DNA polymorphism of the plankton community and its relationships to species composition in the Three Gorges Reservoir Region of the Yangtze River

We examined DNA polymorphism of the plankton community in the Three Gorges Reservoir Region of Yangtze River and studied its relationships to species composition. Samples of the plankton community were collected from nine sampling sites and analyzed by random amplified polymorphic DNA (RAPD). Nine of 60 screened primers generated a total of 88 observable 180 to 1400 by bands, all of which were polymorphic. Cluster analysis of the resulting binary format from DNA banding patterns grouped the target communities into three clusters. The topology of the constructed diagram from species composition data was generally similar to that based on RAPD markers.

Comparison of evolutionary rates in the mitochondrial DNA cytochrome b gene and control region and their implications for phylogeny of the Cobitoidea (Teleostei : Cypriniformes)

It is widely accepted that mitochondrial DNA (mtDNA) control region evolves faster than protein encoding genes with few exceptions. In the present study, we sequenced the mitochondrial cytochrome b gene (cyt b) and control region (CR) and compared their rates in 93 specimens representing 67 species of loaches and some related taxa in the Cobitoidea (Order Cypriniformes). The results showed that sequence divergences of the CR were broadly higher than those of the cyt b (about 1.83 times). However, in considering only closely related species, CR sequence evolution was slower than that of cyt b gene (ratio of CR/cyt b is 0.78), a pattern that is found to be very common in Cypriniformes. Combined data of the cyt b and CR were used to estimate the phylogenetic relationship of the Cobitoidea by maximum parsimony, neighbor-joining, and Bayesian methods. With Cyprinus carpio and Danio rerio as outgroups, three analyses identified the same four lineages representing four subfamilies of loaches, with Botiinae on the basal-most clade. The phylogenctic relationship of the Cobitoidea was ((Catostomidae + Gyrinocheilidae) + (Botiinae + (Balitorinae + (Cobitinae + Nemacheilinae)))), which indicated that Sawada's Cobitidae (including Cobitinae and Botiinae) was not monophyletic. Our molecular phylogenetic analyses are in very close agreement with the phylogenetic results based on the morphological data proposed by Nalbant and Bianco, wherein these four subfamilies were elevated to the family level as Botiidae, Balitoridae, Cobitidae, and Nemacheilidae. (c) 2005 Elsevier Inc. All rights reserved.

De novo RNA synthesis and homology modeling of the classical swine fever virus RNA polymerase

Classical swine fever virus (CSFV) non-structural protein 5B (NS5B) encodes an RNA-dependent RNA polymerase (RdRp), a key enzyme which initiates RNA replication by a de novo mechanism without a primer and is a potential target for anti-virus therapy. We expressed the NS5B protein in Escherichia coli. The rGTP can stimulate de novo initiation of RNA synthesis and mutation of the GDD motif to Gly-Asp-Asp (GAA) abolishes the RNA synthesis. To better understand the mechanism of viral RNA synthesis in CSFV, a three-dimensional model was built by homology modeling based on the alignment with several virus RdRps. The model contains 605 residues folded in the characteristic fingers, palm and thumb domains. The fingers domain contains an N-terminal region that plays an important role in conformational change. We propose that the experimentally observed promotion of polymerase efficiency by rGTP is probably due to the conformational changes of the polymerase caused by binding the rGTP. Mutation of the GDD to GAA interferes with the interaction between the residues at the polymerase active site and metal ions, and thus renders the polymerase inactive. (c) 2005 Elsevier B.V. All rights reserved.

Species richness in a riparian plant community along the banks of the Xiangxi River, the Three Gorges region

The distribution of vascular plant species richness along an altitudinal gradient and their relationships with environmental variables, including slope, aspect, bank (flooding) height, and river width of the Xiangxi River, Hubei Province, were examined. Total vascular plant species richness changed with elevation: it increased at lower elevations, reached a maximum in the midreaches and decreased thereafter. In particular, tree and herbaceous species richness were related to altitude. Correlation analysis (Kendall's tau) between species richness and environmental variables indicated that the change in species richness in the riparian zone was determined by riparian environmental factors and characteristics of regional vegetation distribution along the altitudinal gradient. The low species richness at lower elevations resulted from seasonal flooding and human activities - agriculture and fuel collection - and the higher. Species richness ill (he midreaches reflected transitional zones ill natural vegetation types that had had little disturbance. These results oil species distribution in the riparian community could he utilized as a reference for restoration efforts to improve water quality of the emerging reservoir resulting from the Three Gorges Hydroelectric Dam project.

