Mitochondrial molecular clocks and the origin of the major Otocephalan clades (Pisces : Teleostei): A new insight

The Otocephala, a clade including ostariophysan and clupeomorph telcosts, represents about a quarter of total fish species diversity, with about 1000 gencra and more than 7000 species. A series of recent papers have defended that the origin of this clade and of its major groups may be significantly older than the oldest fossils of each of these groups suggest. Some of these recent papers explicitly defend a Pangean origin for some otocephalan groups Such as the Siluriformes or Cypriniformes. To know whether or not the otocephalans as a whole, and particularly the mainly freshwater, cosmopolitan otophysans could have originated before the splitting of the Pangean Supercontinent is of extreme importance, since otophysan fishes are among the most useful animal groups for the determination of historical continental relationships. In the present work we examined divergence times for each major otocephalan group by an analysis of complete mtDNA sequences, in order to investigate if these divergence times support the hypotheses advanced in recent studies. The complete mtDNA sequences of nine representative non-otocephalan fish species and of twenty-one representative otocephalan species was compared. The present study is thus, among the studies dealing with molecular divergence times of telcosts, the one in which a greater number of otocephalan species are included. The divergence times obtained support that the major otocephalan groups had a much older origin than the oldest fossil records available for these groups suggest. The origin of the Otocephala is estimated as having occurred about 282 Mya, with the origin of the Otophysi being estimated at about 251 Mya. (c) 2005 Elsevier B.V. All rights reserved.

Distribution of the meiofaunal community in a eutrophic shallow lake of China

In a Chinese eutrophic shallow lake, the spatial, temporal and vertical distributions of meiofauna in different lake zones along a eutrophic gradient were analyzed. The spatial distribution of meiofauna among sampling stations changed with nutrient levels. Nematoda were most abundant at the majority of sampling stations comprising 70.6 - 93.2 % meiofaunal abundance except for a hypereutrophic station. The seasonal patterns in abundance of nematodes, oligochaetes, rotifers, chironomids and different nematode feeding groups differed among stations, which revealed that the temporal variations of these meiofaunal groups and the nematode feeding groups may vary with different nutrient loadings. The vertical distributions of meiofaunal groups, nematode species, and nematode trophic groups in the upper and lower sediment layers were similar, suggesting a consistent vertical distribution pattern across different trophic conditions. Nematode species richness, Shannon-Wiener species diversity index, trophic diversity and Maturity Index were significantly correlated with nutrient levels (total phosphorus and nitrogen in lake water and total phosphorus in sediment). Our results suggest the importance of nematode community analyses in the assessment of freshwater eutrophication.

Culture of the terrestrial cyanobacterium, Nostoc flagelliforme (Cyanophyceae), under aquatic conditions

Both colonies and free-living cells of the terrestrial cyanobacterium, Nostoc flagelliforme (Berk. & Curtis) Bornet & Flahault, were cultured under aquatic conditions to develop the techniques for the cultivation and restoration of this endangered resource. The colonial filaments disintegrated with their sheaths ruptured in about 2 days without any desiccating treatments. Periodic desiccation played an important role in preventing the alga from decomposing, with greater delays to sheath rupture with a higher frequency of exposure to air. The bacterial numbers in the culture treated with seven periods of desiccation per day were about 50% less compared with the cultures without the desiccation treatment. When bacteria in the culture were controlled, the colonial filaments did not disintegrate and maintained the integrity of their sheath for about 20 days even without the desiccation treatments, indicating the importance of desiccation for N. flagelliforme to prevent them from being disintegrated by bacteria. On the other hand, when free-living cells obtained from crushed colonial filaments were cultured in liquid medium, they developed into single filaments with sheaths, within which multiple filaments were formed later on as a colony. Such colonial filaments were developed at 15, 25, and 30degreesC at either 20 or 60 mumol photons.m(-2).s(-1); colonies did not develop at 180 mumol photons.m(-2).s(-1), though this light level resulted in the most rapid growth of the cells. Conditions of 60 mumol photons.m(-2).s(-1) and 25degrees C appeared to result in the best colonial development and faster growth of the sheath-held colonies of N. flagelliforme when cultured indoor under aquatic conditions.

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.

