Complete mitochondrial genome of the sea cucumber Apostichopus japonicus (Echinodermata: Holothuroidea): The first representative from the subclass Aspidochirotacea with the echinoderm ground pattern

Complete mitochondrial genome plays an important role in the accurate revelation of phylogenetic relationships among metazoans. Here we present the complete mitochondrial genome sequence from a sea cucumber Apostichopus japonicus (Echinodermata: Holothuroidea), which is the first representative from the subclass Aspidochirotacea. The mitochondrial genome of A. japonicus is 16,096 bp in length. The heavy strand consists of 31.8% A, 20.2% C, 17.9% G, and 30.1% T bases (AT skew = 0.027: GC skew = 0.062). It contains thirteen protein-coding genes (PCGs), twenty-two transfer RNA genes, and two ribosomal RNA genes. There are a total of 3793 codons in all thirteen mitochondrial PCGs, excluding incomplete termination codons. The most frequently used amino acid is Leu (15.77%), followed by Set (9.73%), Met (8.62%), Phe (7.94%), and Ala (7.28%). Intergenetic regions in the mitochondrial genome of A. japonicus are 839 bp in total, with three relatively large regions of Unassigned Sequences (UAS) greater than 100 bp. The gene order of A. japonicus is identical to that observed in the five studied sea urchins, which confirms that the gene order shared by the two classes (Holothuroidea and Echinoidea) is a ground pattern of echinoderm mitochondrial genomes. Bayesian tree based on the cob gene supports the following relationship: (outgroup, (Crinoids, (Asteroids, Ophiuroids, (Echinoids, Holothuroids)))). (C) 2009 Elsevier B.V. All rights reserved.

Expression pattern of dmrt4 from olive flounder (Paralichthys olivaceus) in adult gonads and during embryogenesis

The dmrt (doublesex and mab-3 related transcription factor) gene family comprises several transcription factors that share a conserved DM domain. Dmrt1 is considered to be involved in sexual development, but the precise function of other family members is unclear. In this study, we isolated genomic DNA and cDNA sequences of dmrt4, a member of the dmrt gene family, from olive flounder, Paralichthys olivaceus, through genome walking and real-time reverse transcriptase (RT)-PCR. Sequence analysis indicated that its genomic DNA contains two exons and one intron. A transcriptional factor binding sites prediction program identified a sexual development-related protein, Sox9 (Sry-like HMG box containing 9) in its 5' promoter. Protein alignment and phylogenetic analysis suggested that flounder Dmrt4 is closely related to tilapia Dmo (DM domain gene in ovary). The expression of dmrt4 in adult flounder was sexually dimorphic, as shown by real-time RT-PCR analysis, with strong expression in the testis but very weak expression in the ovary. Its expression was also strong in the brain and gill, but there was only weak or no expression at all in some of the other tissues tested of both sexes. During embryogenesis, its expression was detected in most developmental stages, although the level of expression was distinctive of the various stages. Whole mount in situ hybridization revealed that the dmrt4 was expressed in the otic placodes, forebrain, telencephalon and olfactory placodes of embryos at different developmental stages. These results will improve our understanding of the possible role of flounder dmrt4 in the development of the gonads, nervous system and sense organs.

A fibrinogen-related protein from bay scallop Argopecten irradians involved in innate immunity as pattern recognition receptor

The family of fibrinogen-related proteins (FREPs) is a group of proteins with fibrinogen-like domains. Many members of this family play important roles as pattern recognition receptors in innate immune responses. The cDNA of bay scallop Argopecten irradians FREP (designated as AiFREP) was cloned by rapid amplification of cDNA ends (RACE) method based on the expressed sequence tag (EST). The full-length cDNA of AiFREP was of 990 bp. The open reading frame encoded a polypeptide of 251 amino acids, including a signal sequence and a 213 amino acids fibrinogen-like domain. The fibrinogen-like domain of AiFREP was highly similar to those of mammalian ficolins and other FREPs. The temporal expression of AiFREP mRNA in hemolymph was examined by fluorescent quantitative real-time PCR. The mRNA level of scallops challenged by Listonella anguillarum was significantly up-regulated, peaked to 9.39-fold at 9 h after stimulation, then dropped back to 4.37-fold at 12 h, while there was no significant change in the Micrococcus luteus challenged group in all periods of treatment. The function of AiFREP was investigated by recombination and expression of the cDNA fragment encoding its mature peptide in Escherichia coli Rosetta gami (DE3). The recombinant AiFREP (rAiFREP) agglutinated chicken erythrocytes and human A, B, O-type erythrocytes. The agglutinating activities were calcium-dependent and could be inhibited by acetyl group-containing carbohydrates. rAiFREP also agglutinated Gram-negative bacteria E. coli JM109, L anguillarum and Gram-positive bacteria M. luteus in the presence of calcium ions. These results collectively suggested that AiFREP functions as a pattern recognition receptor in the immune response of bay scallop and contributed to nonself recognition in invertebrates, which would also provide clues for elucidating the evolution of the lectin pathway of the complement system. (C) 2008 Elsevier Ltd. All rights reserved.

