EST-based identification of genes expressed in the hypothalamus of male orange-spotted grouper (Epinephelus coioides)

The orange-spotted grouper, Epinephelus coioides, is an important marine aquaculture fish, but its large-scale aquaculture has been hindered by the rarity of natural males because it is a protogynous hermaphroditic fish. Hypothalamus-pituitary-gonad is an important endocrine axis in regulating reproduction and sex differentiation. To reveal the molecular mechanism of hypothalamic physiological functions, we performed he studies on identification of genes expressed in the hypothalamus of male orange-spotted grouper using EST and RT-PCR strategy. A total of 1006 ESTs were sequenced, and 402 (39.96%) clones were identified as known genes and 604 (60.04%) as unknown genes. The 402 clones of known gene products represent transcripts of 18 1 genes. Moreover, the expression patterns of 26 unknown genes were analyzed in various tissues, such as liver, kidney, spleen, fat, heart, muscle, pituitary, hypothalamus, telencephalon, cerebellum, midbrain, medulla oblongata, ovary and testes. Five different categories of expression patterns were observed from them. Several unknown ESTs, such as DN551996, DN551998, DN552082, and DN552070, were detected to be hypothalamus-specific, brains-specific, or hypothalamus and gonad-specific genes. Interestingly, DN551996, not only exhibiting expression differences between ovary and testis, but also showing sex-dependent differences in hypothalamus of grouper, might play significant role in grouper reproduction or sex inversion. Further functional studies on these genes will provide more information on molecule regulation mechanism of sex inversion in groupers. (c) 2006 Elsevier B.V All fights reserved.

semantic oriented ontology cohesion metrics for ontology-based systems

Ontologies play a core role to provide shared knowledge models to semantic-driven applications targeted by Semantic Web. Ontology metrics become an important area because they can help ontology engineers to assess ontology and better control project management and development of ontology based systems, and therefore reduce the risk of project failures. In this paper, we propose a set of ontology cohesion metrics which focuses on measuring (possibly inconsistent) ontologies in the context of dynamic and changing Web. They are: Number of Ontology Partitions (NOP), Number of Minimally Inconsistent Subsets (NMIS) and Average Value of Axiom Inconsistencies (AVAI). These ontology metrics are used to measure ontological semantics rather than ontological structure. They are theoretically validated for ensuring their theoretical soundness, and further empirically validated by a standard test set of debugging ontologies. The related algorithms to compute these ontology metrics also are discussed. These metrics proposed in this paper can be used as a very useful complementarity of existing ontology cohesion metrics.

A new structure of In-based ohmic contacts to n-type GaAs

Electrical, structural and reaction characteristics of In-based ohmic contacts to n-GaAs were studied. Attempts were made to form a low-band-gap interfacial phase of InGaAs to reduce the barrier height at the metal/semiconductor junction, thus yielding low-resistance, highly reliable contacts. The contacts were fabricated by e-beam sputtering Ni, NiIn and Ge targets on VPE-grown n(+)-GaAs film (approximate to 1 mu m, 2 x 10(18) cm(-3)) in ultrahigh vacuum as the structure of Ni(200 Angstrom)/NiIn(100 Angstrom)/Ge(40 Angstrom)/n(+)-GaAs/SI-GaAs, followed by rapid thermal annealing at various temperatures (500-900 degrees C). In this structure, a very thin layer of Ge was employed to play the role of heavily doping donors and diffusion limiters between In and the GaAs substrate. Indium was deposited by sputtering NiIn alloy instead of pure In in order to ensure In atoms to be distributed uniformly in the substrate; nickel was chosen to consume the excess indium and form a high-temperature alloy of Ni3In. The lowest specific contact resistivity (rho(c)) of (1.5 +/- 0.5)x 10(-6) cm(2) measured by the Transmission Line Method (TLM) was obtained after annealing at 700 degrees C for 10 s. Auger sputtering depth profile and Transmission Electron Microscopy (TEM) were used to analyze the interfacial microstructure. By correlating the interfacial microstructure to the electronical properties, InxGa1-xAs phases with a large fractional area grown epitaxially on GaAs were found to be essential for reduction of the contact resistance.

