New insights into the karyotypic relationships of Chinese muntjac (Muntiacus reevesi), forest musk deer (Moschus berezovskii) and gayal (Bos frontalis)

To investigate the karyotypic relationships between Chinese muntjac (Muntiacus reevesi), forest musk deer (Moschus berezovskii) and gayal (Bos frontalis), a complete set of Chinese muntjac chromosome-specific painting probes has been assigned to G-banded chromosomes of these three species. Sixteen autosomal probes (i.e. 6-10, 12-22) of the Chinese muntjac each delineated one pair of conserved segments in the forest musk deer and gayal, respectively. The remaining six autosomal probes (1-5, and 11) each delineated two to five pairs of conserved segments. In total, the 22 autosomal painting probes of Chinese muntjac delineated 33 and 34 conserved chromosomal segments in the genomes of forest musk deer and gayal, respectively. The combined analysis of comparative chromosome painting and G-band comparison reveals that most interspecific homologous segments show a high degree of conservation in G-banding patterns. Eleven chromosome fissions and five chromosome fusions differentiate the karyotypes of Chinese muntjac and forest musk deer; twelve chromosome fissions and six fusions are required to convert the Chinese muntjac karyotype to that of gayal; one chromosome fission and one fusion separate the forest musk deer and gayal. The musk deer has retained a highly conserved karyotype that closely resembles the proposed ancestral pecoran karyotype but shares none of the rearrangements characteristic for the Cervidae and Bovidae. Our results substantiate that chromosomes 1-5 and 11 of Chinese muntjac originated through exclusive centromere-to-telomere fusions of ancestral acrocentric chromosomes. Copyright (C) 2005 S. Karger AG, Basel.

KARYOTYPE EVOLUTION OF SHREW MOLES (SORICOMORPHA: TALPIDAE)

The Chinese long-tailed mole (Scaptonyx fusicaudus) closely resembles American (Neurotrichus gibbsii) and Japanese (Dymecodon pilirostris and Urotrichus talpoides) shrew moles in size, appearance, and ecological habits, yet it has traditionally been classified either together with (viz subfamily Urotrichinae) or separately (tribe Scaptonychini) from the latter genera (tribe Urotrichini sensu lato). We explored the merit of these competing hypotheses by comparing the differentially stained karyotypes of S.fusicaudus and N. gibbsii with those previously reported for both Japanese taxa. With few exceptions, diploid chromosome number (2n = 34), fundamental autosomal number (FNa = 64), relative size, and G-banding pattern of S. fusicaudus were indistinguishable from those of D. pilirostris and U. talpoides. In fact, only chromosome 15 differed significantly between these species, being acrocentric in D. pilirostris, subtelocentric in U. talpoides, and metacentric in S. fusicaudus. This striking similarity is difficult to envisage except in light of a shared common ancestry, and is indicative of an exceptionally low rate of chromosomal evolution among these genera. Conversely, the karyotype of N. gibbsii deviates markedly in diploid chromosome and fundamental autosomal number (2n = 38 and FNa = 72, respectively), morphology, and G-banding pattern from those of Scaptonyx and the Japanese shrew moles. These differences cannot be explained by simple chromosomal rearrangements, and Suggest that rapid chromosomal reorganization Occurred ill the karyotype evolution of this species, possibly due to founder or bottleneck events.

