Molecular modeling on some human interleukins sharing gamma c of interleukin-2 receptor, and structure-function relationships

Five models for human interleukin-7 (HIL-7), HIL-9, HIL-13, HIL-15 and HIL-17 have been generated by SYBYL software package. The primary models were optimized using molecular dynamics and molecular mechanics methods. The final models were optimized using a steepest descent algorithm and a subsequent conjugate gradient method. The complexes with these interleukins and the common gamma chain of interleukin-2 receptor (IL-2R) were constructed and subjected to energy minimization. We found residues, such as Gln127 and Tyr103, of the common gamma chain of IL-2R are very important. Other residues, e.g. Lys70, Asn128 and Glu162, are also significant. Four hydrophobic grooves and two hydrophilic sites converge at the active site triad of the gamma chain. The binding sites of these interleukins interaction with the common gamma chain exist in the first helical and/or the fourth helical domains. Therefore, we conclude that these interleukins binds to the common gamma chain of IL-2R by the first and the fourth helix domain. Especially at the binding sites of some residues (lysine, arginine, asparagine, glutamic acid and aspartic acid), with a discontinuous region of the common gamma chain of IL-2R, termed the interleukins binding sites (103-210). The study of these sites can be important for the development of new drugs. (C) 2000 Elsevier Science B.V. All rights reserved.

Abundance and conservation status of the Yangtze finless porpoise in the Yangtze River, China

middle and lower reaches of the Yangtze River, China. It is the only freshwater population of porpoises in the world and is currently listed as Endangered by IUCN. In November and December 2006 we used two boats and line transect methods to survey the entire current range of the population, except for two lakes (Poyang and Dongting). Sighting results were similar for both boats, so we pooled all data and analyzed them using two line transect models and a strip transect model. All models produced similar estimates of abundance (1111, 1225 and 1000). We then added independent estimates of the number of porpoises from the two lakes for a total estimate of approximately 1800 porpoises. Our findings indicate that the population continues to decline and that its distribution is becoming more fragmented. Our current estimate in the main river is slightly less than half the estimate from surveys between 1984 and 1991 (which was probably an underestimate). We also found an apparent gap in the distribution of porpoises between Yueyang and Shishou (similar to 150 km), where sightings had previously been common. Continued threats to Yangtze finless porpoises include bycatch in unregulated and unselective fishing, habitat degradation through dredging, pollution and noise, vessel strikes and water development. Immediate protective measures are urgently needed to ensure the persistence of finless porpoises in the Yangtze River. The survey design and analytical methods developed in this study might be appropriate for surveys of cetaceans in other river systems. (c) 2008 Elsevier Ltd. All rights reserved.

Cloning and characterization of interferon stimulated genes Viperin and ISG15, and their promoters from snakehead Channa argus

By suppression subtractive hybridization, rapid amplification of cDNA ends and gene walking methods, interferon stimulated genes (ISGs), Viperin and ISG15, and their promoters have been cloned and characterized from snakehead Channa argus. The Viperin cDNA was found to be 1474 nt and contain an open reading frame (ORF) of 1059 nt that translates into a putative peptide of 352 amino acid (aa). The putative peptide of Viperin shows high identity to that in teleosts and mammals except for the N-terminal 70 aa. The ISG15 cDNA was found to be 758 nt and contain an ORF of 468 nt that translates into a putative peptide of 155 aa. The putative peptide of ISG15 is composed of two tandem repeats of ubiquitin-like (UBL) domains, and a canonical conjugation motif (LRGG) at C-terminal. Viperin and ISG15 promoter regions were characterized by the presence of interferon stimulating response elements (ISRE) and gamma-IFN activation sites (GAS). ISRE is a feature of IFN-induced gene promoter and partially overlaps interferon regulatory factor (IRF) 1 and IRF2 recognition sites. GAS is responsible for the gamma-IFN mediated transcription. One conserved site for NF-kappa B was found in the promoter region of Viperin. This is the first report of conservative binding motif for NF-kappa B in accordance with the consensus sequence (GGGRN-NYYCC) among teleost ISG promoters. Moreover, there were also TATA, CAAT and Sp1 transcription factor sites in Viperin and ISG15 promoters. In 5' untranslated region (UTR), snakehead ISG15 gene contains a single intron, which differs from Viperin gene. The transcripts of Vipeirn and ISG15 mRNA were mainly expressed in head kidney, posterior kidney, spleen and gill. The expression levels in liver were found to increase obviously in response to induction by IFN-inducer poly I : C.