Wide-band underwater acoustic absorption based on locally resonant unit and interpenetrating network structure

The interpenetrating network structure provides an interesting avenue to novel materials. Locally resonant phononic crystal (LRPC) exhibits excellent sound attenuation performance based on the periodical arrangement of sound wave scatters. Combining the LRPC concept and interpenetrating network glassy structure, this paper has developed a new material which can achieve a wide band underwater strong acoustic absorption. Underwater absorption coefficients of different samples were measured by the pulse tube. Measurement results show that the new material possesses excellent underwater acoustic effects in a wide frequency range. Moreover, in order to investigate impacts of locally resonant units, some defects are introduced into the sample. The experimental result and the theoretical calculation both show that locally resonant units being connected to a network structure play an important role in achieving a wide band strong acoustic absorption.

Range-based attacks on links in random scale-free networks

Range and load play key roles in the problem of attacks on links in random scale-free (RSF) networks. In this paper we obtain the approximate relation between range and load in RSF networks by the generating function theory, and then give an estimation about the impact of attacks on the efficiency of the network. The results show that short-range attacks are more destructive for RSF networks, and are confirmed numerically.

Large current gain and low operational voltage permeable metal-base organic transistors based on Au/Al double layer metal base

In order to realize the common-emitter characteristics of the tris(8-hydroxyquinoline) aluminium (Alq(3))-based organic transistors, we used Au/Al double metal layer as the base, thus the vertical metal-base transistors with structure of Al/n-Si/Au/Al/Alq(3)/LiF/Al were constructed. It was found that the contact properties between the base and the organic semiconductors play an important role in the device performance. The utilization of Au/Al double layer metal base allows the devices to operate at high gain in the common-emitter and common-base mode at low operational voltage.

Robust core-shell supramolecular assemblies based on cationic vesicles and ring-shaped {Mo-154} polyoxomolybdate nanoclusters: Template-directed synthesis and characterizations

Substantial progress has been made recently in extending the supramolecular assembly of biomimetic structures to vesicle-based sophisticated nanocomposites and mesostructures. We report herein the successful preparation of unilamellar surfactant vesicles coated with a monolayer of ring-shaped {Mo-154} polyoxometalate (POM) nanoclusters, (NH4)(28)[Mo-154 (NO)(14)O(448)Hi(4)(H2O)(70)].approximate to 350H(2)O, by coulomb attractions using preformed didodecyldimethylammonium bromide (DDAB) surfactant vesicles as templates. The resultant vesicle-templated supramolecular assemblies are robust (they do not disintegrate upon dehydration) both at room-temperature ambient and vacuum conditions, as characterized by conventional transmission electron microscopy (TEM) and atomic force microscopy (AFM). The flexibility of the complex soft assemblies was also revealed by AFM measurements. The effect of POM-vesicle coulomb attractions on the dimensions of the templating vesicles was also investigated by using dynamic light scattering (DLS).Although origins of the structure stability of the as-prepared supramolecular assemblies are not clear yet, the nanometer scale cavities and the related properties of macroions of the POM clusters may play an important role in it.

One-step polyelectrolyte-based route to well-dispersed gold nanoparticles: Synthesis and insight

Polyelectrolytes have been widely used as building blocks for the creation of thickness-controllable multilayer thin films in a layer-by-layer fashion, and also been used as flocculants or stabilizer of colloids. This paper reports novel finding that a kind of polyelectrolyte, polyamines, can facilely induce HAuCl4 to spontaneously form well-stabilized gold nanoparticles without the additional step of introducing a reducing reagent during the elevation of temperature, even at room temperature in some cases. The polymer chain-confined microenvironment and the acid-induced evolution of amide of such kind of polyelectrolyte solution play an important role in the nucleation and growth of gold nanoparticles. This method would not only be helpful to gain an insight into the formation of gold nanoparticles in polyelectrolyte systems, but also provide a novel and facile one-step polyelectrolyte-based synthetic route to polyelectrolyte protected gold nanoparticles in aqueous media for potential applications. More importantly, this strategy will be general to the preparation of other nanoparticles.