Complete genome sequence of lymphocystis disease virus isolated from China

Lymphocystis diseases in fish throughout the world have been extensively described. Here we report the complete genome sequence of lymphocystis disease virus isolated in China (LCDV-C), an LCDV isolated from cultured flounder (Paralichthys olivaceus) with lymphocystis disease in China. The LCDV-C genome is 186,250 bp, with a base composition of 27.25% G+C. Computer-assisted analysis revealed 240 potential open reading frames (ORFs) and 176 nonoverlapping putative viral genes, which encode polypeptides ranging from 40 to 1,193 amino acids. The percent coding density is 67%, and the average length of each ORF is 702 bp. A search of the GenBank database using the 176 individual putative genes revealed 103 homologues to the corresponding ORFs of LCDV-1 and 73 potential genes that were not found in LCDV-1 and other iridoviruses. Among the 73 genes, there are 8 genes that contain conserved domains of cellular genes and 65 novel genes that do not show any significant homology with the sequences in public databases. Although a certain extent of similarity between putative gene products of LCDV-C and corresponding proteins of LCDV-1 was revealed, no colinearity was detected when their ORF arrangements and coding strategies were compared to each other, suggesting that a high degree of genetic rearrangements between them has occurred. And a large number of tandem and overlapping repeated sequences were observed in the LCDV-C genome. The deduced amino acid sequence of the major capsid protein (MCP) presents the highest identity to those of LCDV-1 and other iridoviruses among the LCDV-C gene products. Furthermore, a phylogenetic tree was constructed based on the multiple alignments of nine MCP amino acid sequences. Interestingly, LCDV-C and LCDV-1 were clustered together, but their amino acid identity is much less than that in other clusters. The unexpected levels of divergence between their genomes in size, gene organization, and gene product identity suggest that LCDV-C and LCDV-1 shouldn't belong to a same species and that LCDV-C should be considered a species different from LCDV-1.

Comparative cytogenetics of bats (Chiroptera): The prevalence of Robertsonian translocations limits the power of chromosomal characters in resolving interfamily phylogenetic relationships

Although the monophyly of Chiroptera is well supported by many independent studies, higher-level systematics, e.g. the monophyly of microbats, remains disputed by morphological and molecular studies. Chromosomal rearrangements, as one type of rare genomic changes, have become increasingly popular in phylogenetic studies as alternatives to molecular and other morphological characters. Here, the representatives of families Megadermatidae and Emballonuridae are studied by comparative chromosome painting for the first time. The results have been integrated into published comparative maps, providing an opportunity to assess genome-wide chromosomal homologies between the representatives of eight bat families. Our results further substantiate the wide occurrence of Robertsonian translocations in bats, with the possible involvement of whole-arm reciprocal translocations (WARTs). In order to search for valid cytogenetic signature(s) for each family and superfamily, evolutionary chromosomal rearrangements identified by chromosomal painting and/or banding comparison are subjected to two independent analyses: (1) a cladistic analysis using parsimony and (2) the mapping of these chromosomal changes onto the molecularly defined phylogenetic tree available fromthe literature. Both analyses clearly indicate the prevalence of homoplasic events that reduce the reliability of chromosomal characters for resolving interfamily relationships in bats.

Strain rate-dependent shear band behavior in bulk metallic glasses

In this article, we review our recent advances in understanding the deformation behavior of a typical tough Zr41.2Ti13.8Cu12.5Ni10Be22.5 (Vit 1) bulk metallic glass (BMG), as a model material, under various loading modes and strain rates, focusing particularly on the rate-dependence and formation mechanism of shear-banding. Dynamic and quasi-static mechanical experiments, including plate shear, shear punch and spherical indentation, and continuum as well as atomistic modeling on shear-banding are discussed. The results demonstrate that higher strain rate slows down the annihilation process of free volume, but promotes the free-volume coalescence, which is responsible for the rate-dependent shear banding. The physical origin of shear bands, that is the free volume softening underpinned by irreversible rearrangements of atoms, is unveiled. Finally, some concluding remarks are given.

First synthesis of single and mixed alpha-oxo ketene dithioacetals from active methenyl precursors

beta-Dioxodithioate were produced easily from active methenyl precursors, carbondisulfide and RX with potassium carbonate as base. By a selective basic assistant cleavage of a carbon-carbon bond at the beta-dicarbonyl unit of beta-dioxodithioate and the subsequent alkylation with RX/R'X in situ, single or mixed alpha-oxo ketene dithioacetals were, obtained in good yields.