The spatial pattern of the small fish community in the Biandantang Lake - a small shallow lake along the middle reach of the Yangtze River, China

The spatial pattern of the small fish community was studied seasonally in 1996 in the Biandantang Lake. Based on plant cover, the lake was divided into five habitats, arranged in the order by plant structure complexity from complex to simple: Vallisneria spiralis habitat (V habitat), Vallisneria spiralis-Myriophyllum spicatum habitat (V-M habitat), Myriophyllum spicatum habitat (M habitat), Nelunbo nucefera habitat (N habitat), and no vegetation habitat (NV habitat). A modified popnet was used for quantitative sampling of small fishes. A total of 16 fish species were collected; Hypseleotris swinhonis, Ctenogobius giurinus, Pseudorasbora parva, Carassius auratus and Paracheilognathus imberis were the five numerically dominant species. In both summer and autumn, the total density of small fishes was about 10 ind m(-2). Generally, Ctenogobius giurinus, a sedatory, benthic fish, was distributed more or less evenly among the five habitats, while the other four species had lower densities in the N habitat and NV habitat, which had the simplest structures. The distribution of the small fish species showed seasonal variations. In winter, most species concentrated in the V habitat, which had the most complex structure. In spring, the fish had low densities in the N and NV habitat, and were more or less evenly distributed in the other habitats. In summer, the fish had a low density in the NV habitat, and were evenly distributed in the other habitats. In autumn, the fish had higher densities in the V-M and M habitats than in the others. Generally, spatial overlaps between the dominant species were higher in winter than in the other seasons. It was suggested that the variations in the importance of predation risk and resource competition in habitat choice determined the seasonal changes of spatial patterns in the small fishes in the Biandantang Lake.

Theoretical analysis of the bandgap for the intermixed GaInP/AlGaInP quantum wells

Compositional distribution of the quantum well and barrier after quantum well intermixing for GaInP/AlGaInP system was theoretically analyzed on the basis of atom diffusion law. With the compositional distribution result, the valence subband structure of the intermixed quantum well was calculated on the basis of 6x6 Luttinger-Kohn Hamiltonian, including spin-orbit splitting effects. TO get more accurate results in the calculation, a full 6-band problem was solved without axial approximation, which had been widely used in the Luttinger-Kohn model to simplify the computational efforts, since there was a strong warping in the GaInP valence band. At last, the bandgap energy of the intermixed quantum well was obtained and the calculation result is of much importance in the analysis of quantum well intermixing experiments.

Segmented All-Platinum Nanowires with Controlled Morphology through Manipulation of the Local Electrolyte Distribution in Fluidic Nanochannels during Electrodeposition

Synthesis of segmented all-Pt nanowires is achieved by a template-assisted method. The combination of a suitably chosen electrolyte/template system with pulse-reverse electrodeposition allows the formation of well-defined segments linked to nanowires. Manipulation of the morphology is obtained by controlling the electrokinetie effects on the local electrolyte distribution inside the nanochannels during the nanowire growth process, allowing a deviation from the continuously cylindrical geometry given by the nanoporous template. The length of the segments can be adjusted as a function of the cathodic pulse duration. Applying constant pulses leads to segments with homogeneous shape and dimensions along most of the total wire length. X-ray diffraction demonstrates that the preferred crystallite orientation of the polycrystalline wires varies with the average segment length. The results are explained considering transitions in texture formation with increasing thickness of the electrodeposit. A mechanism of segment formation is proposed based on structural characterizations. Nanowires with controlled segmented morphology are of great technological importance, because of the possibility to precisely control their substructure as a means of tuning their electrical, thermal, and optical properties. The concept we present in this work for electrodeposited platinum and track-etched polycarbonate membranes can be applied to other selected materials as well as templates and constitutes a general method to controlled nanostructuring and synthesis of shape controlled nanostructures.

Spatial variability in water quality and surface sediment diatom assemblages in a complex lake basin,lake of the woods,ontario,canada

Lake of the Woods (LOW) is an international waterbody spanning the Canadian provinces of Ontario and Manitoba, and the U.S. state of Minnesota. In recent years, there has been a perception that water quality has deteriorated in northern regions of the lake, with all increase in the frequency and intensity of toxin-producing cyanobacterial blooms. However, given the lack of long-term data these trends are difficult to verify. As a first step, we examine spatial and seasonal patterns in water quality in this highly complex lake on the Canadian Shield. Further, we examine surface sediment diatom assemblages across multiple sites to determine if they track within-take differences in environmental conditions. Our results show that there are significant spatial patterns in water quality in LOW. Principal Component Analysis divides the lake into three geographic zones based primarily on algal nutrients (i.e., total phosphorus, TP), with the highest concentrations at sites proximal to Rainy River. This variation is closely tracked by sedimentary diatom assemblages, with [TP] explaining 43% of the variation in diatom assemblages across sites. The close correlation between water quality and the surface sediment diatom record indicate that paleoecological models could be used to provide data on the relative importance of natural and anthropogenic sources of nutrients to the lake.

