Secondary structures of mRNAs and splicing of introns in eukaryotes.

After analyzing the secondary structures of 68 exon-intron-exon and the corresponding exon-exon sequence segments, it is found that about 90% of 5' and 3' terminal bases G (splicing sites) of introns are situated in the loops of secondary structures or at the ends of stems near the loops, and most of "G" s in loops are closed to the ends of loops. Approximately 92% of the connecting sites of the adjoining exons also show the similar features. About 82% of the branch point "A" s are situated in loops or at the ends of stems near the loops. Splicing sites and branch points approach each other in space because of the folding.

Word boundary modelling and full covariance gaussians for Arabic Speech-to-Text systems

This paper describes recent improvements to the Cambridge Arabic Large Vocabulary Continuous Speech Recognition (LVCSR) Speech-to-Text (STT) system. It is shown that wordboundary context markers provide a powerful method to enhance graphemic systems by implicit phonetic information, improving the modelling capability of graphemic systems. In addition, a robust technique for full covariance Gaussian modelling in the Minimum Phone Error (MPE) training framework is introduced. This reduces the full covariance training to a diagonal covariance training problem, thereby solving related robustness problems. The full system results show that the combined use of these and other techniques within a multi-branch combination framework reduces the Word Error Rate (WER) of the complete system by up to 5.9% relative. Copyright © 2011 ISCA.

Progress towards the design and numerical analysis of a 3D microchannel biochip separator

This paper reports the design and numerical analysis of a three-dimensional biochip plasma blood separator using computational fluid dynamics techniques. Based on the initial configuration of a two-dimensional (2D) separator, five three-dimensional (3D) microchannel biochip designs are categorically developed through axial and plenary symmetrical expansions. These include the geometric variations of three types of the branch side channels (circular, rectangular, disc) and two types of the main channel (solid and concentric). Ignoring the initial transient behaviour and assuming that steady-state flow has been established, the behaviour of the blood fluid in the devices is algebraically analysed and numerically modelled. The roles of the relevant microchannel mechanisms, i.e. bifurcation, constriction and bending channel, on promoting the separation process are analysed based on modelling results. The differences among the different 3D implementations are compared and discussed. The advantages of 3D over 2D separator in increasing separation volume and effectively depleting cell-free layer fluid from the whole cross section circumference are addressed and illustrated. © 2011 John Wiley & Sons, Ltd.

Biofluid behaviour in 3D microchannel systems: Numerical analysis and design development of 3D microchannel biochip separators

This paper describes the design and development cycle of a 3D biochip separator and the modelling analysis of flow behaviour in the biochip microchannel features. The focus is on identifying the difference between 2D and 3D implementations as well as developing basic forms of 3D microfluidic separators. Five variants, based around the device are proposed and analysed. These include three variations of the branch channels (circular, rectangular, disc) and two variations of the main channel (solid and concentric). Ignoring the initial transient behaviour and assuming steady state flow has been established, the efficiencies of the flow between the main and side channels for the different designs are analysed and compared with regard to relevant biomicrofluidic laws or effects (bifurcation law, Fahraeus effect, cell-free phenomenon, bending channel effect and laminar flow behaviour). The modelling results identify flow features in microchannels, a constriction and bifurcations and show detailed differences in flow fields between the various designs. The manufacturing process using injection moulding for the initial base case design is also presented and discussed. The work reported here is supported as part of the UK funded 3D-MINTEGRATION project. © 2010 IEEE.

Establishment of a Chinese sturgeon Acipenser sinensis tail-fin cell line and its susceptibility to frog iridovirus

Chinese sturgeon Acipenser sinensis, a cartilaginous ganoid, is a 'living fossil' on a deeply isolated evolutionary branch. A cell line was established from Chinese sturgeon tail-fin tissue (CSTF) . These epithelial CSTF cells grew well in Dulbecco's modified Eagle's medium at 25 degrees C. Karyotypic analysis revealed a normal diploid karyotype with 2n = 264 and large numbers of punctate chromosomes. A strain of frog iridoviruses [Rana grylio virus (RGV)] was used to test the susceptibility of this cell line to infection. Infection was confirmed by cytopathic effect, immunofluorescence and electron-microscope observations, which detected the viral antigens or particles in the cytoplasm of RGV-infected cells. Molecular analysis further suggested that c. 550 bp DNA fragment could be cloned from the RGV-infected CSTF cells' DNA with major capsid protein gene polymerase chain reaction primers. Furthermore, after transfection with pEGFP vector DNA, the CSTF cell line produced significant fluorescent signals indicating its utility in exogenous studies.