External field induced crystallization of poly(3-dodecylthiophene)

In order to investigate the effect of external field on the crystallization behavior of poly(3-dodecylthiopliene) (P3DDT), the samples were recrystallized with different electrostatic field intensity, different pressure and different solidification direction in temperature gradient field. Measurements of differential scanning calorimetry and X-ray diffraction were operated to characterize these samples for analysis. The results suggest that after recrystallization, whether the external field is added or not, a more compact packing of molecular chains in P3DDT could be obtained without the change of the crystal structure model. Moreover, the addition of electrostatic field has greater effects on the crystallization of rigid main chains than on that of flexible side chains, Merely great pressure field can effect the rearrangements of molecular chains greatly. As for the temperature gradient field induced crystallization, different oriented solidification direction will lead to different effects on the compact degree and perfect degree of molecular chains packing,

Studies of the ortho effect in fragmentations of acetyl ion adducts of disubstituted benzenes

The ion-molecule reactions of disubstituted benzenes under chemical ionization conditions with acetyl chloride as reagent gas were examined, and the fragmentation reactions of the adduct ions (mostly proton and acetyl ion adducts) were studied by collision-induced dissociation. Electron-releasing substituents favored the adduct reactions, and electron-withdrawing groups did not. The position and properties of substituting groups had an effect on the relative abundances of the adduct ions. Several examples of the ortho effect were observed. The fragmentation reaction of the adduct ions formed by ortho-benzenediamine with the acetyl ion was similar to the reductive alkylation reaction of amines in the condensed phase. Copyright (C) 2001 John Wiley & Sons, Ltd.

Mass spectrometry study combined with theoretical calculation on the unimolecular fragmentation of tetrahydroimidazole-substituted methylene beta-diketones

Studies of low-energy collision-induced dissociation and isotopic labeling on ionized tetrahydroimidazole-substituted methylene P-diketones by tandem mass spectrometry showed that their unimolecular fragmentations may involve the reactions of intermediate ion/neutral complexes and multistep rearrangements. The corresponding mechanisms were proved by semiemipirical calculations of PM3 and AM1 methods.

Ion/neutral complex-mediated reactions generated from some ionized tetrahydroimidazole-substituted methylene beta-diketones

The dissociation of gaseous metastable ions of m/z 153 and the formation of ions of m/z 139 from the unimolecular fragmentations of ionized tetrahydroimidazole-substituted methylene beta-diketones were examined by tandem mass spectrometry. In addition, some other fragments accompanying the elimination of either an H2O molecule or an CHO. radical were also observed in the collision-induced dissociation spectra of molecular ions of the compounds bearing an aromatic ring. Collision-induced dissociation and isotopic labeling showed that these processes may involve reactions of intermediate ion/neutral complexes and multistep rearrangements. The corresponding mechanisms are discussed. (C) 1997 by John Wiley & Sons, Ltd.

The complete mitochondrial genomes of two common shrimps (Litopenaeus vannamei and Fenneropenaeus chinensis) and their phylogenomic considerations

Complete mitochondrial genomes have proven extremely valuable in helping to understand the evolutionary relationships among metazoans. However, uneven taxon sampling may lead to unclear or even erroneous phylogenetic topologies. The decapod crustaceans are relatively well-sampled, but sampling is still uneven within this group. We have sequenced the mitochondrial genomes of two shrimps Litopenaeus vannamei and Fenneropenaeus chinensis. As seen in other metazoans, the genomes contain a standard set of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and an AT-rich non-coding region. The gene arrangements are consistent with the pancrustacean ground pattern. Both the pattern of gene rearrangements and phylogenomic analyses using concatenated nucleic acid and amino acid sequences of the 13 mitochondrial protein-coding genes strengthened the support that Caridea and Palinura are primitive members of Pleocyemata. These sequences, in combination with two previously published penaeid mitochondrial genomes, suggest that genera within the family Penaeidae have the following relationship: (((Penaeits + Fenneropenaett.) + Litopeiiaelts) + Marsupenaeus). The analyses of nucleic acid and amino acid sequences of the mitochondrial genomes also strongly support the monophyly of Penaeidae, Brachyura and Pleocyemata. In addition, the analyses of the average Ka/Ks in the 13 mitochondrial protein-coding genes of penaeid shrimps indicated a strong purifying selection within this group.