Phylogeny of freshwater parasitic copepods in the Ergasilidae (Copepoda : Poecilostomatoida) based on 18S and 28S rDNA sequences

The phylogenetic relationships among the Ergasilidae genera are poorly understood. In this study, 14 species from four genera in the Ergasilidae including Sinergasilus, Ergasilus, Pseudergasilus, and Paraergasilus were collected in China, and their phylogenetic relationships were examined using neighbor-joining, maximum parsimony, maximum likelihood, and Bayesian inference methods based on partial sequences of 18S and 28S ribosomal deoxyribonucleic acid, respectively. All the analyses suggest that the Sinergasilus and Paraergasilus are both monophyletic, but the Ergasilus is polyphyletic rather than monophyletic. Considering the relationships among the four genera, the phylogenetic analyses and subsequent hypothesis tests all suggest that Pseudergasilus clustered with some Ergasilus species may have a closer relationship with Sinergasilus rather than with Paraergasilus. It is proposed that the Sinergasilus and the Pseudergasilus species might have evolved from Ergasilus species.

Biogeography and molecular phylogeny of the genus Schizothorax (Teleostei : Cyprinidae) in China inferred from cytochrome b sequences

Aim: To test a vicariant speciation hypothesis derived from geological evidence of large-scale changes in drainage patterns in the late Miocene that affected the drainages in the south-eastern Tibetan Plateau. Location: The Tibetan Plateau and adjacent areas. Methods: The cytochrome b DNA sequences of 30 species of the genus Schizothorax from nine different river systems were analysed. These DNA sequences were analysed using parsimony, maximum likelihood and Bayesian methods. The approximately unbiased and Shimodaira-Hasegawa tests were applied to evaluate the statistical significance of the shortest trees relative to alternative hypotheses. Dates of divergences between lineages were estimated using the nonparametric rate smoothing method, and confidence intervals of dates were obtained by parametric bootstrapping. Results: The phylogenetic relationships recovered from molecular data were inconsistent with traditional taxonomy, but apparently reflected geographical associations with rivers. Within the genus Schizothorax, we observed a divergence between the lineages from the Irrawaddy-Lhuit and Tsangpo-Parlung rivers, and tentatively dated this vicariant event back to the late Miocene (7.3-6.8 Ma). We also observed approximately simultaneous geographical splits within drainages of the south-eastern Tibetan Plateau, the Irrawaddy, the Yangtze and the Mekong-Salween rivers in the late Miocene (7.1-6.2 Ma). Main conclusions: Our molecular evidence tentatively highlights the importance of palaeoriver connections and the uplift of the Tibetan Plateau in understanding the evolution of the genus Schizothorax. Molecular estimates of divergence times allowed us to date these vicariant scenarios back to the late Miocene, which agrees with geological suggestions for the separation of these drainages caused by tectonic uplift in south-eastern Tibet. Our results indicated the substantial role of vicariant-based speciation in shaping the current distribution pattern of the genus Schizothorax.

Determination of 266 pesticide residues in apple juice by matrix solid-phase dispersion and gas chromatography-mass selective detection

A macro matrix solid-phase dispersion (MSPD) method was developed to extract 266 pesticides from apple juice samples prior to gas chromatography-mass selective detection (GC-MSD) determination. A 10 g samples was mixed with 20 g diatomaceous earth. The mixture was transferred into a glass column. Pesticide residues were leached with a 160 mL hexane-dichloromethane (1:1) at 5 mL/min. Two hundred and sixty-six pesticides were divided into three groups and detected by GC-MSD under selective ion monitoring. The proposed method takes advantage of both liquid-liquid extraction and conventional MSPD methods. Application was illustrated by the analysis of 236 apple juice samples produced in Shaanxi province China mainland this year. (C) 2004 Elsevier B.V. All rights reserved.