Three-stage transformation of chlorophyll transient fluorescence pattern under sustained dehydration and the discovery of critical water content in seaweeds

The chlorophyll fluorescence kinetics of marine red alga Grateloupia turutunt Yamada, green alga Ulva pertusa Kjellm and brown alga Laminaria japonica Aresch during natural sustained dehydration were monitored and investigated. The pulse amplified modulation (PAM) system was used to analyze the distinct fluorescence parameters during thallus dehydration. Results proved that the fluorescence kinetics of different seaweed all showed three patterns of transformation with sustained water loss. These were: 1) peak kinetic pattern (at the early stage of dehydration fluorescence enhanced and quenched subsequently, representing a normal physiological state). 2) plateau kinetic pattern (with sustained water loss fluorescence enhanced continuously but quenching became slower, finally reaching its maximum). 3) Platform kinetic pattern (fluorescence fell and the shape of kinetic curve was similar to plateau kinetic pattern). A critical water content (CWC) could be found and defined as the percentage of water content just prior to the fluorescence drop and to be a significant physiological index for evaluation of plant drought tolerance. Once thallus water content became lower than this value the normal peak pattern can not be recovered even through rehydration, indicating an irreversible damage to the thylakoid membrane. The CWC value corresponding to different marine species were varied and negatively correlated with their desiccation tolerance, for example. Laminaria japonica had the highest CWC value (around 90%) and the lowest dehydration tolerance of the three. In addition, a fluorescence "burst" was found only in red algae during rehydration. The different fluorescence parameters F-o, F-v and F-v, F-m were measured and compared during water loss. Both F-o and F-v increased in the first stage of dehydration but F-v/F-m. kept almost constant. So the immediate response of in vivo chlorophyll fluorescence to dehydration was an enhancement. Later with sustained dehydration F-o increased continuously while F-v decreased and tended to become smaller and smaller. The major changes in fluorescence (including fluorescence drop during dehydration and the burst during rehydration) were all attributed to the change in F-o instead of F-v This significance of F-o indicates that it is necessary to do more research on F-o as well as on its relationship with the state of thylakoid membrane.

Early expressed genes showing a dichotomous developing pattern in the lancelet embryo

Lancelets (amphioxus), although showing the most similar anatomical features to vertebrates, never develop a vertebrate-like head but rather several structures specific to this animal. The lancelet anatomical specificity seems to be traceable to early developmental stages, such as the vertebrate dorsal and anterior-posterior determinations. The BMP and Wnt proteins play important roles in establishing the early basis of the dorsal structures and the head in vertebrates. The early behavior of BMP and Wnt may be also related to the specific body structures of lancelets. The expression patterns of a dpp-related gene, Bbbmp2/4, and two wnt-related genes, Bbwnt7 and Bbwnt8, have been studied in comparison with those of brachyury and Hnf-3 beta class genes The temporal expression patterns of these genes are similar to those of vertebrates; Bbbmp2/4 and Bbwnt8 are first expressed in the invaginating primitive gut and the equatorial region. respectively, at the initial gastrula stage. However, spatial expression pattern of Bbbmp2/4 differs significantly from the vertebrate cognates. It is expressed in the mid-dorsal inner layer of gastrulae and widely in the anterior region, in which vertebrates block BMP signaling, The present study suggests that the lancelet embryo may have two distinct developmental domains from the gastrula stage, the domains of which coincide later with the lateral diverticular and the somitocoelomic regions. The embryonic origin of the anterior-specific structures in lancelets corresponds to the anterior domain where Bbbmp2/4 is continuously expressed.