Domain analysis of the Edwardsiella tarda ferric uptake regulator

Recent studies have shown that the ferric uptake regulator (Fur) of Edwardsiella tarda (Fur(Et)) shares high sequence identity with the Escherichia coli Fur (Fur(Ec)) at the N-terminal DNA-binding region. In the present study, the functional importance of the C-terminal region of Fur(Et) was investigated. It was found that Fur(Et) bearing deletion of the C-terminal 12 residues still possesses most of the repressor activity, whereas Fur(Et) bearing deletions of the C-terminal 16 and more than 16 residues are severely affected in activity. Domain swapping analyses indicated that the chimeric Fur proteins (Et75Ec73 and Et75Vh74) consisting of the N-terminal 1-75 region of Fur(Et) fused to the C-terminal 76-148 region of Fur(Ec) and the C-terminal 76-149 region of the Vibrio harveyi Fur (Fur(Vh)), respectively, are fully active. C92 of Fur(Ec) and C137 of Fur(Vh), which are functionally essential in Fur(Ec) and Fur(Vh), respectively, are also essential in Et75Ec73 and Et75074, respectively. Further study identified an artificial Fur protein, EtMF54, which is composed of the N-terminal 49 residues of Fur(Et) and five artificial residues. Compared to Fur(Et), EtMF54 possesses partial Fur activity that is iron-dependent. These results (I) indicate that there exist certain functional/structural compatibilities among Fur(Et), Fur(Ec), and Fur(Vh) at the C-terminal region; (ii) provide insights to the potential location of the regulatory ion-binding site of Fur(Et).

Regulation of the Edwardsiella tarda Hemolysin Gene and luxS by EthR

Edwardsiella tarda is a pathogen with a broad host range that includes human and animals. The E. tarda hemolysin (Eth) system, which comprises EthA and EthB, is a noted virulence element that is widely distributed in pathogenic isolates of E. tarda. Previous study has shown that the expression of ethB is regulated by iron, which suggests the possibility that the ferric uptake regulator (Fur) is involved in the regulation of ethB. The work presented in this report supports the previous findings and demonstrates that ethB expression was decreased under conditions when the E. tarda Fur (Fur(Et)) was overproduced, and enhanced when Fur(Et) was inactivated. We also identified a second ethB regulator, EthR, which is a transcription regulator of the GntR family. EthR represses ethB expression by direct interaction with the ethB promoter region. In addition to ethB, EthR also modulates, but positively, luxS expression and AI-2 production by binding to the luxS promoter region. The expression of ethR itself is subject to negative autoregulation; interference with this regulation by overexpressing ethR during the process of infection caused (i) drastic changes in ethB and luxS expressions, (ii) vitiation in the tissue dissemination and survival ability of the bacterium, and (iii) significant attenuation of the overall bacterial virulence. These results not only provide new insights into the regulation mechanisms of the Eth hemolysin and LuxS/AI-2 quorum sensing systems but also highlight the importance of these systems in bacterial virulence.

Complete mitochondrial genome of the Asian paddle crab Charybdis japonica (Crustacea: Decapoda: Portunidae): gene rearrangement of the marine brachyurans and phylogenetic considerations of the decapods

Given the commercial and ecological importance of the Asian paddle crab, Charybdis japonica, there is a clearly need for genetic and molecular research on this species. Here, we present the complete mitochondrial genome sequence of C. japonica, determined by the long-polymerase chain reaction and primer walking sequencing method. The entire genome is 15,738 bp in length, encoding a standard set of 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes, plus the putative control region, which is typical for metazoans. The total A+T content of the genome is 69.2%, lower than the other brachyuran crabs except for Callinectes sapidus. The gene order is identical to the published marine brachyurans and differs from the ancestral pancrustacean order by only the position of the tRNA (His) gene. Phylogenetic analyses using the concatenated nucleotide and amino acid sequences of 13 protein-coding genes strongly support the monophyly of Dendrobranchiata and Pleocyemata, which is consistent with the previous taxonomic classification. However, the systematic status of Charybdis within subfamily Thalamitinae of family Portunidae is not supported. C. japonica, as the first species of Charybdis with complete mitochondrial genome available, will provide important information on both genomics and molecular ecology of the group.