Inhibition of no tail (ntl) gene expression in zebrafish by external guide sequence (EGS) technique

External guide sequence (EGS) technique, a branch of ribozyme strategy, can be enticed to cleave the target mRNA by forming a tRNA-like structure. In the present study, no tail gene (ntl), a key gene participating in the formation of normal tail, was used as a target for ribonuclease (RNase) P-mediated gene disruption in zebrafish in vivo. Transient expression of pH1-m3/4 ntl-EGS or pH1-3/4 ntl-EGS produced the full no tail phenotype at long-pec stage in proportion as 24 or 35%, respectively. As is expected that the full-length ntl mRNA of embryos at 50% epiboly stage decreased relative to control when injected the embryos with 3/4 EGS or m3/4 EGS RNA. Interestingly, ntl RNA transcripts, including the cleaved by EGS and the untouched, increased. Taken together, these results indicate that EGS strategy can work in zebrafish in vivo and becomes a potential tool for degradation of targeted mRNAs.

Characterization of two genes encoding leucine-rich repeat-containing proteins in grass carp Ctenopharyngodon idellus

The cDNAs and genes of two different types of leucine- rich repeat-containing proteins from grass carp ( Ctenopharyngodon idellus) were cloned. Homology search revealed that the two genes, designated as GC-GARP and GC-LRG, have 37% and 32% deduced aminoacid sequence similarities with human glycoprotein A repetitions predominant precursor ( GARP) and leucine-rich alpha2-glycoprotein (LRG), respectively. The cDNAs of GC-GARP and GC-LRG encoded 664 and 339 amino acid residues, respectively. GC-GARP and GC-LRG contain many distinct structural and/or functional motifs of the leucine- rich repeat (LRR) subfamily, such as multiple conserved 11-residue segments with the consensus sequence LxxLxLxxN/CxL ( x can be any amino acid). The genes GC-GARP and GC-LRG consist of two exons, with 4,782 bp and 2,119 bp in total length, respectively. The first exon of each gene contains a small 5'-untranslated region and partial open reading frame. The putative promoter region of GC-GARP was found to contain transcription factor binding sites for GATA-1, IRF4, Oct-1, IRF-7, IRF-1, AP1, GATA-box and NFAT, and the promoter region of GC-LRG for MYC-MAX, MEIS1, ISRE, IK3, HOXA9 and C/EBP alpha. Phylogenetic analysis showed that GC-GARP and mammalian GARPs were clustered into one branch, while GC-LRG and mammalian LRGs were in another branch. The GC-GARP gene was only detected in head kidney, and GC-LRG in the liver, spleen and heart in the copepod ( Sinergasilus major)- infected grass carp, indicating the induction of gene expression by the parasite infection. The results obtained in the present study provide insight into the structure of fish LRR genes, and further study should be carried out to understand the importance of LRR proteins in host - pathogen interactions.

Manopt, a matlab toolbox for optimization on manifolds

Optimization on manifolds is a rapidly developing branch of nonlinear optimization. Its focus is on problems where the smooth geometry of the search space can be leveraged to design effcient numerical algorithms. In particular, optimization on manifolds is well-suited to deal with rank and orthogonality constraints. Such structured constraints appear pervasively in machine learning applications, including low-rank matrix completion, sensor network localization, camera network registration, independent component analysis, metric learning, dimensionality reduction and so on. The Manopt toolbox, available at www.manopt.org, is a user-friendly, documented piece of software dedicated to simplify experimenting with state of the art Riemannian optimization algorithms. By dealing internally with most of the differential geometry, the package aims particularly at lowering the entrance barrier. © 2014 Nicolas Boumal.

Characterization of cDNA encoding immunoglobulin light chain of the Mandarin fish (Siniperca chuatsi)

Immunoglobulin light chain cDNA sequences of a perciform fish, the mandarin fish Siniperca chuatsi were amplified from head kidney mRNA by reverse transcription (RT)-PCR and RACE methods using degenerated primer and gene specific ones. In cDNA sequences of the VL region, nucleotide exchanges were present mainly within CDRs, although a lesser degree of variability was also found in FRs. Moreover, the length of CDRI and CDR3 in the mandarin fish is shorter than in most other fish species. In the middle of S. chuatsi CL region, a microsatellite sequence (AGC)(6-8) was found, which is also present in another perciform species, the spotted wolffish (Anarhichas minor). The comparison of amino acid sequence of the mandarin fish CL domain with those of other vertebrates showed the highest degree of similarity of 94.5% to the spotted wolffish, while the similarity with rainbow trout (Oncorhynchus mykiss) Ig L1 (62.7%) and channel catfish (Ictalurus punctatus) Ig LG (55.9%) isotypes is also higher. However, there is only 50% identity in the VL regions between the mandarin fish and the wolffish. The sequence similarity of the mandarin fish CL domain with those of higher vertebrate did not readily allow it to be classified as kappa or lambda isotype. The phylogenetic analyses also demonstrated that the CL genes of the mandarin fish and most other teleost fish cluster as a separate branch out of the mammal kappa and lambda branches. (C) 2003 Elsevier B.V. All rights reserved.

