Discovery of Highly Excited Long-Lived Isomers in Neutron-Rich Hafnium and Tantalum Isotopes through Direct Mass Measurements

A study of cooled Au-197 projectile-fragmentation products has been performed with a storage ring. This has enabled metastable nuclear excitations with energies up to 3 MeV, and half-lives extending to minutes or longer, to be identified in the neutron-rich nuclides Hf-183,Hf-184,Hf-186 and Ta-186,Ta-187. The results support the prediction of a strongly favored isomer region near neutron number 116.

Expressed sequence tags from the zhikong scallop (Chlamys farreri): Discovery and annotation of host-defense genes

A high-quality cDNA library was constructed from whole body tissues of the zhikong scallop, Chlamys farreri, challenged by Listonella anguillarum. A total of 5720 clones were sequenced, yielding 5123 expressed sequence tags (ESTs). Among the 3326 unique genes identified, 2289 (69%) genes had no significant (E-value < 1e-5) matches to known sequences in public databases and 194 (6%) matched proteins of unknown functions. The remaining 843 (25%) genes that exhibited homology with genes of known functions, showed broad involvement in metabolic processes (31%), cell structure and motility (20%), gene and protein expression (12%), cell signaling and cell communication (8%), cell division (4%), and notably, 25% of those genes were related to immune function. They included stress response genes, complement-like genes, proteinase and proteinase inhibitors, immune recognition receptors and immune effectors. The EST collection obtained in this study provides a useful resource for gene discovery and especially for the identification of host-defense genes and systems in scallops and other molluscs. (C) 2009 Elsevier Ltd. All rights reserved.

Discovery of immune related factors in Fenneropenaeus chinensis by annotation of ESTs

A total of 10446 expressed sequence tags (ESTs) are obtained by a large-scale sequencing of a cDNA library from cephalothorax of adult Fenneropenaeus chinensis. An EST analysis platform was built up based on local computers and bioinformatic techniques were used to annotate these ESTs in order to promptly find possible functional genes, especially for immune related factors. About 4% of the ESTs show similarity to the coding sequences of such factors, including lectin, serine protease, serpin, lysozyme, etc. These ESTs provide a partial profile of the immune system in F. chinensis and useful information for further study on these genes.

Three-stage transformation of chlorophyll transient fluorescence pattern under sustained dehydration and the discovery of critical water content in seaweeds

The chlorophyll fluorescence kinetics of marine red alga Grateloupia turutunt Yamada, green alga Ulva pertusa Kjellm and brown alga Laminaria japonica Aresch during natural sustained dehydration were monitored and investigated. The pulse amplified modulation (PAM) system was used to analyze the distinct fluorescence parameters during thallus dehydration. Results proved that the fluorescence kinetics of different seaweed all showed three patterns of transformation with sustained water loss. These were: 1) peak kinetic pattern (at the early stage of dehydration fluorescence enhanced and quenched subsequently, representing a normal physiological state). 2) plateau kinetic pattern (with sustained water loss fluorescence enhanced continuously but quenching became slower, finally reaching its maximum). 3) Platform kinetic pattern (fluorescence fell and the shape of kinetic curve was similar to plateau kinetic pattern). A critical water content (CWC) could be found and defined as the percentage of water content just prior to the fluorescence drop and to be a significant physiological index for evaluation of plant drought tolerance. Once thallus water content became lower than this value the normal peak pattern can not be recovered even through rehydration, indicating an irreversible damage to the thylakoid membrane. The CWC value corresponding to different marine species were varied and negatively correlated with their desiccation tolerance, for example. Laminaria japonica had the highest CWC value (around 90%) and the lowest dehydration tolerance of the three. In addition, a fluorescence "burst" was found only in red algae during rehydration. The different fluorescence parameters F-o, F-v and F-v, F-m were measured and compared during water loss. Both F-o and F-v increased in the first stage of dehydration but F-v/F-m. kept almost constant. So the immediate response of in vivo chlorophyll fluorescence to dehydration was an enhancement. Later with sustained dehydration F-o increased continuously while F-v decreased and tended to become smaller and smaller. The major changes in fluorescence (including fluorescence drop during dehydration and the burst during rehydration) were all attributed to the change in F-o instead of F-v This significance of F-o indicates that it is necessary to do more research on F-o as well as on its relationship with the state of thylakoid membrane.

