Multiple maternal origins of chickens: Out of the Asian jungles

Domestic chickens have long been important to human societies for food, religion, entertainment, and decorative uses, yet the origins and phylogeography of chickens through Eurasia remain uncertain. Here, we assessed their origins and phylogeographic hist

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.

Sequence variations of the S7 ribosomal protein gene in primitive cyprinid fishes: Implication on phylogenetic analysis

Cyprinidae is the largest fish family in the world and contains about 210 genera and 2010 species. Appropriate DNA markers must be selected for the phylogenetic analyses of Cyprinidae. In present study, the 1st intron of the S7 ribosomal protein (r-protein) gene is first used to examine the relationships among cyprinid fishes. The length of the 1st intron obtained by PCR amplification ranges from 655 to 859 by in the 16 cyprinid species investigated, and is 602 by in Myxocyprinus asiaticus. Out of the alignment of 925 nucleotide sites obtained, the parsimony informative sites are 499 and occupy 54% of the total sites. The results indicate that the 1st intron sequences of the S7 r-protein gene in cyprinids are rich in informative sites and vary remarkably in sequence divergence from 2.3% between close species to 66.6% between distant species. The bootstrap values of the interior nodes in the NJ (neighbor-joining) and MP (most-parsimony) trees based on the present S7 r-protein gene data are higher than those based on cytochrome b and the d-loop region respectively. Therefore, the 1st intron sequences of the S7 r-protein gene in cyprinids are sensitive enough for phylogenetic analyses, and the 1st intron is an appropriate genetic marker for the phylogenetic reconstruction of the taxa in different cyprinid subfamilies. However, attempts to discuss whether the present S7 r-protein gene data can be applied to the phylogeny of the taxa at the level of the family or the higher categories in Cypriniformes need further studies.

Improvement of the radiation hardness of SIMOX buried layers using nitrogen implantation

An investigation of hardening the buried oxides (BOX) in separation by implanted oxygen (SIMOX) silicon-on-insulator (SOI) wafers to total-dose irradiation has been made by implanting nitrogen into the BOX layers with a constant dose at different implantation energies. The total-dose radiation hardness of the BOX layers is characterized by the high frequency capacitance-voltage (C-V) technique. The experimental results show that the implantation of nitrogen into the BOX layers can increase the BOX hardness to total-dose irradiation. Particularly, the implantation energy of nitrogen ions plays an important role in improving the radiation hardness of the BOX layers. The optimized implantation energy being used for a nitrogen dose, the hardness of BOX can be considerably improved. In addition, the C-V results show that there are differences between the BOX capacitances due to the different nitrogen implantation energies.

Isolation and mapping of telomeric pentanucleotide (TAACC)(n) repeats of the pacific whiteleg shrimp, Penaeus vannamei, using fluorescence in situ hybridization

To develop genetic and physical maps for shrimp, accurate information on the actual number of chromosomes and a large number of genetic markers is needed. Previous reports have shown two different chromosome numbers for the Pacific whiteleg shrimp, Penaeus vannamei, the most important penaeid shrimp species cultured in the Western hemisphere. Preliminary results obtained by direct sequencing of clones from a Sau3A-digested genomic library of P. vannamei ovary identified a large number of (TAACC/GGTTA)-containing SSRs. The objectives of this study were to (1) examine the frequency of (TAACC)(n) repeats in 662 P. vannamei genomic clones that were directly sequenced, and perform homology searches of these clones, (2) confirm the number of chromosomes in testis of P. vannamei, and (3) localize the TAACC repeats in P. vannamei chromosome spreads using fluorescence in situ hybridization (FISH). Results for objective I showed that 395 out of the 662 clones sequenced contained single or multiple SSRs with three or more repeat motifs, 199 of which contained variable tandem repeats of the pentanucleotide (TAACC/GGTTA),, with 3 to 14 copies per sequence. The frequency of (TAACC)n repeats in P. vannamei is 4.68 kb for SSRs with five or more repeat motifs. Sequence comparisons using the BLASTN nonredundant and expressed sequence tag (EST) databases indicated that most of the TAACC-containing clones were similar to either the core pentanucleotide repeat in PVPENTREP locus (GenBank accession no. X82619) or portions of 28S rRNA. Transposable elements (transposase for Tn1000 and reverse transcriptase family members), hypothetical or unnamed protein products, and genes of known function such as 18S and 28S rRNAs, heat shock protein 70, and thrombospondin were identified in non-TAACC-containing clones. For objective 2, the meiotic chromosome number of P. vannamei was confirmed as N = 44. For objective 3, four FISH probes (P1 to P4) containing different numbers of TAACC repeats produced positive signals on telomeres of P. vannamei chromosomes. A few chromosomes had positive signals interstitially. Probe signal strength and chromosome coverage differed in the general order of P1 > P2 > P3 > P4, which correlated with the length of TAACC repeats within the probes: 83, 66, 35, and 30 bp, respectively, suggesting that the TAACC repeats, and not the flanking sequences, produced the TAACC signals at chromosome ends and TAACC is likely the telomere sequence for P. vannamei.

