which describes the detailed structure and the corresponding physical process of Micro-Mesh Gaseous Structure (Micromegas) detector, the macro commands and the control structures based on the Garfield program has been developed. And using the Garfield program controlled by this batch file, the detector's gain and spatial resolution have been investigated under different conditions. These results obtained by the simulation program not only exhibit the influences of the mesh and drift voltage, the mixture gas proportion, the distance between the mesh cathode and the printed circuit board readout anode, and the Lines Per Inch of the mesh cathode on the gain and spatial resolution of the detector, but also are very important to optimize the design, shorten the experimental period, and save cost during the detector development. Additionally, they also indicate that the Garfield program is a powerful tool for the Micromegas detector design and optimization.

HIRFL-CSR PHYSICS PROGRAM

The research activities at HIRFL-CSR cover the fields of the radio-biology, material science, atomic physics, and nuclear physics. This talk will mainly concentrate on the program on nuclear physics with the existing and planned experimental setups at HIRFL-CSR.

Nuclear physics program at HIRFL

With the commissioning of HIRFL-CSR, HIRFL can provide heavy ion beams with energy covering the range of several MeV/u to 1 GeV/u. In this talk, the experiments on nuclear physics at different energies to be carried out with different experimental setups at HIRFL will be introduced.