Discovery of genes involved in defense/immunity functions in a haemocytes cDNA library from Fenneropenaeus chinensis by ESTs annotation

Crustacean haemocytes play important roles in the host immune response including recognition, phagocytosis, melanization, cytotoxicity and inter-cellular signal communication. Expressed sequence tags (ESTs) analysis is proved to be an efficient approach not only for gene discovery, but also for gene expression profiles performance. In order to further understand the innate immune system and defense mechanisms of Chinese shrimp at molecular level, complementary DNA library is constructed from the haemocyte tissue of Fenneropenaeus chinensis. A total of 2371 cDNA clones are successfully sequenced and the average sequence length is 460 bp. About 50% are identified as orthologs of known genes from other organisms by BLASTx and BLASTn program. By sequences comparability and analysis, 34 important genes including 177 ESTs are identified that may be involved in defense or immune functions in shrimp based on the known knowledge. These genes are categorized into five categories according to their putative functions in shrimp immune system: 13 genes are different types of antimicrobial peptides (AMP, penaeidin, antilipopolysaccharide factor, etc.), and their proportion is about 3 8%; 11 genes belong to prophenoloxidase system (prophenoloxidase, serine proteinase, serine proteinase inhibitor, etc.), and their proportion is about 32%; five genes have high homology with clotting protein (lectin, transglutaminase, etc), and their proportion is about 15%; three genes may be involved in inter-cell signal communication (peroxinectin, integrin), and their proportion is about 9%; two genes have been identified to be chaperone proteins (Hsc70, thioredoxin peroxidase), and their proportion is about 6%. These EST sequences enrich our understanding of the immune genes of F chinensis and will help farther experimental research into immune factors and improve our knowledge of the immune mechanisms of shrimp. (c) 2007 Elsevier B.V. All rights reserved.

Discovery of the genes in response to white spot syndrome virus (WSSV) infection in Fenneropenaeus chinensis through cDNA microarray

We used microarray technology to study differentially expressed genes in white spot syndrome virus (WSSV)-infected shrimp. A total of 3136 cDNA targets, including 1578 unique genes from a cephalothorax cDNA library and 1536 cDNA clones from reverse and forward suppression subtractive hybridization (SSH) libraries of Fenneropenaeus chinensis, plus 14 negative and 8 blank control clones, were spotted onto a 18 x 18 mm area of NH2-modified glass slides. Gene expression patterns in the cephalothorax of shrimp at 6 h after WSSV injection and moribund shrimp naturally infected by WSSV were analyzed. A total of 105 elements on the arrays showed a similar regulation pattern in artificially infected shrimp and naturally infected moribund shrimp; parts of the results were confirmed by semiquantitative reverse transcriptase-polymerase chain reaction (RT-PCR). The up-regulated expression of immune-related genes, including heat shock proteins (HSP70 and HSP90), trehalose-phosphate synthase (TPS), ubiquitin C, and so forth, were observed when shrimp were challenged with WSSV. Genes including myosin LC2, ATP synthase A chain, and arginine kinase were found to be down-regulated after WSSV infection. The expression of housekeeping genes such as actin, elongation factor, and tubulin is not stable, and so these genes are not suitable as internal standards for semiquantitative RT-PCR when shrimp are challenged by WSSV. As a substitute, we found that triosephosphate isomerase (TPI) was an ideal candidate of interstandards in this situation.

Discovery of Late Cretaceous garnet two-pyroxene granulite in the southern Lhasa terrane, Tibet and its tectonic significances

The Lhasa terrane, located between the Bangonghu-Nujiang suture zone and the Indus-Yalung Tsangpo suture zone in the southern Tibetan Plateau, was considered previously as a Precambrian continental block. Mesozoic and Cenozoic tectonic evolution of the Lhasa terrane is closely related to the subduction of the Tethys ocean and the collision between the Indian and European continents; so it is one of the keys to reveal the formation and evolution of the Tibetan plateau. The garnet two-pyroxene granulite which was found at the Nyingtri rock group of the southeastern Lhasa terrene consists of garnet, clinopyroxene, orthopyroxene, labradorite, Ti-rich amphibolite and biotite, with a chemical composition of mafic rock. The metamorphic conditions were estimated to be at T = 747 similar to 834 degrees C and P = 0.90 similar to 1.35GPa, suggesting a formation depth of 45km. The zircon U-Pb dating for the garnet amphibolite and marble associated with the granulite give a metamorphic age of 85 similar to 90Ma. This granulite-facies metamorphic event together with a contemporaneous magmatism demonstrated that the southern Lhasa terrane has undergone an Andean-type orogeny at Late Mesozoic time.

Determination of five pharmacologically active compounds extracted from Rhodiola for natural product drug discovery with HPLC-APCI-MS

A rapid and sensitive liquid chromatography-atmospheric pressure chemical ionization mass spectrometry (HPLC-APCI-MS) assay for the determination of five pharmacologically active compounds (PAC) extracted from the traditional Chinese medicine, Rhodiola , namely salidroside, tyrosol, rhodionin, gallic acid, and ethyl gallate has been developed. In this method, PAC could be baseline separated and detected with DAD at 275 nm. The validation of the method, including sensitivity, linearity, repeatability, and recovery, was examined. The linear calibration curves were acquired with correlation coefficient >0.999 and the limits of detection LOD (at a signal-to-noise ratio=3:1) were between 0.058 and 1.500 mu mol/L. It was found, that the amounts of PAC varied with different species of Rhodiola . The established method is rapid and reproducible for the separation of five natural pharmacologically active compounds from extracts of Rhodiola with satisfactory results.