ISOTOPIC CHARACTERISTICS AND AGE DATING OF THE PUMICE IN OKINAWA TROUGH

The data on the isotope compositions of rubidium, strontium and oxygen in the pumice of Okinawa Trough are reported for the first time. The ages of the pumice were successfully dated with the method of U-series disequilibrium. Then, the material source, crystallization evolution of magma and activity cycles of volcanos are explored. Isotopic data show that pumice magma was originally from the mantle, but had undergone a full crystallization differentiation and had been contaminated to a fair extent by crust-derived materials before the magma was erupted out of the sea floor. According to the dating results available so far, the earliest volcanic eruption in Okinawa Trough occurred about 70,000 a ago and the latest eruption was about 10,000 a B.P. During this period, there were three volcanic eruption cycles which were respectively corresponding to the middle Late Pleistocene, the late Late Pleistocene and the Early Holocene.

Scour of the seabed under a pipeline in oscillating flow

The scour of the seabed under a pipeline is studied experimentally in this paper. Tests are carried out in a U-shaped oscillatory water tunnel with a box imbedded in the bottom of the test section. By use of the standard sand, clay and plastic grain as the seabed material, the influence of the bed material on the scour is studied. The relationship between the critical initial gap-to-diameter ratio above which no scour occurs and the parameters of the oscillating flow is obtained. The self-burial phenomenon. which occurs for the pipeline not fixed to two sidewalls of the test section, is not observed for the Bred pipeline. The effect of the pipe on sand wave formation is discussed. The maximum equilibrium scour depths For different initial gap-to-diameter ratios, different Kc numbers and different bed sands are also given in this paper.

Mode analysis of the UV-written channel waveguide - art. no. 60340J

The effective index method (EIM) was adopted to model the channel waveguide patterned by the UV in photosensitive silica film. The effective indexes of the different dimension symmetrical and asymmetrical channel waveguides were calculated, and the resource of the error of the method was pointed out. At last, the dimension rang to propagate single mode was presented.

Influence of crystal perfection on the reverse leakage current of the SiGe Si p-n heterojunction diodes

Double-crystal X-ray diffraction and I-V characterization have been carried out on the GSMBE grown SiGe/Si p-n heterojunction materials. Results show that the SiGe alloys crystalline quality and the misfit dislocations are critical influences on the reverse leakage current. The crystal perfection and/or the degree of metastability of the Sice alloys have been estimated in terms of the model proposed by Tsao with the experimental results. High-quality p-n heterojunction diodes can be obtained by optimizing the SiGe alloy structures, which limit the alloys in the metastable states. (C) 1999 Elsevier Science B.V. All rights reserved.

The neutron/proton ratio of squeezed-out nucleons and the high density behavior of the nuclear symmetry energy

Within a transport model it is shown that the neutron/proton ratio of squeezed-out nucleons perpendicular to the reaction plane, especially at high transverse momenta, in heavy-ion reactions induced by high energy neutron-rich nuclei can be a useful tool for studying the high density behavior of the nuclear symmetry energy.