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.

断陷湖盆缓坡带成藏模式研究

Halfgraben-like depressions have multiple layers of subtle traps, multiple coverings of oil-bearing series and multiple types of reservoirs. But these reservoirs have features of strong concealment and are difficult to explore. For this reason, many scholars contribute efforts to study the pool-forming mechanism for this kind of basins, and establish the basis for reservoir exploration and development. However, further study is needed. This paper takes HuiMin depression as an example to study the pool-forming model for the gentle slope belts of fault-depression lake basins. Applying multi-discipline theory, methods and technologies including sedimentary geology, structural geology, log geology, seismic geology, rock mechanics and fluid mechanics, and furthermore applying the dynamo-static data of oil reservoir and computer means in maximum limitation, this paper, qualitatively and quantitatively studies the depositional system, structural framework, structural evolution, structural lithofacies and tectonic stress field, as well as fluid potential field, sealing and opening properties of controlling-oil faults and reservoir prediction, finally presents a pool-forming model, and develops a series of methods and technologies suited to the reservoir prediction of the gentle slope belt. The results obtained in this paper richen the pool-forming theory of a complex oil-gas accumulative area in the gentle slope belt of a continental fault-depression basin. The research work begins with the study of geometric shape of fracture system, then the structural form, activity stages and time-space juxtaposition of faults with different level and different quality are investigated. On the basis of study of the burial history, subsidence history and structural evolution history, this paper synthesizes the studied results of deposition system, analyses the structural lithofacies of the gentle slope belt in the HuiMing Depression and its controlling roles to oil reservoir in the different structural lithofacies belts in time-space, and presents their evolution patterns. The study of structural stress field and fluid potential field indicates that the stress field has a great change from the Dong Ying stages to nowadays. One marked point among them is that the Dong Ying double peak- shaped nose structures usually were the favorable directional area for oil and gas migration, while the QuDi horst became favorable directional area since the GuanTao stage. Based on the active regular of fractures and the information of crude oil saturation pressure, this paper firstly demonstrates that the pool-forming stages of the LingNan field were prior to the stages of the QuDi field, whici provides new eyereach and thinking for hydrocarbon exploration in the gentle slope belt. The BeiQiao-RenFeng buried hill belt is a high value area with the maximum stress values from beginning to end, thus it is a favorable directional area for oil and gas migration. The opening and sealing properties of fractures are studied. The results obtained demonstrate their difference in the hydrocarbon pool formation. The seal abilities relate not only with the quality, direction and scale of normal stress, with the interface between the rocks of two sides of a fault and with the shale smear factor (SSF), but they relate also with the juxtaposition of fault motion stage and hydrocarbon migration. In the HuiMin gentle slope belt, the fault seal has difference both in different stages, and in different location and depth in the same stage. The seal extent also displays much difference. Therefore, the fault seal has time-space difference. On the basis of study of fault seal history, together with the obtained achievement of structural stress field and fluid potential field, it is discovered that for the pool-forming process of oil and gas in the studied area the fault seal of nowadays is better than that of the Ed and Ng stages, it plays an important role to determine the oil column height and hydrocarbon preservation. However, the fault seal of the Ed and Ng stages has an important influence for the distribution state of oil and gas. Because the influential parameters are complicated and undefined, we adopt SSF in the research work. It well reflects synthetic effect of each parameter which influences fault seal. On the basis of the above studies, three systems of hydrocarbon migration and accumulation, as well as a pool-forming model are established for the gentle slope belt of the HuiMin depression, which can be applied for the prediction of regular patterns of oil-gas migration. Under guidance of the pool-forming geological model for the HuiMin slope belt, and taking seismic facies technology, log constraint evolution technology, pattern recognition of multiple parameter reservoir and discrimination technology of oil-bearing ability, this paper develops a set of methods and technologies suited to oil reservoir prediction of the gentle slope belt. Good economic benefit has been obtained.