Cloning and sequencing of the growth hormone gene of large yellow croaker and its phylogenetic significance

Using conserved primers and the PCR reaction, the growth hormone (GH) gene and the 3'-UTR of the large yellow croaker (Pseudosciaena crocea) were amplified and sequenced. The gene structure was analyzed and compared to the GH genes of 5 other percoid fish downloaded from Genbank. Also the GH gene of the large yellow croaker and the genes from 14 Percoidei and 2 Labroidei species were aligned using Clustal X. A matrix of 564 bp was used to construct the phylogenetic tree using maximum parsimony and neighbor-joining methods. Phylogenetic trees by the two methods are identical in most of the clades with high bootstrap support. The results are also identical to those from morphological data. In general, this analysis does not support the monophyly of the families Centropomidae and Carangidae. But our GH gene tree indicates that the representative species of the families Sparidae and Sciaenidae are a monophyletic group.

Calculation of light delay for coupled microrings by FDTD technique and Pade approximation

The Pade approximation with Baker's algorithm is compared with the least-squares Prony method and the generalized pencil-of-functions (GPOF) method for calculating mode frequencies and mode Q factors for coupled optical microdisks by FDTD technique. Comparisons of intensity spectra and the corresponding mode frequencies and Q factors show that the Pade approximation can yield more stable results than the Prony and the GPOF methods, especially the intensity spectrum. The results of the Prony method and the GPOF method are greatly influenced by the selected number of resonant modes, which need to be optimized during the data processing, in addition to the length of the time response signal. Furthermore, the Pade approximation is applied to calculate light delay for embedded microring resonators from complex transmission spectra obtained by the Pade approximation from a FDTD output. The Prony and the GPOF methods cannot be applied to calculate the transmission spectra, because the transmission signal obtained by the FDTD simulation cannot be expressed as a sum of damped complex exponentials. (C) 2009 Optical Society of America

Structure and device characteristics of AlxGa1-xAs/GaAs solar cells

AlGa1-xAs/GaAs heterostructures have been grown by two different liquid phase epitaxy (LPE) modes, i.e. the supercooled and melt-etch methods, for the fabrication of highly efficient solar cells. Typical structural characteristics observed under a transmission electron microscope (TEM), an Auger energy spectrometer (AES) and corresponding device parameters were presented. The results indicated that the P+PNN+ configuration grown by the melt-etch method could be used to produce high performance, large area solar cells with effectively reducing the defects of the substrate and improving the minority carrier collection by forming a compositionally graded region in the window layer.

Development of functionalized terbium fluorescent nanoparticles for antibody labeling and time-resolved fluoroimmunoassay application

Silica-based functionalized terbium fluorescent nanoparticles were prepared, characterized and developed as a fluorescence probe for antibody labeling and time-resolved fluoroimmunoassay. The nanoparticles were prepared in a water-in-oil (W/O) microemulsion containing a strongly fluorescent Tb3+ chelate. N,N.N-1,N-1-12,6-bis(3'-aminomethyl-1'-pyrazolyl)phenylpyridine] tetrakis(acetate)-Tb3+ (BPTA-Tb3+), Triton X-100, octanol, and cyclohexane by controlling copolymerization of tetraethyl orthosilicate (TEOS) and 3-[2-(2- aminoethylamino)-ethylamino]propyl-trimethoxysilane (AEPS) with ammonia water. The characterizations by transmission electron microscopy and fluorometric quantum methods show that the nanoparticles are spherical and uniform in size, 45 +/- 3 nm in diameter, strongly fluorescent with fluorescence yield of 10% and a long fluorescence lifetime of 2.0 ms. The amino groups directly introduced to the nanoparticle's surface by using AEPS in the preparation made the surface modification and bioconjugation of the nanoparticles easier. The nanoparticle-labeled anti-human alpha-fetoprotein antibody was prepared and used for time-resolved fluoroimmunoassay of (x-fetoprotein (AFP) in human serum samples. The assay response is linear from 0.10 ng ml(-1) to about 100 ng ml(-1) with the detection limit of 0.10 ng ml(-1). The coefficient variations (CVs) of the method are less than 9.0%. and the recoveries are in the range of 84-98% for human serum sample measurements. (C) 2004 Elsevier B.V. All rights reserved.