Synthesis and characterization of novel bipolar PPV-based copolymer containing triazole and carbazole units

Two new blue light-emitting PPV-based conjugated copolymers containing both an electron-withdrawing unit (triazole-TAZ) and electron-rich moieties (carbazole-CAR and bicarbazole-BCAR) were prepared by Wittig condensation polymerization between the triazole diphosphonium salt and the corresponding dialdehyde monomers. Their structures and properties were characterized by FT-IR, TGA, DSC, UV-Vis, PL spectroscopy and electrochemical measurements. The resulting copolymers are soluble in common organic solvents and thermally stable with a T-g of 147degreesC for TAZ-CAR-PPV and of 157degreesC for TAZ-BCAR-PPV. The maximum photoluminescence wavelengths of TAZ-CAR-PPV and TAZ-BCAR-PPV film appear at 460 nm and 480 nm, respectively. Cyclic voltammetry measurement demonstrates that TAZ-BCAR-PPV has good electrochemical reversibility, while TAZ-CAR-PPV exhibits the irreversible redox process. The triazole unit was found to be an effective pi-conjugation interrupter and can play the rigid spacer role in determining the emission colour of the resulting copolymer.

Sequence analysis of Arthrospira maxima based on fosmid library

Arthrospira (Spirulina) (Setchell& Gardner) is an important cyanobacterium not only in its nutritional potential but in its special biological characteristics. An unbiased fosmid library of Arthrospira maxima FACHB438 that contains 4300 clones was constructed. The size distribution of insert fragments is from 15.5 to 48.9 kb and the average size is 37.6 kb. The recombination frequency is 100%. Therefore the library is 29.9 equivalents to the Arthrospira genome size of 5.4 Mb. A total of 719 sample clones were randomly chosen from the library and 602 available sequences, which consisted of 307,547 bases, covering 5.70% of the whole genome. The codon usage of A. maxima was not strongly biased. GC content at the first position of codons (46.9%) was higher than the second (39.8%) and the third (45.5%) positions. GC content of the genome was 43.6%. Of these sequences, 287 (47.7%) showed high similarities to known genes, 63 (10.5%) to hypothetical genes and the remaining 252 (41.8%) had no significant similarities. The assigned genes were classified into 22 categories with respect to different biological roles. Remarkably, the high presence of 25 sequences (4.2%) encoding reverse transcriptase indicates the RT gene may have multiple copies in the A. maxima genome and might play an important role in the evolutionary history and metabolic regulation. In addition, the sequences encoding the ATP-binding cassette transport system and the two-component signal transduction system were the second and third most frequent genes, respectively. These genomic features provide some clues as to the mechanisms by which this organism adapts to the high concentration of bicarbonate and to the high pH environment.

PenBase, the shrimp antimicrobial peptide penaeidin database: Sequence-based classification and recommended nomenclature

Antimicrobial peptides play a major role in innate immunity. The penaeidins, initially characterized from the shrimp Litopenaeus vannamei, are a family of antimicrobial peptides that appear to be expressed in all penaeid shrimps. As of recent, a large number of penaeid nucleotide sequences have been identified from a variety of penaeid shrimp species and these sequences currently reside in several databases under unique identifiers with no nomenclatural continuity. To facilitate research in this field and avoid potential confusion due to a diverse number of nomenclatural designations, we have made a systematic effort to collect, analyse, and classify all the penaeidin sequences available in every database. We have identified a common penaeidin signature and subsequently established a classification based on amino acid sequences. In order to clarify the naming process, we have introduced a 'penaeidin nomenclature' that can be applied to all extant and future penaeidins. A specialized database, PenBase, which is freely available at http://www.penbase.immunaqua.com, has been developed for the penaeidin family of antimicrobial peptides, to provide comprehensive information about their properties, diversity and nomenclature. (c) 2005 Elsevier Ltd. All rights reserved.