流动单元四维模型和剩余油预测以濮城油田为例

This study is aimed to reveal macroscopic and microscopic anisotropism by using new theories, new methods and new technology. In order to reveal the forming mechanism and distribution pattern of remaining oil, flow units 4-dimension model and realistic model was established according the data over 20 years development of the Pucheng Oil field. Based on theories of multi-discipline subject, methods and technologies, by using correspondent 4-D data body and computer, combining quantity and quality study, static and development data, macroscopic and microscopic data, the two different geneses' reservoir, eg., braided delta and lake delta, are studied. The two different geneses' reservoir flow units models were established. Main achievement of this thesis are summarized as following: The standard of parameter optimization, identification and appreciation of two different geneses' reservoir were established. Based on the standard, the reservoir were classed into four flow units class as G,E,F and P. The flow unit static models of two different geneses' reservoir were established, and the relation of geometric shape, space distribution and macroscopic remaining oil was revealed. the flow units microscopic model were established, which tells that the changes of all the microscopic factor in the development. (4) Accordig BP arithmetic method, an adapt arithmetic method were designed, and the reservoir flow units were simulated based on the new method. (5) Reservoir realistic model of flow unit were established. Based on the model the microscopic development is simulated, which reveals the oil and water seepage in the reservoir and the mechanism of the microscopic oil formation. (6) The spatial residual oil distribution patterns were summarized. The remaided oil is mainly in the places as not being affected by the injected water, high part of the structures and the place near the sealed faults. There are 3 kinds and 9 distribution modes of microscopic remaining oil. The forming mechanism and distribution rule were pointed out. The study has developed a set of theories, technology and methods for flow units study, including flow units description, characterization and prediction. The study is also an improvement of the development geology theory in continental fault depression lake basin.

下扬子北缘前陆盆地形成演化与油气赋存条件

The foreland basin on the northern margin of the lower reach of the Yangtze river (the lower Yangtze foreland basin) is tectonically situated in the basin-mountain transitional area along the southeastern flank of the Dabie mountains. The early formation and development of the basin is closely related to the open-up of the Mian-Lue paleo-oceanic basin on the southern margin of the Central Orogenic System represented by Qinling-Dabei orogenic belt, while the tectonic evolution of the middle-late stage of the basin is mainly related to development of the Mian-Lue tectonic zone that occurred on the basis of the previous Mian-Lue paleo-suture. The foreland basin of the northern rim of the lower reach of the Yangtze river was formed during the middle-Triassic collision between the Yangtze and North China plates and experienced an evolution of occuirence-development-extinction characterized by marine facies to continental facies and continental margin to intracontinent in terms of tectonic setting.The foreland basin (T2-J2) was developed on the basis of the passive continental marginal basin on the south side of the Mian-Lue paleo-ocean and superimposed by late Jurassic-Tertiary fault basin. The tectonic setting underwent a multiple transformation of rifting-collisional clososing-tensional faulting and depression, which resulted in changes of the property for the basin and the final formation of the superposed compose basin in a fashion of 3-story-building. According to the tectonic position and evolution stages of plate collision happening on the southeastern margin of the Dabie mountains, and tectono-tratigraphic features shown by the foreland basin in its main formational period, the evolution of the foreland basin can be divided into four stages: 1) pre-orogenic passive margin (P2-Ti). As the Mian-Lue ocean commenced subduction in the late-Permian, the approaching of the Yangtze and North China plates to each other led to long-periodical and large-scale marine regression in early Triassic which was 22 Ma earlier than the global one and generated I-type mixed strata of the clastic rocks and carbonate, and I-type carbonate platform. These represent the passive stratigraphy formed before formation of the foreland basin. 2) Foreland basin on continental margin during main orogenic episode (T2.3). The stage includes the sub-stage of marine foreland basin (T2X remain basin), which formed I-type stratigrphy of carbonate tidal flat-lagoon, the sub-stage of marine-continental transition-molasse showing II-type stratigraphy of marine-continental facies lake - continental facies lake. 3) Intracontinental foreland basin during intracontinental orogeny (Ji-2)- It is characterized by continental facies coal-bearing molasses. 4) Tensional fault and depression during post-orogeny (J3-E). It formed tectono-stratigraphy post formation of the foreland basin, marking the end of the foreland evolution. Fold-thrust deformation of the lower Yangtze foreland basin mainly happened in late middle-Jurassic, forming ramp structures along the Yangtze river that display thrusting, with deformation strength weakening toward the river from both the Dabie mountains and the Jiangnan rise. This exhibits as three zones in a pattern of thick-skinned structure involved the basement of the orogenic belt to decollement thin-skinned structure of fold-thrust from north to south: thrust zone of foreland basin on northern rim of the lower reach of the Yangtze river, foreland basin zone and Jiannan compose uplift zone. Due to the superposed tensional deformation on the earlier compressional deformation, the structural geometric stratification has occurred vertically: the upper part exhibits late tensional deformation, the middle portion is characterized by ramp fault -fold deformation on the base of the Silurian decollement and weak deformation in the lower portion consisting of Silurian and Neo-Proterozoic separated by the two decollements. These portions constitutes a three-layered structural assemblage in a 3-D geometric model.From the succession of the lower reach of the Yangtze river and combined with characteristics of hydrocarbon-bearing rocks and oil-gas system, it can be seen that the succession of the continental facies foreland basin overlies the marine facies stratigraphy on the passive continental margin, which formed upper continental facies and lower marine facies hydrocarbon-bearing rock system and oil-gas forming system possessing the basic conditions for oil-gas occurrence. Among the conditions, the key for oil-gas accumulation is development and preservation of the marine hydrocarbon-bearing rocks underlying the foreland basin. The synthetic study that in the lower Yangtze foreland basin (including the Wangjiang-Qianshan basin), the generation-reservoir-cover association with the Permian marine facies hydrocarbon-bearing rocks as the critical portion can be a prospective oil-gas accumulation.Therefore, it should aim at the upper Paleozoic marine hydrocarbon-bearing rock system and oil-gas forming system in oil-gas evaluation and exploration. Also, fining excellent reservoir phase and well-preserved oil-gas accumulation units is extremely important for a breakthrough in oil-gas exploration.