Tandem duplication-random loss is not a real feature of oyster mitochondrial genomes

Duplications and rearrangements of coding genes are major themes in the evolution of mitochondrial genomes, bearing important consequences in the function of mitochondria and the fitness of organisms. Yu et al. (BMC Genomics 2008, 9: 477) reported the complete mt genome sequence of the oyster Crassostrea hongkongensis (16,475 bp) and found that a DNA segment containing four tRNA genes (trnK(1), trnC, trnQ(1) and trnN), a duplicated (rrnS) and a split rRNA gene (rrnL5') was absent compared with that of two other Crassostrea species. It was suggested that the absence was a novel case of "tandem duplication-random loss" with evolutionary significance. We independently sequenced the complete mt genome of three C. hongkongensis individuals, all of which were 18,622 bp and contained the segment that was missing in Yu et al.'s sequence. Further, we designed primers, verified sequences and demonstrated that the sequence loss in Yu et al.'s study was an artifact caused by placing primers in a duplicated region. The duplication and split of ribosomal RNA genes are unique for Crassostrea oysters and not lost in C. hongkongensis. Our study highlights the need for caution when amplifying and sequencing through duplicated regions of the genome.

Minor sesquiterpenes with new carbon skeletons from the brown alga Dictyopteris divaricata

Five minor sesquiterpenes (1-5) with two novel carbon skeletons, together with a minor new oplopane sesquiterpene ( 6), have been isolated from the brown alga Dictyopteris divaricata. By means of spectroscopic data including IR, HRMS, 1D and 2D NMR, and CD, their structures including absolute configurations were assigned as (+)-(1R, 5S, 6S, 9R)3- acetyl-1-hydroxy-6-isopropyl-9-methylbicyclo[4.3.0] non-3-ene ( 1), (+)-(1R, 3S, 4S, 5R, 6S, 9R)-3-acetyl-1,4-dihydroxy-6- isopropyl-9-methylbicyclo[4.3.0] nonane (2), (+)-(1R, 3R, 4R, 5R, 6S, 9R)-3-acetyl-1,4-dihydroxy-6-isopropyl-9-methylbicyclo[ ;4.3.0] nonane ( 3), (+)-(1S, 2R, 6S, 9R)-1-hydroxy-2-(1-hydroxyethyl)-6-isopropyl-9-methylbicyclo[4.3.0] non-4-en-3-one (4), (-)-( 5S, 6R, 9S)-2-acetyl-5-hydroxy-6-isopropyl-9-methylbicyclo[4.3.0] non-1-en-3-one ( 5), and (-)-( 1S, 6S, 9R)- 4-acetyl- 1-hydroxy-6-isopropyl-9-methylbicyclo[ 4.3.0] non-4-en-3-one ( 6). Biogenetically, the carbon skeletons of 1-6 may be derived from the co-occurring cadinane skeleton by different ring contraction rearrangements. Compounds 1-6 were inactive (IC50 > 10 mu g/mL) against several human cancer cell lines.

Chromosomal rearrangement in Pectinidae revealed by rRNA loci and implications for bivalve evolution

Karyotype and chromosomal localization of major (18-5.8-28S) and minor (5S) ribosomal RNA genes were studied in two species of Pectinidae, zhikong (Chlamys farreri) and bay (Argopecten irradians irradians) scallops. using fluorescence in situ hybridization (FISH). C. farreri had a haploid number of 19 with a karyotype of 3m + 4sm + 7sm-st + 4st + 1st-t, and A. i. irradians had a haploid number of 16 with a karyotype of 5st + 11t. In C. farreri, the major and minor rRNA genes had one locus each and were mapped to the same chromosome-Chromosome 5. In A. i. irradians, the major rRNA genes had two loci, located on Chromosomes 4 and 8, and the 5S rRNA gene was found at a third chromosome-Chromosome 10. Results of this and other studies indicate that karyotype of A. i. irradians (n = 16, 21 arms) is secondary and derived from an ancestral karyotype similar to that of C. farreri (n = 19, 38 arms) through considerable chromosomal loss and rearrangements. The ability to tolerate significant chromosomal loss suggests that the modal karyotype of Pectinidae and possibly other bivalves with a haploid number of 19 is likely tetraploid; i.e., at least one genome duplication has occurred during the evolution of Bivalvia.