Molecular cloning of TRAF2 binding protein gene and its promoter region from the grass carp Ctenopharyngodon idellus

A tumor necrosis factor receptor-associated factor 2 binding protein (T2BP) gene was isolated from the grass carp (Ctenopharyngodon idellus) by utilizing suppression subtractive hybridization (SSH) and rapid amplification of cDNA ends (RACE). The grass carp T2BP (GT2BP) gene contains an open reading frame of 579 nucleotide(s) (nt), encoding 193 amino acids, with 23 nt 5'-untranslated region and a long 3'-untranslated region of 434 nt including poly (A), 1 AUUUA motif and 4 AUUUUA motifs. No signal peptide has been detected in the predicted GT2BP, but a characteristic forkhead associated domain is present. The GT2BP mRNA shares 83% identity with the zebrafish DNA sequence, and they both have no introns in the genomic DNA. The putative transcription factor binding sites of GT2BP include two C/EBP alpha binding sites, and one c-Jun binding, one AP-1 binding, and one nuclear factor kappa B (NF kappa B) binding sites. Southern blot analysis revealed that the GT2BP was a single-copy gene. Individual difference was observed in GT2BP expression in examined organs of healthy grass carp. However, the expression of GT2BP in all examined organs in a fish with the highest copepod infection level and the significantly higher expression level in spleen and liver in infected fish may indicate its up-regulation with the parasite infection. (c) 2005 Elsevier B.V. All rights reserved.

Phylogenetic relationships of the Chinese cyprinid genus Rhinogobio Bleeker (Teleostei : Cyprinidae) based on sequences of the mitochondrial DNA control region, with comments on character adaptations

Rhinogobio is a cyprinid genus restricted to the river drainages of China. Sequences of the mitochondrial DNA control region were determined for four Rhinogohio species and one outgroup species, Coreius heterodon, to investigate the phylogenetic relationships within the genus. The control region of the Rhinogobio species ranges from 922 to 930 base pairs and comprises 930 base pairs in Coreius. Our phylogenetic analysis indicates two distinct lineages in the genus Rhinogobio. The first includes only R. ventralis. In the second lineage there are three species, two closely related species R. cylindricus and R. hunanensis, and their sister species R. typus. An analysis of character adaptations suggests an evolutionary trend in this genus towards a relatively lower body and caudal peduncle depth, a shorter dorsal fin, and a more anterior anus. In addition, there is a trend towards shorter barbels and relatively larger eyes. Some or all of these traits may be associated with a habitat shift from fast-flowing turbid rivers to slower-flowing clear river habitats.

Molecular phylogeny of three subspecies of common carp Cyprinus carpio, based on sequence analysis of cytochrome b and control region of mtDNA

The complete cytochrome b and the control region of mtDNA (about 2070 bp in total) of 10 strains belonging to three subspecies of the common carp, including three wild subspecies (the Yangtze River wild common carp - Cyprinus carpio haematopterus, Yuanjiang River wild common carp Cyprinus carpio rubrofuscus and Volga River wild common carp - Cyprinus carpio carpio) and seven domestic strains (Xingguo red carp, Russian scattered scaled mirror carp, Qingtian carp, Japanese Koi carp, purse red carp, Big-belly carp, German mirror carp) were sequenced. Phylogenetic analysis indicated that the 10 strains form three distinct clades, corresponding to C. c. haematopterus, C. c. rubrofuscus and C. c. carpio respectively. Purse red carp, an endemic domestic strain in Jiangxi province of China, showed a higher evolution rate in comparison with the other strains of C. c. haematopterus, most probably because of intensive selection and a long history of domestication. Base variation ratios among the three subspecies varied from 0.78% (between C. c. haematopterus and C. c. rubrofuscus) to 1.47%(between C. c. carpio and C. c. rubrofuscus). The topography of the phylogenetic tree and the geographic distribution of three subspecies closely resemble each other. The divergence time between C. c. carpio and the other two subspecies was estimated to be about 0.9 Myr and about 0.5 Myr between C. c. haematopterus and C. c. rubrofuscus. Based on phylogenetic analysis, C. c. rubrofuscus might have diverged from C. c. haematopterus.

