Construction and characterization of bacterial artificial chromosome library of black-handed spider monkey (Ateles geoffroyi)

The large-insert genomic DNA library is a critical resource for genome-wide genetic dissection of target species. We constructed a high-redundancy bacterial artificial chromosome (BAC) library of a New World monkey species, the black-handed spider monkey

Construction and characterization of a Lipotes vexillifer genomic DNA BAC library

We constructed a genomic DNA library for Lipotes vexillifer (L. vexillifer), the Baiji or Yangtze River dolphin, one of the most endangered mammals in the world. The library consists of 149,000 BAC clones, with an average insert size of 83 kb, representing approximately 3.4 haploid genome equivalents. PCR amplification of four known L. vexillifer genes yielded two to four positive clones each. To demonstrate the utility of this library, we isolated and sequenced the L. vexillifer alpha lactalbumin gene, which is a gene specific to mammals and one which has been widely used as molecular tool in phylogenetic analysis. We also end-sequenced 20 randomly selected clones, resulting in the identification of at least five new L. vexilliter genes, five SSR loci, and one SINE locus. These results suggest that this library is a valuable resource for candidate gene cloning, physical mapping, and genome sequencing of this important and threatened species.

Biotransfer of persistent organic pollutants from a large site in China used for the disassembly of electronic and electrical waste

Samples of groundwater, river water, river sediment, paddy soil, rice seeds, hen eggs, fish, umbilical cord blood, and newborn meconium were collected from October 2002 to October 2003 near a large site in China used for the disassembly of obsolete transformers and other electronic or electrical waste. Six indicator PCB congeners, three non-ortho dioxin-like PCB congeners, and six organochlorine pesticides were determined in the samples by GC with electron capture detector. The results demonstrated that the local environment and edible foods had been seriously polluted by toxic PCBs and organochlorine pesticides. The actual daily intakes (ADIs) of these pollutants were estimated for local residents living in the area. The intake data showed that the contents of PCBs in these local residents were substantial, as the ADI estimates greatly exceed the reference doses set by the World Health Organization and the United States Agency for Toxic Substances and Disease Registry. The presence of the indicator PCB congeners in the cord blood and the meconium samples, as well as significant correlations (r(2) > 0.80, p < 0.05) between these levels, suggests a potential biotransfer of these indicators from mothers to their newborns. This preliminary study showed that obsolete transformers and other electronic or electrical waste can be an important source for the emission of persistent organic pollutants into the local environment, such as through leakage, evaporation, runoff, and leaching. Contamination from this source appears to have reached the level considered to be a serious threat to environmental and human health around the disassembly site.

Construction and characterization of a novel recombinant single-chain variable fragment antibody against White Spot Syndrome Virus from shrimp

An antibody phage display library against White Spot Syndrome Virus (WSSV) was constructed. After four rounds of panning against WSSV, 192 out of 480 clones displayed WSSV binding activity. One of the positive clones, designated A1, had relatively higher activity specifically binding to WSSV A1-soluble, single-chain fragment variable (scFv) antibody has an affinity constant (K-aff) of 2.02 +/- 0.42 x 10(9) M-1. Dot blot assays showed that A1-soluble scFv could detect WSSV directly from shrimp hemolymph after 24-h feeding infection by WSSV. A1 scFv has potential for the development of a cheap, simple and sensitive diagnostic kit for WSSV in the field. (C) 2003 Elsevier Science B.V. All rights reserved.

Construction and analysis of a high-CO2-requiring mutant of the cyanobacterium Anabaena sp strain PCC7120

A mutant of Anabaena sp. strain PCC7120 requiring high CO2 was generated using Tn5 mutagenesis. This is the first data for a filamentous cyanobacterium. The mutant was capable of growing at 5% CO2, but incapable of growing at air levels of CO2. Southern hybridization analysis indicated that the Anabaena genome was inserted by the transposon at one site. The apparent photosynthetic affinity of the mutant to external dissolved inorganic carbon (DIC) was about 300 times lower that of the wild type (WT), and the medium alkalization rate as well as the carboxysomal carbonic anhydrase activity of the mutant was also lower than those of the WT. When the mutant was transferred from the culture medium bubbled with 5% CO2 to higher DIC (8.4% CO2) or 1% CO2, it showed similar responses to the WT. However, aberrant carboxysomes were found in the mutant cells through ultrastructural analysis, indicating it was most probably the wrong organization of the carboxysomes that eventually led to the inefficient operation of carboxysomal carbonic anhydrase and the subsequent defectiveness of the mutant in utilizing DIC.