空间情境模型中以观察者为中心的空间关系表征

Human being built and updated the representations of spatial distances and spatial relations between protagonist and the around things in language comprehension. The representations of the spatial relations in egocentric spatial situational models were important in spatial cognition, narrative comprehension and psycholinguistic. Using imagery searching paradigm, Franklin and Tversky (1990) studied the representations of the spatial relations in egocentric spatial situational models and found the standard RT pattern of searching the objects in different directions around the observer (frontpattern based on the findings in perceptual space(Hintzman, 1981). Eight experiments were conducted to distinguish the factors that affected the RT pattern in imagery searching. Rt. patterns in experiments 1, 2, 3, showed that there were two factors in identify which object was currently located beyond the observer's front, back, right, and left. The first factor (called direction effect) was for identifying the referred direction of probing noun, with a pattern of process time frontpattern of process time focuspattern was found in reacting to direction nouns in Experiment 4, whereas another RT pattern (left=right=frontpattern (focusgeometric distance between them determined the psychological distance between two objects. As a conclusion, the structural natures of the spatial representation determined the nature of spatial relations.

Affine Matching with Bounded Sensor Error: A Study of Geometric Hashing and Alignment

Affine transformations are often used in recognition systems, to approximate the effects of perspective projection. The underlying mathematics is for exact feature data, with no positional uncertainty. In practice, heuristics are added to handle uncertainty. We provide a precise analysis of affine point matching, obtaining an expression for the range of affine-invariant values consistent with bounded uncertainty. This analysis reveals that the range of affine-invariant values depends on the actual $x$-$y$-positions of the features, i.e. with uncertainty, affine representations are not invariant with respect to the Cartesian coordinate system. We analyze the effect of this on geometric hashing and alignment recognition methods.

Some Extensions of the K-Means Algorithm for Image Segmentation and Pattern Classification

In this paper we present some extensions to the k-means algorithm for vector quantization that permit its efficient use in image segmentation and pattern classification tasks. It is shown that by introducing state variables that correspond to certain statistics of the dynamic behavior of the algorithm, it is possible to find the representative centers fo the lower dimensional maniforlds that define the boundaries between classes, for clouds of multi-dimensional, mult-class data; this permits one, for example, to find class boundaries directly from sparse data (e.g., in image segmentation tasks) or to efficiently place centers for pattern classification (e.g., with local Gaussian classifiers). The same state variables can be used to define algorithms for determining adaptively the optimal number of centers for clouds of data with space-varying density. Some examples of the applicatin of these extensions are also given.