Clemaps: Multiple Alignment Of Protein Structures Based On Conformational Letters

CLEMAPS is a tool for multiple alignment of protein structures. It distinguishes itself from other existing algorithms for multiple structure alignment by the use of conformational letters, which are discretized states of 3D segmental structural states. A letter corresponds to a cluster of combinations of three angles formed by C-alpha pseudobonds of four contiguous residues. A substitution matrix called CLESUM is available to measure the similarity between any two such letters. The input 3D structures are first converted to sequences of conformational letters. Each string of a fixed length is then taken as the center seed to search other sequences for neighbors of the seed, which are strings similar to the seed. A seed and its neighbors form a center-star, which corresponds to a fragment set of local structural similarity shared by many proteins. The detection of center-stars using CLESUM is extremely efficient. Local similarity is a necessary, but insufficient, condition for structural alignment. Once center-stars are found, the spatial consistency between any two stars are examined to find consistent star duads using atomic coordinates. Consistent duads are later joined to create a core for multiple alignment, which is further polished to produce the final alignment. The utility of CLEMAPS is tested on various protein structure ensembles.

Measuring spin diffusion of electrons in bulk n-GaAs using circularly dichromatic absorption difference spectroscopy of spin gratings

Circular dichromatic absorption difference spectroscopy is developed to measure the spin diffusion dynamics of electrons in bulk n-GaAs. This spectroscopy has higher detection sensitivity over homodyne detection of spin-grating-diffracted signal. A model to describe circular dichromatic absorption difference signal is derived and used to fit experimental signal to retrieve decaying rate of spin gratings. A spin diffusion constant of D-s=201 +/- 25 cm(2)/s for bulk n-GaAs has been measured at room temperature using this technique and is close to electron diffusion constant (D-c), which is much different from the case in GaAs quantum wells where D-s is markedly less than D-c.

Suspended particulate matter fluxes through the Straits of Dover, English Channel: observations and modelling

Suspended Particulate Matter (SPM) concentrations at various levels within the water column, together with salinity and temperature, were measured using water samples collected from six stations across the Straits of Dover. The sampling programme covered a 16-month period, undertaken during 23 cruises. On the basis of the spatial variability in the concentrations, the water bodies are divided by several boundaries, controlled by tidal and wind conditions. Within the water column, SPM concentrations were higher near the sea bed than in the surface waters. Throughout the cross-section, maximum concentrations occurred adjacent to the coastlines. Temporal variability in the SPM concentration exists on daily and seasonal scales within the coastal waters (4.2 to 74.5 mg L-1): resuspension processes, in response to semi-diurnal tidal cycles (with a period of around 12.4 h) and spring-neap cycles (with a period of 15 days) make significant contributions. Distinctive seasonal/annual concentration changes have also been observed. In the offshore waters, such variability is much less significant (0.9 to 6.0 mg L-1). In the summer the English Coastal Zone is associated with relatively high SPM concentrations: the Central Zone has a low and stable SPM concentration between these zones, there is a Transitional Zone, where there is a rapid response of SPM concentration to wind forcing. Finally, the French Coastal Zone is characterized by variable (sometimes high) SPM concentrations. Because of the zonation, SPM fluxes within the Dover Strait are controlled by different transport mechanisms. Within the Central Zone, the flux can be represented by the product of mean water discharges and SPM concentrations. However, within the coastal zones fluctuations in SPM concentrations on various time-scales must be considered. In order to calculate the maximum and minimum SPM fluxes, 10 cells were divided in the strait. A simple modelling calculation has been proposed for this complex area. The effect of spring-neap tidal cycles and seasonal changes can contribute significantly to the overall flux, which is of the order of 20 x 10(6) t.yr(-1) (through the Dover Strait, towards the North Sea). Such an estimate is higher than most obtained previously. (C) 2000 Ifremer/CNRS/IRD/Editions scientifiques et medicales Elsevier SAS.

Resuspension and advection processes affecting suspended particulate matter concentrations in the central English Channel

Suspended particulate matter (SPM) measurements obtained along a cross-section in the central English Channel (Wight-Cotentin transect) indicate that the area may be differentiated into: (1) an English coastal zone, associated with the highest concentrations; (2) a French coastal zone, with intermediate concentrations; and (3) the offshore waters of the Channel, characterised by a very low suspended-sediment load. The SPM particle-size distribution was modal close to the English coast (main mode 10-12 mu m); the remainder of the area was characterised by flat SPM distributions. Examination of the diatom communities in the SPM suggest:; that material resuspended in the intertidal zone and the estuarine environments was advected towards the offshore waters of the English Channel. Considerable variations in SPM concentrations occurred during a tidal cycle: maximum concentrations were sometimes up to 3 times higher than the minimum concentrations, Empirical orthogonal function (EOF) analysis of the SPM concentration time series indicates that, although the bottom waters were more turbid than the surficial waters, this was not likely to be the result of in situ sediment resuspension. Instead, the observed variations appear to be controlled mainly by advective mechanisms. The limited resuspension was probably caused by: (1) the limited availability of fine-grained material within the bottom sediments, and (2) 'bed-armouring' processes which protect the finer-grained fractions of the seabed material from erosion and entrainment within the overlying flow during the less energetic stages of the tide.

A new species of the genus Rhopalotettix Hancock (Orthoptera, Tetrigoidea, Metrodoridae) from Taiwan (in English)

This paper describes a new species of Metrodoridae, Rhopalotettix taipeieiisis sp. nov. , collected from (lie (arm of Taiwan University in Taipei, Taiwan, and provides a key to the 6 species of the genus Rhopnloteltix Hancock, 1910. Type specimens are deposited in the Department ol Entomology, Taiwan University, Taipei, Taiwan.