Diversity and spatial distribution of amoA-encoding archaea in the deep-sea sediments of the tropical West Pacific Continental Margin

The ecological characteristics of the deep-sea amoA-encoding archaea (AEA) are largely unsolved. Our aim was to study the diversity, structure and distribution of the AEA community in the sediments of the tropical West Pacific Continental Margin, to develop a general view of the AEA biogeography in the deep-sea extreme environment. Archaeal amoA clone libraries were constructed. Diverse and novel amoA sequences were identified, with the Bohol Sea, Bashi Strait and Sibuyan Sea harbouring the highest and the Bicol Shelf the lowest AEA diversity. Phylogenetic and statistical analyses illustrate a heterogeneous distribution of the AEA community, probably caused by the differential distribution of the terrestrial or estuarine AEA in the various sampling sites. The deep-sea sedimentary environments potentially harbour diverse and novel AEA in the tropical West Pacific Continental Margin. The stations in the Philippine inland seas (including station 3043) may represent AEA assemblages with various terrestrial influences and the stations connected directly to the open Philippine Sea may represent marine environment-dominant AEA assemblages. Our study indicates the potential importance of geological and climatic events in the transport of terrestrial micro-organisms to the deep-sea sedimentary environments, almost totally neglected previously.

Sea surface height and transport stream function of the South China Sea from a variable-grid global ocean circulation model

A fine-grid model (1/6degrees) covering the South China Sea (SCS), East China Sea and Japan/East Sea, which is embedded into a coarse-grid (3degrees) global model, was established to study the SCS circulation. In the present paper, we report the model-produced monthly and annual mean transport stream functions and sea surface heights(SSH) and their anomalies of the SCS. Comparison to the TOPEX/Poseidon data shows that the model-produced monthly sea surface height anomalies (SSHA) are in good agreement with altimeter measurements. Based on the results, the circulation of the SCS, especially the upper layer circulation, is discussed. In the surface layer, the western Philippine Sea water intrudes into the SCS through the Luzon Strait in autumn, winter and spring, but not in summer. However, as far as the whole water column is concerned, the water intrudes into the SCS through the Luzon Strait all the year round. This indicates that in summer the water still intrudes into the SCS in the subsurface and intermediate layers. The area near the northern continental slope of the SCS is dominated by a cyclonic circulation all the year round. The SCS Southern Anticyclonic Gyre, SE Vietnam Off-Shore Current in summertime and SCS Southern Cyclonic Gyre in wintertime are reproduced reasonably. The difference between the monthly averaged SSH and SSHA is significant, indicating the importance of the mean SSH in the SCS circulation.

Genetic diversity of the subterranean Gansu zokor in a semi-natural landscape

We studied the relationship between genetic diversity of the subterranean Gansu zokor Myospalax cansus and habitat variability in the Loess Plateau, Qinghai Province, China. We used a combination of geographic information systems and molecular techniques to assess the impact of habitat composition and human activities on the genetic diversity of zokor populations in this semi-natural landscape. Although they occurred relatively infrequently in the landscape, woodland and high-coverage grassland habitats were the main positive contributors to the genetic diversity of zokor populations. Rural residential land, plain agricultural land and low-coverage grassland had a negative effect on genetic diversity. Hilly agricultural land and middle-coverage grassland had little impact on zokor genetic diversity. There were also interactions between some habitat types, that is, habitat types with relatively better quality together promoted conservation of genetic diversity, while the interaction between (among) bad habitat types made situations worse. Finally, habitat diversity, measured as patch richness and Shannon's diversity index, was positively correlated with the genetic diversity. These results demonstrated that: (1) different habitat types had different effects on the genetic diversity of zokor populations and (2) habitat quality and habitat heterogeneity were important in maintaining genetic diversity. Habitat composition was closely related to land use thus emphasizing the importance of human activities on the genetic diversity of subterranean rodent populations in this semi-natural landscape. Although the Gansu zokor was considered to be a pest species in the Loess Plateau, our study provides insights for the management and conservation of other subterranean rodent species.