Strategy for analysis and screening of bioactive compounds in traditional Chinese medicines

Traditional Chinese medicines (TCMs), due to their long time clinic test and reliable therapeutic efficacy, are attracting increased global attention served as excellent pools of bioactive compounds for the discovery of new drugs. However, hundreds or even thousands of components are usually contained in traditional Chinese medicines and only a few compounds are responsible for the pharmaceutical and/or toxic effects. The large numbers of other components in traditional Chinese medicines make the screening and analysis of the bioactive components extremely difficult. By the way, the combination effect of bioactive components on the pharmacological activity makes it very difficult to clear the therapeutic mechanism of TCMs. Therefore, some strategies have to design for screening of bioactive compounds in traditional Chinese medicines, which further leads to disclose the therapeutic mechanism of TCMs in molecular level. The review will summarize the present state of the art of screening strategy for active compounds in traditional Chinese medicines, and the chromatography methods for screening and analysis of bioactive compounds in traditional Chinese medicines will be emphasized. (C) 2004 Elsevier B.V. All rights reserved.

Determination of 1-phenyl-3-methyl-5-pyrazolone-labeled carbohydrates by liquid chromatography and micellar electrokinetic chromatography

In this paper, the method for the derivatization of carbohydrates with 1-phenyl-3-methyl-5-pyrazolone (PMP) was simplified. One-third of the derivatization time was saved. Five monosaccharide derivatives have been well separated by MEKC and HPLC under optimized conditions. Good reproducibility could be obtained with relative standard deviation (RSD) values of the migration times within 5.0 and 2.3%, respectively. Furthermore, the developed methods have been successfully applied to the analysis of carbohydrates in Aloe powder and food. These methods are quite useful for routine analysis of monosaccharides and oligosaccharides in real samples. (C) 2003 Elsevier B.V. All rights reserved.

Fast Haar Transform Based Feature Extraction for Face Representation and Recognition

Subspace learning is the process of finding a proper feature subspace and then projecting high-dimensional data onto the learned low-dimensional subspace. The projection operation requires many floating-point multiplications and additions, which makes the projection process computationally expensive. To tackle this problem, this paper proposes two simple-but-effective fast subspace learning and image projection methods, fast Haar transform (FHT) based principal component analysis and FHT based spectral regression discriminant analysis. The advantages of these two methods result from employing both the FHT for subspace learning and the integral vector for feature extraction. Experimental results on three face databases demonstrated their effectiveness and efficiency.

Metal nanomaterials and carbon nanotubes - synthesis, functionalization and potential applications towards electrochemistry

This review focuses on the synthesis, assembly, surface functionalization, as well as application of inorganic nanostructures. Electrochemical and wet- chemical methods are demonstrated to be effective approaches to make metal nanostructures under control without addition of a reducing agent or protecting agent. Owing to the unique physical and chemical properties of the nano-sized materials, novel applications are introduced using inorganic nanomaterials, such as electrocatalysis, photoelectricity, spectrochemistry, and analytical chemistry.

Structural stability and magnetic coupling in CaCu3Co4O12 from first principles

The structural, electronic and magnetic properties of CaCu3Co4O12 were studied by use of the full-potential linearized augmented plane wave method. The calculated results indicate that CaCu3Co4O12 is stable both thermodynamically and mechanically. Both GGA (generalized gradient approximation) and GGA + U methods predict that CaCu3Co4O12 is metallic. The ferromagnetic configuration is only slightly more stable in energy compared with the non-magnetic configuration (3.7 meV), suggesting that they are competitive for being the ground state. Co is in the low spin state (S = 1/2).