Analysis of five pharmacologically active compounds from Rhodiola for natural product drug discovery with capillary electrophoresis

A rapid capillary electrophoresis method for the separation of five natural pharmacologically active compounds from extracted Rhodiola, namely salidroside, tyrosol, rhodionin, gallic acid and ethyl gallate has been developed. The separation of five natural pharmacologically active compounds was carried out in a fused-silica capillary with 14 mM boric acid, 30 mM SDS and 2.5% acetonitrile, adjusted to pH 10.7 with NaOH. Applied potential was 21 kV. The temperature of the capillary was maintained at 25 degreesC by the instrument thermostating system, with the correlation coefficients of 0.9805-0.9989 for migration time, and relative standards of < 3.52% for peak areas. The established method is rapid and reproducible for the separation of five natural pharmacologically compounds from extracts of Rhodiola with satisfactory results.

Delegation, Arbitration and High-Level Service Discovery as Key Elements of a Software Infrastructure for Pervasive Computing

The dream of pervasive computing is slowly becoming a reality. A number of projects around the world are constantly contributing ideas and solutions that are bound to change the way we interact with our environments and with one another. An essential component of the future is a software infrastructure that is capable of supporting interactions on scales ranging from a single physical space to intercontinental collaborations. Such infrastructure must help applications adapt to very diverse environments and must protect people's privacy and respect their personal preferences. In this paper we indicate a number of limitations present in the software infrastructures proposed so far (including our previous work). We then describe the framework for building an infrastructure that satisfies the abovementioned criteria. This framework hinges on the concepts of delegation, arbitration and high-level service discovery. Components of our own implementation of such an infrastructure are presented.

TYPICAL: A Knowledge Representation System for Automated Discovery and Inference

TYPICAL is a package for describing and making automatic inferences about a broad class of SCHEME predicate functions. These functions, called types following popular usage, delineate classes of primitive SCHEME objects, composite data structures, and abstract descriptions. TYPICAL types are generated by an extensible combinator language from either existing types or primitive terminals. These generated types are located in a lattice of predicate subsumption which captures necessary entailment between types; if satisfaction of one type necessarily entail satisfaction of another, the first type is below the second in the lattice. The inferences make by TYPICAL computes the position of the new definition within the lattice and establishes it there. This information is then accessible to both later inferences and other programs (reasoning systems, code analyzers, etc) which may need the information for their own purposes. TYPICAL was developed as a representation language for the discovery program Cyrano; particular examples are given of TYPICAL's application in the Cyrano program.

On Genetic Programming and Knowledge Discovery in Transcriptome

Rowland, J. J. (2004) On Genetic Programming and Knowledge Discovery in Transcriptome Data. Proc. IEEE Congress on Evolutionary Computation, Portland, Oregon. pp 158-165. ISBN 0-7803-8515-2

Information Fusion and Hierarchical Knowledge Discovery by ARTMAP Neural Networks

Mapping novel terrain from sparse, complex data often requires the resolution of conflicting information from sensors working at different times, locations, and scales, and from experts with different goals and situations. Information fusion methods help resolve inconsistencies in order to distinguish correct from incorrect answers, as when evidence variously suggests that an object's class is car, truck, or airplane. The methods developed here consider a complementary problem, supposing that information from sensors and experts is reliable though inconsistent, as when evidence suggests that an objects class is car, vehicle, or man-made. Underlying relationships among objects are assumed to be unknown to the automated system of the human user. The ARTMAP information fusion system uses distributed code representations that exploit the neural network's capacity for one-to-many learning in order to produce self-organizing expert systems that discover hierarchial knowledge structures. The system infers multi-level relationships among groups of output classes, without any supervised labeling of these relationships. The procedure is illustrated with two image examples.

Self-Organizing Hierarchical Knowledge Discovery by an ARTMAP Image Fusion System

Classifying novel terrain or objects front sparse, complex data may require the resolution of conflicting information from sensors working at different times, locations, and scales, and from sources with different goals and situations. Information fusion methods can help resolve inconsistencies, as when evidence variously suggests that an object's class is car, truck, or airplane. The methods described here consider a complementary problem, supposing that information from sensors and experts is reliable though inconsistent, as when evidence suggests that an object's class is car, vehicle, and man-made. Underlying relationships among objects are assumed to be unknown to the automated system or the human user. The ARTMAP information fusion system used distributed code representations that exploit the neural network's capacity for one-to-many learning in order to produce self-organizing expert systems that discover hierarchical knowledge structures. The system infers multi-level relationships among groups of output classes, without any supervised labeling of these relationships.