A Dicer-1 gene from white shrimp Litopenaeus vannamei: Expression pattern in the processes of immune response and larval development

Dicer is a member of the RNAase III family which catalyzes the cleavage of double-stranded RNA to small interfering RNAs and micro RNAs, and then directs sequence-specific gene silencing. In this paper, the full-length cDNA of Dicer-1 was cloned from white shrimp Litopenaeus vannamei (designated as LvDcr1). It was of 7636 bp, including a poly A tail, a 5' UTR of 136 bp, a 3' UTR of 78 bp, and an open reading frame (ORF) of 7422 bp encoding a putative protein of 2473 amino acids. The predicted amino acid sequence comprised all recognized functional domains found in other Dicer-1 homologues and showed the highest (97.7%) similarity to the Dicer-1 from tiger shrimp Penaeus mondon. Quantitative real-time PCR was employed to investigate the tissue distribution of LvDcr1 mRNA, and its expression in shrimps under virus challenge and larvae at different developmental stages. The LvDcr1 mRNA could be detected in all examined tissues with the highest expression level in hemocyte, and was up-regulated in hemocytes and gills after virus injection. These results indicated that LvDcr1 was involved in antiviral defense in adult shrimp. During the developmental stages from fertilized egg to postlarva VII, LvDcr1 was constitutively expressed at all examined development stages, but the expression level varied significantly. The highest expression level was observed in fertilized eggs and followed a decrease from fertilized egg to nauplius I stage. Then, the higher levels of expression were detected at nauplius V and postlarva stages. LvDcr1 expression regularly increased at the upper phase of nauplius, zoea and mysis stages than their prophase. The different expression of LvDcr1 in the larval stages could provide clues for understanding the early innate immunity in the process of shrimp larval development. (C) 2010 Elsevier Ltd. All rights reserved.

Broader pattern of tandem repeats in the mitochondrial control region of Perciformes

Perciformes, the largest order of vertebrates with 20 suborders, is the most diverse fish order that dominates vertebrate ocean life. The complete mitochondrial control region (CR) of Trichiurus japonicus (Trichiuridae, Scombroidei) and Pampus sp. (Stromateidae, Stromateoidei) were amplified and sequenced. Together with data from GenBank, the tandem repeats in the mitochondrial CR from 48 species, which covered nine suborders of Perciformes, are reported in this study. The tandem repeats tend to be long in the suborder Percoidei and Stromateoidei. The identical repeats in 21 species of Cichlidae suggest a common origin and have existed before species divergence. Larimichthys crocea shows tandem repeats instead of the typical structure of the central conserved sequence blocks, which was first reported in Perciformes and vertebrates. This might have resulted from interruption of the polymerase activity during the H-strand synthesis. The four broader patterns presented here for the tandem repeats, including those in both the 5' and 3' ends, only in the either 5' or 3' end, and in the central conserved domain of the control region, will be useful for understanding the evolution of species.

CfLGBP, a pattern recognition receptor in Chlamys farreri involved in the immune response against various bacteria

Lipopolysaccharide and beta-1, 3-glucan binding protein (LGBP) is a kind of pattern recognition receptor, which can recognize and bind LPS and beta-1, 3-glucan, and plays curial roles in the innate immune defense against Gram-negative bacteria and fungi. In this study, the functions of LGBP from Zhikong scallop Chlamys farreri performed in innate immunity were analyzed. Firstly, the mRNA expression of CfLGBP in hemocytes toward three typical PAMPS stimulation was examined by realtime PCR. It was up-regulated extremely (P < 0.01) post stimulation of LPS and beta-glucan, and also exhibited a moderate up-regulation (P < 0.01) after PGN injection. Further PAMPs binding assay with the polyclonal antibody specific for CfLGBP proved that the recombinant CfLGBP (designated as rCfLGBP) could bind not only LPS and beta-glucan, but also PGN in vitro. More importantly, rCfLGBP exhibited obvious agglutination activity towards Gram-negative bacteria Escherichia coil, Gram-positive bacteria Bacillus subtilis and fungi Pichia pastoris. Taking the results of immunofluorescence assay into account, which displayed CfLGBP was expressed specifically in the immune cells (hemocytes) and vulnerable organ (gill and mantle), we believed that LGBP in C farreri, serving as a multi-functional PRR, not only involved in the immune response against Gram-negative and fungi as LGBP in other invertebrates, but also played significant role in the event of anti-Gram-positive bacteria infection. As the first functional research of LGBP in mollusks, our study provided new implication into the innate immune defense mechanisms of C. farreri and mollusks. (C) 2010 Elsevier Ltd. All rights reserved.