CONSTRUCTION AND APPLICATIONS OF A DUAL MASS-SELECTED LOW-ENERGY ION-BEAM SYSTEM

A direct ion beam deposition system designed for heteroepitaxy at a low substrate temperature and for the growth of metastable compounds has been constructed and tested. The system consists of two mass-resolved low-energy ion beams which merge at the target with an incident energy range 50-25 000 eV. Each ion beam uses a Freeman ion source for ion production and a magnetic sector for mass filtering. While a magnetic quadrupole lens is used in one beam for ion optics, an electrostatic quadrupole lens focuses the other beam. Both focusing approaches provide a current density more than 100-mu-A/cm2, although the magnetic quadrupole gives a better performance for ion energies below 200 eV. The typical current of each beam reaches more than 0.3 mA at 100 eV, with a ribbon beam of about 0.3-0.5 x 2 cm2. The target is housed in an ultrahigh vacuum chamber with a base pressure of 1 x 10(-7) Pa and a typical pressure of 5 x 10(-6) Pa when a noncondensable beam like argon is brought into the chamber. During deposition, the target can be heated to 800-degrees-C and scanned mechanically with an electronic scanning control unit. The dual beam system has been used to grow GaN using a Ga+ and a N+ beam, and to study the oxygen and hydrogen ion beam bombardment effects during carbon ion beam deposition. The results showed that the simultaneous arrival of two beams at the target is particularly useful in compound formation and in elucidation of growth mechanisms.

Advanced superconducting electron cyclotron resonance ion source SECRAL: Design, construction, and the first test result

Superconducting electron cyclotron resonance (ECR) ion source with advanced design in Lanzhou (SECRAL) is a next generation ECR ion source and aims for developing a very compact superconducting ECR ion source with a structure and high performances for highly charged ion-beam production. The ion source was designed to be operated at 18 GHz at initial operation and finally will be extended to 28 GHz. The superconducting magnet confinement configuration of the ion source consists of three axial solenoid coils and six sextupole coils with a cold iron structure as field booster and clamping. At full excitation, this magnet assembly can produce peak mirror fields on the axis of 3.6 T at injection, 2.2 T at extraction, and a radial sextupole field of 2.0 T at plasma chamber wall. What is different from the traditional design, such as LBNL VENUS and LNS SERSE, is that the three axial solenoid coils are located inside of the sextupole bore in order to reduce the interaction forces between the sextupole coils and the solenoid coils. SECRAL may open the way for building a compact and high-performance 18-28 GHz superconducting ECR ion source. Very preliminary commissioning results are promising. Detailed design, construction issues and very preliminary test results of the ion source at 18 GHz are presented.

Construction and test of Wien-filter combined with RIBLL

A recoil separator Wien-filter which was developed for the Radioactive Ion Beam Line in Lanzhou (RIBLL) as an extension is described. It consists of 2 quadruple triplets and a standard Wien-filter. It was designed for study of the fusion-evaporation reactions. The overall design, background suppression, the transmission efficiency, the angular acceptance and the momentum acceptance have been described. All the performances fulfil the designed requirements. Based on the test results, with some modifications the investigations of the nuclei with Z <= 110 and the drip-line nuclei in the medium-heavy mass region can be carried out with this facility.

Construction and Photoluminescence of Monophase Hybrid Materials Derived from a Urea-Based Bis-Silylated Bipyridine

A urea-based bis-silylated bipyridine ligand derived from 4,4'-diamino-2,2'-bipyridine has been prepared. Organic-inorganic hybrid materials with a high loading of lanthanide 2,2-bipyridine moieties were obtained by using the silylated bipyridine as the only siloxane network precursor in the presence of lanthanide ions (or lanthanide complexes). The in-situ formation of lanthanide complexes from lanthanide ions and the silylated bipyridine during the sol-gel processing was confirmed by the luminescence behavior of the obtained hybrid materials and that of the corresponding pure lanthanide complex [Ln(bpy)(2)Cl-3 center dot 2H(2)O].