Studies on polysaccharides from three edible species of Nostoc (Cyanobacteria) with different colony morphologies: Comparison of monosaccharide compositions and viscosities of polysaccharides from field colonies and suspension cultures

Hot water-soluble polysaccharides woe extracted from field colonies and suspension cultures of Nostoc commune Vaucher, Nostoc flagelliforme Berkeley et Curtis, and Nostoc sphaeroides Kutzing. Excreted extracellular polymeric substances (EPS) were isolated from the media in which the suspension cultures were grown. The main monosaccharides of the field colony polysaccharides from the three species were glucose, xylose, and galactose, with an approximate ratio of 2:1:1. Mannose was also present, but the levels varied among the species, and arabinose appeared only in N. flagelliforme. The compositions of the cellular polysaccharides and EPS from suspension cultures were more complicated than those of the field samples and varied among the different species. The polysaccharides from the cultures of N. flagelliforme had a relatively simple composition consisting of mannose, galactose, glucose, and glucuronic acid, but no xylose, as was found in the field colony polysaccharides. The polysaccharides from cultures of N. sphaeroides contained glucose (the major component), rhamnose, fucose, xylose, mannose, and galactose. These same sugars were present in the polysaccharides from cultures of N. commune, with xylose as the major component. Combined nitrogen in the media had no qualitative influence on the compositions of the cellular polysaccharides but affected those of the EPS of N. commune and N. flagelliforme. The EPS of N. sphaeroides had a very low fetal carbohydrate content and thus was not considered to be polysaccharide in nature. The field colony polysaccharides could be separated by anion exchange chromatography into neutral and acidic fractions having similar sugar compositions. Preliminary linkage analysis showed that 1) xylose, glucose, and galactose were 1-->4 linked, 2) mannose, galactose, and xylose occurred as terminal residues, and 3) branch points occurred in glucose as 1-->3,4 and 1-->3,6 linkages and in xylose as a 1-->3,4 linkage. The polymer preparations from field colonies had higher kinematic viscosities than those from corresponding suspension cultures. The high viscosities of the polymers suggested that they might DE suitable for industrial uses.

Optical microwave generation based on DFB lasers

A new device of two parallel distributed feedback ( DFB) laser integrated monolithically with Y-branch waveguide coupler was fabricated by means of quantum well intermixing. Optical microwave signal was generated in the Y-branch waveguide coupler through frequency beating of the two laser modes coming from two DFB lasers in parallel, which had a small difference in frequency. Continuous rapidly tunable optical microwave signals from 13 GHz to 42 GHz were realized by adjusting independently the driving currents injected into the two DFB lasers.

Frequency mixing and phase detection functionalities of three-terminal ballistic junctions

Three-terminal ballistic junctions (TBJs) are fabricated from a high-mobility InP/In0.75Ga0.25As heterostructure by electron-beam lithography. The voltage output from the central branch is measured as a function of the voltages applied to the left and right branches of the TBJs. The measurements show that the TBJs possess an intrinsic nonlinearity. Based on this nonlinearity, a novel room-temperature functional frequency mixer and phase detector are realized. The TBJ frequency mixer and phase detector are expected to have advantages over traditional circuits in terms of simple structure, small size and high speed, and can be used as a new type of building block in nanoelectronics.

In-plane propagation of cavity polaritons in a quantum semiconductor microcavity

Considering that the coupling among the heavy-hole exciton, light-hole exciton and the cavity photon can form bipolaritons in a quantum semiconductor microcavity, we calculate the group velocities of the cavity polaritons at different incident angles using the coupling model of three harmonic oscillators. The result indicates that the group velocities of the low and middle branches of the cavity polaritons have extrema, but the group velocities of the high branch increase with the increasing incident angle.

Experimental investigation of photoluminescence dynamics of cavity polaritons under nonresonant excitation

Low-temperature time-resolved photoluminescence (PL) experiments have been performed on a semiconductor planar microcavity, which contains two sets of three In0.13Ga0.87As/GaAs quantum wells embedded in a 3 lambda /2 GaAs cavity. The spontaneous emission dynamics of both lower- and upper-branch polaritons is investigated as a function of exciton-cavity detuning under nonresonant optical excitation. It is found that the PL decay times of both branches are independent of cavity detuning while the PL rising kinetics of the lower- and upper-branch polaritons exhibits a significant difference. The rise time of the upper polarition branch shows a strong dependence on cavity detuning, while the rise time of the lower polarition branch is less sensitive to cavity detuning. Our results can be well understood in the framework of the theoretical prediction of Tassone et al.

Anomaly of the current self-oscillation frequency in the sequential tunneling of a doped GaAs/AlAs superlattice

An anomalous behavior of the current self-oscillation frequency is observed in the dynamic de voltage bands, emerging from each sawtoothlike branch of the current-voltage characteristic of a doped GaAs/A1As superlattice in the transition process from static to dynamic electric field domain formations. Varying the applied de voltage at a fixed temperature, we find that the frequency increases while the averaged current decreases. Inside each voltage band, the frequency has a strong voltage dependence in the temperature range where the averaged current changes with the applied de voltage. This dependence can be understood in terms of motion of the system along a limit cycle.