Cflec-5, a pattern recognition receptor in scallop Chlamys farreri agglutinating yeast Pichia pastoris

C-type lectins are a superfamily of carbohydrate-recognition proteins which play crucial roles as pattern recognition receptors (PRRs) in the innate immunity. In this study, the full-length cDNA of a C-type lectin was cloned from scallop Chlamys farreri (designated as Cflec-5) by expression sequence tag (EST) analysis and rapid amplification of cDNA ends (RACE) approach The full-length cDNA of Cflec-5 was of 1412 bp. The open reading frame encoded a polypeptide of 153 amino acids, including a signal sequence and a conserved carbohydrate-recognition domain with the EPN motif determining the mannose-binding specificity The deduced amino acid sequence of Cflec-5 showed high similarity to members of C-type lectin superfamily. The quantitative real-time PCR was performed to investigate the tissue distribution of Cflec-5 mRNA and its temporal expression profiles in hemocytes post pathogen-associated molecular patterns (PAMPs) stimulation. In healthy scallops, the Cflec-5 mRNA was mainly detected in gill and mantle, and marginally in other tissues The mRNA expression of Cflec-5 could be significantly induced by lipopolysaccharide (LPS) and glucan stimulation and reached the maximum level at 6 h and 12 h, respectively But its expression level did not change significantly during peptidoglycan (PGN) stimulation The function of Cflec-5 was investigated by recombination and expression of the cDNA fragment encoding its mature peptide in Escherichia coli Rosetta Gami (DE3) The recombinant Cflec-5 agglutinated Pichia pastoris in a calcium-independent way The agglutinating activity could be inhibited by D-mannose. LPS and glucan, but not by D-galactose or PGN. These results collectively suggested that Cflec-5 was involved in the innate Immune response of scallops and might contribute to nonself-recognition through its interaction with various PAMPs (C) 2010 Elsevier Ltd All rights reserved

Tectonic and geodynamic pattern of marginal seas on the West Pacific inferred from multi-satellite altewetry geoid

With the rapid development of satellite observations, we can use the altimetry geoid to study submarine tectonics and geodynamics. On the basis of the 4' x 4' geoid undulation calculated from altimeter data of Geosat, ERS-1/2 and Topex/Poseidon on the West Pacific, located between 0degreesN similar to 45degreesN, 100degreesC similar to 150degreesE, Bouguer, Glenni and isostatic geoid undulation are obtained from correction of gravitational potential of the global topography and isostacy. Moho discontinuity depth is inversed by the Glenni geoid undulation, and the stress field from small-scale mantle convection is reasonably calculated from the isostatic geoid undulation. The results show that within the Philippine Sea and the South China Sea, short-wavelength lineations of the geoid undulation are parallel or cross to magnetic lineations and rifting ridges. The Moho depth of marginal sea basins becomes shallow southward, and its values are similar to that of the Philippine Sea. These facts show that strength of tectonic activities are almost the same on the both sides of the Ryukyu-Taiwan-Philippine are. Various kinds of tectonic features with different driving mechanisms of small-middle and large-scale of mantle convection, however, display a special pattern of tectonics and geodynamics of the continental marginal seas distinguished from oceans and continents.

Distribution pattern of marine flagellate and its controlling factors in the central and north part of the Huanghai Sea in early summer

A survey was carried out in the central and north part of the Huanghai Sea (34.5degrees similar to 37.0degreesN, 120.5degrees similar to124.0degreesE) during June 12 similar to 27, 2000. It was found that the abundance of marine flagellate ranged from 45 to 1278 cell/ml, 479 cell/ml in average. Flagellate was more abundant in the central part than in the north part of Huanghai Sea, and the abundance decreased with the increasing distance from the coast, showing a similar distribution pattern with isotherm. Vertically, high density of flagellate was always presented in the bottom of thermocline, and formed a dense accumulation in the central area of the Huanghai Sea Cold Water Mass. The effects of physical and biological factors on the distribution of marine flagellate in early summer were discussed. Water temperature (especially the existence of thermocline) rather than salinity showed significant effect on the distribution pattern of marine flagellate in the Huanghai Sea in early summer. When comparing the abundance of marine flagellate with that of other microorganisms, it revealed a comparatively stable relationship among these organhisms, with a ratio of heterotrophic bacteria: cyanobacteria: flagellate: dinoflagellate: ciliate being 10(5) 10(3):10(2):10(1):10(0).