Molecular cloning of the viperin gene and its promoter region from the mandarin fish Siniperca chuatsi

A viperin gene has been cloned from the mandarin fish (Siniperca chuatsi). From the first transcription initiation site, the mandarin fish viperin gene extends 3163 nucleotides to the end of the 3' untranslated region, and it contains six exons and five introns. The open reading frame of the viperin transcript has 1062 nucleotides which encode a 354 amino acid peptide. The amino acid sequence of mandarin fish viperin shows high identities with its homologues in teleosts and mammals except for the first 70 amino acids. A characteristic feature in the viperin promoter region was the presence of five putative ICSBP (IRF8) binding sites and one IRFI binding site. The viperin gene expressed mainly in lymphoid tissues before stimulation, but its expression can be examined in almost all the organs investigated after stimulation with virus or Poly I:C. The expression pattern and promoter sequence may be considered as the indirect evidence that the transcription of viperin is regulated by interferons or interferon induced genes. (C) 2004 Elsevier B.V. All rights reserved.

A survey of the gomphonemaceae and cymbellaceae (Bacillariophyta) from the Jolmolungma Mountain (Everest) region of China

Gomphonemaceae and Cymbellaceae from Jolmolungma Mountain region of China, comprised 79 taxa belonging to five genera. The dominant species were Gomphonema angustatum var. productum, G. gracile var. gracile, G. parvulum var. parvulum, G. hedini, Cymbella aequalis var. pisciculus, C. delicatula, C. cistula, C. cistula var. hebetata, C. cesatii, C. cymbiformis, C microcephala, C. minuta var. minuta., C. minuta var. silesiaca, C. pusilla, C. affinis. Some arctic and alpine forms also occurred, and the following taxa were unique to this region: Cymbella delicatula, C. naviculiformis, C. gracilis, C. minuta var. minuta, C. affinis, C. cistula, C. cymbiformis, C. cistula var. hebetata, C. arctica, Didymosphenia geminata, Gomphonema hedinii, G. olivaceum. Numbers of taxa in each samples varied greatly, It appears that species diversity of diatoms is related not only to macro-environments (e.g., geographic zonation) but also to microenvironments (e.g., microhabitats and microclimates). Cymbella spp. are not only comparatively widespread in the region but also outnumber Gomphonema spp. A large number of species found in the Jolmolungma Mountain region are also found in Tibet and the headwaters of Yangtze River.

Phylogeny of the East Asian cyprinids inferred from sequences of the mitochondrial DNA control region

With 210 genera and 2010 species, Cyprinidae is the largest freshwater fish family in the world. Several papers, based on morphological and molecular data, have been published and have led to some solid conclusions, such as the close relationships between North American phoxinins and European leuciscins. However, the relationships among major subgroups of this family are still not well resolved, especially for those East Asian groups. In the present paper, the mitochondrial DNA (mtDNA) control region, 896-956 base pairs, of 17 representative species of East Asian cyprinids was sequenced and compared with those of 21 other cyprinids to study their phylogenetic relationships. After alignment, there were 1051 sites. The comparison between pairwise substitutions and HKY distances showed that the mtDNA control region was suitable for phylogenetic study. Phylogenetic analysis indicated that there are two principal lineages in Cyprinidae: Cyprinine and Leuciscine. In Cyprinine, the relationships could be a basal Labeoinae, an intermediate Cyprininae, and a diversified Barbinae (including Schizothroaxinae). In Leuciscine, Rasborinae is at the basal position; Gobioninae and Leuciscinae are sister groups; the East Asian cultrin-xenocyprinin taxa form a large monophyletic group with some small affiliated groups; and the positions of Acheilognathinae and Tincinae are still uncertain.