Construction and control of plasmid DNA network

The influences of different cations on plasmid DNA network structures on a mica substrate were investigated by atomic force microscopy (AFM). Interactions between the DNA strands and mica substrate, and between the DNA strands themselves were more strongly influenced by the complex cations (Fe(phen)(3)(2+), Ni(phen)(3)(2+), and Co(phen)(3)(3+)) than by the simple cations (Mg2+, Mn2+, Ni2+, Ca2+, Co3+). The mesh height of the plasmid DNA network was higher when the complex cations were added to DNA samples. The mesh size decreased with increasing DNA concentration and increased with decreasing DNA concentration in the same cation solution sample. Hence, plasmid DNA network height can be controlled by selecting different cations, and the mesh size can be controlled by adjusting plasmid DNA concentration.

Construction and characterization of a fosmid library for pathogenic bacterium Vibrio anguillarum

Vibrio anguillarum is a common bacterial pathogen in fish. However, little is known about its pathogenic mechanism, in part, because the entire genome has not been completely sequenced. We constructed a fosmid library for V. anguillarum containing 960 clones with an average insert size of 37.7 kb and 8.6-fold genome coverage. We characterized the library by end-sequencing 50 randomly selected clones. This generated 93 sequences with a total length of 57 485 by covering 1.4% of the whole genome. Of these sequences, 58 (62.4%) were homologous to known genes, 30 (32.3%) were genes with hypothetical functions, and the remaining 5 (5.3%) were unknown genes. We demonstrated the utility of this library by PCR screening of 10 genes. This resulted in an average of 6.2 fosmid clones per screening. This fosmid library offers a new tool for gene screening and cloning of V. anguillarum, and for comparative genomic studies among Vibrio species.

Construction and evaluation of DNA vaccines encoding Edwardsiella tarda antigens

Edwardsiella tarda is an opportunistic pathogen that can infect humans, animal, and fish. Two E. tarda antigens, Eta6 and FliC, which are homologues to an ecotin precursor and the FliC flagellin, respectively, were identified by in vivo-induced antigen technology from a pathogenic E. tarda strain isolated from diseased fish. When used as a subunit vaccine, purified recombinant Eta6 was moderately protective against lethal challenge of E. tarda in a Japanese flounder model, whereas purified recombinant FliC showed no apparent immunciprotectivity. Similarly, DNA vaccines based on eta6 and fliC in the form of plasmids pEta6 and pFliC induced, respectively, moderate and marginal protection against E. tarda infection. To improve the vaccine efficacy of eta6, a chimeric DNA vaccine, pCE6, was constructed, which encodes Eta6 fused in-frame to FliC. pCE6 was found to induce significantly higher level of protection than pEta6. Likewise, another chimeric DNA vaccine, pCE18, which expresses FliC fused to a previously identified E. tarda antigen Et18, elicited significantly stronger protective immunity than the DNA vaccine based on et18 alone. Fish immunized with pEta6 and pCE6 produced specific serum antibodies and exhibited significantly enhanced expression of the genes encoding elements that are involved in both innate and adaptive immune responses. Furthermore, the induction magnitudes of most of these genes were significantly higher in pCE6-vaccinated fish than in pEta6-vaccinated fish. (C) 2009 Elsevier Ltd. All rights reserved.

Construction and characterization of a bacterial artificial chromosome library of marine macroalga Porphyra yezoensis (Rhodophyta)

A large-DNA-fragment library is necessary for research into the Porphyra genome. In this study, a bacterial artificial chromosome (BAC) library of Porphyra yezoensis was constructed and characterized. The library contains 54,144 BAC clones with an average insert size of about 65 kb and fewer than 0.7% of clones without large inserts. Therefore, its capacity is more than 6.6 P. yezoensis genome equivalents, and the probability of recovering any nuclear DNA sequence from the library is higher than 99%. The library shows good fidelity and stability. A putative trehalose-6-phosphate synthase (TPS) gene was successfully screened out from the library. The above results show that the library is useful for gene cloning and genomic research in P. yezoensis.