Preliminary study of the dynamic origin of the distribution pattern of bottom sediments on the continental shelves of the Bohai Sea, Yellow Sea and East China Sea

The bottom sediment types in the Bohai Sea, Yellow Sea and East China Sea (BYECS) are diversified, and their distribution pattern is very complicated. However, the bottom sediment types can be simplified to be sandy sediment, clayey sediment and mixed sediment, which comprise the complicated distribution pattern of bottom sediment in the BYECS. The continental shelves of the BYECS are broad, with shallow water depths and tidal currents which are permanent and dominate the marine dynamics in the BYECS. Based on numerical simulation of tidal elevations and currents in the BYECS, the rates of suspended load transport and bed load transport during a single tidal cycle for sediments of eight different grain size ranges are calculated. The results show that any sediment, whose threshold velocity is less than that of tidal current, has the same transport trend. Suspended load transport rare, bed load transport rate, and the ratio of the former to the latter decrease with grain size becoming coarser and coarser. The erosion/accretion patterns of sediments with different grain sizes are determined by the sediment transport rate divergences, and the results show that the patterns are the same for sediments with different grain sizes. Three main bottom sediment types, i.e. sandy sediment mainly composed of fine sand, clayey sediment mainly composed of silty clay, and mixed sediment mainly composed of fine sand, silt, and clay, are obtained by computation. The three bottom sediment types and their distribution pattern are consistent not only with sediment transport field and the sea bed erosion/accretion pattern obtained by simulation, but also with field data of bottom sediment types and divisions. In the BYECS, sand ridges form mainly in the areas with strong rectilinear tidal currents, sand sheets form mainly in the areas dominated by strong rotatory tidal currents, and clayey sediments, i.e. mud patches, form mainly in the areas with weak tidal currents. Hence, not only the sandy sediments but also the clayey sediments in the BYECS are formed under the control of the whole tidal current field of the BYECS. The three main bottom sediment types are not isolated respectively-in fact, they constitute a whole tidal depositional system. Under the condition with no cyclonic cold eddy, the clayey sediments in the BYECS can form in weak tidal current environments. Therefore, a cold eddy is not necessary for the deposition of clayey sediments in the BYECS. (C) 2000 Academic Press.

地下水流动数值模拟的并行计算方法研究

Numerical modeling of groundwater is very important for understanding groundwater flow and solving hydrogeological problem. Today, groundwater studies require massive model cells and high calculation accuracy, which are beyond single-CPU computer’s capabilities. With the development of high performance parallel computing technologies, application of parallel computing method on numerical modeling of groundwater flow becomes necessary and important. Using parallel computing can improve the ability to resolve various hydro-geological and environmental problems. In this study, parallel computing method on two main types of modern parallel computer architecture, shared memory parallel systems and distributed shared memory parallel systems, are discussed. OpenMP and MPI (PETSc) are both used to parallelize the most widely used groundwater simulator, MODFLOW. Two parallel solvers, P-PCG and P-MODFLOW, were developed for MODFLOW. The parallelized MODFLOW was used to simulate regional groundwater flow in Beishan, Gansu Province, which is a potential high-level radioactive waste geological disposal area in China. 1. The OpenMP programming paradigm was used to parallelize the PCG (preconditioned conjugate-gradient method) solver, which is one of the main solver for MODFLOW. The parallel PCG solver, P-PCG, is verified using an 8-processor computer. Both the impact of compilers and different model domain sizes were considered in the numerical experiments. The largest test model has 1000 columns, 1000 rows and 1000 layers. Based on the timing results, execution times using the P-PCG solver are typically about 1.40 to 5.31 times faster than those using the serial one. In addition, the simulation results are the exact same as the original PCG solver, because the majority of serial codes were not changed. It is worth noting that this parallelizing approach reduces cost in terms of software maintenance because only a single source PCG solver code needs to be maintained in the MODFLOW source tree. 2. P-MODFLOW, a domain decomposition–based model implemented in a parallel computing environment is developed, which allows efficient simulation of a regional-scale groundwater flow. The basic approach partitions a large model domain into any number of sub-domains. Parallel processors are used to solve the model equations within each sub-domain. The use of domain decomposition method to achieve the MODFLOW program distributed shared memory parallel computing system will process the application of MODFLOW be extended to the fleet of the most popular systems, so that a large-scale simulation could take full advantage of hundreds or even thousands parallel processors. P-MODFLOW has a good parallel performance, with the maximum speedup of 18.32 (14 processors). Super linear speedups have been achieved in the parallel tests, indicating the efficiency and scalability of the code. Parallel program design, load balancing and full use of the PETSc were considered to achieve a highly efficient parallel program. 3. The characterization of regional ground water flow system is very important for high-level radioactive waste geological disposal. The Beishan area, located in northwestern Gansu Province, China, is selected as a potential site for disposal repository. The area includes about 80000 km2 and has complicated hydrogeological conditions, which greatly increase the computational effort of regional ground water flow models. In order to reduce computing time, parallel computing scheme was applied to regional ground water flow modeling. Models with over 10 million cells were used to simulate how the faults and different recharge conditions impact regional ground water flow pattern. The results of this study provide regional ground water flow information for the site characterization of the potential high-level radioactive waste disposal.