Cymbellaceae and Gomphonemataceae (Bacillariophyta) from the Hengduan Mountains region (southwestern China)

We present a species list of the Gomphonemataceae and Cymbellaceae occurring in the Hengduan Mountains re-ion. These two families were found to be presented in the area by 117 species, varieties and forms belonging to four genera (Amphora, Cymbella, Didymosphenia and Gomphonema). Size, striae density, habitat and distribution in China are given for each taxon. The common taxa were Cymbella aequalis var. piscicultis. C. affinis, C. cesatii, C. cistula var. gibbosa, C. delicatula. C. gracilis, C. hustedtii, C. minuta f. latens, C. minita var. silesiaca, C. naviculiformis, C. parva. C. turgidida, Gomphonema acuminatum var. acuminatum, G. gracile, G. intricatum, G. olivaceum. G. parvulum and G. truncatum var. capitatum. Some morphological features of Cymbella cistula var. capitata, Cymbella sinica var. miyiensis, Gomphonema hedinii and G. kaznakowii were found to differ from previously published descriptions. Taxa typical of high latitude climates encountered during the present study were Cymbella affinis, C. alpina, C. cistula var. cistida, C. delicatula. C. naviculiformis. Didymosphenia geminata, Gomphonema acuminatum var. pusillum, G. constrictum var. capitatum f. turgidum, G. kaznakowii, G. olivaceum, G. subtile var. subtile, G. tergestinum and G. ventricosum.

PCR-RFLP analysis of mitochondrial DNA ND5/6 region among 3 subspecies of common carp (Cyprinus carpio L.) and its application to genetic discrimination of subspecies

Mitochondrial DNA ND5/6 region was studied by PCR-RFLP analysis among ten representative strains belonging to three subspecies (Cyprinus carpio carpio, Cyprinus carpio haematopterus and Cyprinus carpio rubrofuscus) of common carp (Cyprinus carpio L.). A total of 2.4 kb fragment was amplified and subjected to restriction endonuclease analysis with nine restriction endonucleases subsequently. The results indicated that each subspecies owned one hyplotype and four restriction enzymes (Dde I, HaeIII, Taq I and Mbo I) produced diagnostic restriction sites which could be used for discriminating the three subspecies and as molecular genetic markers for assistant selective breeding of common carp.

Sequence variations in the mitochondrial DNA control region and their implications for the phylogeny of the Cypriniformes

The mitochondrial DNA control region of six cobitids and two catostomids was sequenced and compared with sequences of other cypriniforms to study their sequence variations. The extended termination associated sequence (ETAS) domain, central domain, and conserved sequence block (CSB) domain were partitioned and the ETAS sequence, CSB-D, CSB-E, ECSB-F, CSB1, CSB2, and CSB3 were identified. It is suggested that the "hairpin" TACAT-ATGTA is the key sequence of ETAS and GACATA is the symbol of CSB1. Phylogenetic analysis based on the CSB domain showed that all cyprinids evolved as one monophyletic group, while the non-cyprinid Cypriniformes could be another monophyly that is in accordance with the hypothesis proposed by Siebert. Further analysis of the phylogeny of the Cobitoidei was also conducted and it is tentatively suggested that their relationships are Catostomidae + (Gyrinocheilidae + (Botiinae + (Homalopteridae + (Cobitinae + Nemacheilinae)))).

Characteristics of rDNA intergenic spacer region from a waterbloom cyanobacteria species Oscillatoria sp.

Sequence of rDNA intergenic spacer region (ISR) from a waterbloom cyanobacterial species Oscillatoria sp, was determined and analyzed. The results of sequence comparison showed that the spacer had a high level sequence divergence, suggesting the sequence may be a target sequence for developing cyanobacteria genus- and species-specific oligonucleotide probes. In addition, a 20bp sequence of rDNA ISR was found highly conserved in all species of cyanobacteria, which was not found in other eubacteria. This conserved sequence within a variable region indicates that it might be a functional oligonucleotide in the processing of the rRNA precursor.

Low threshold lasing of GaN-based vertical cavity surface emitting lasers with an asymmetric coupled quantum well active region

We have fabricated and characterized GaN-based vertical cavity surface emitting lasers (VCSELs) with a unique active region structure, in which three sets of InGaN asymmetric coupled quantum wells are placed in a half-wavelength (0.5 lambda) length. Lasing action was achieved under optical pumping at room temperature with a threshold pumping energy density of about 6.5 mJ/cm(2). The laser emitted a blue light at 449.5 nm with a narrow linewidth below 0.1 nm and had a high spontaneous emission factor of about 3.0x10(-2). The results indicate that this active region structure is useful in reducing the process difficulties and improving the threshold characteristics of GaN-based VCSELs.