Discovery of the genes in response to white spot syndrome virus (WSSV) infection in Fenneropenaeus chinensis through cDNA microarray

We used microarray technology to study differentially expressed genes in white spot syndrome virus (WSSV)-infected shrimp. A total of 3136 cDNA targets, including 1578 unique genes from a cephalothorax cDNA library and 1536 cDNA clones from reverse and forward suppression subtractive hybridization (SSH) libraries of Fenneropenaeus chinensis, plus 14 negative and 8 blank control clones, were spotted onto a 18 x 18 mm area of NH2-modified glass slides. Gene expression patterns in the cephalothorax of shrimp at 6 h after WSSV injection and moribund shrimp naturally infected by WSSV were analyzed. A total of 105 elements on the arrays showed a similar regulation pattern in artificially infected shrimp and naturally infected moribund shrimp; parts of the results were confirmed by semiquantitative reverse transcriptase-polymerase chain reaction (RT-PCR). The up-regulated expression of immune-related genes, including heat shock proteins (HSP70 and HSP90), trehalose-phosphate synthase (TPS), ubiquitin C, and so forth, were observed when shrimp were challenged with WSSV. Genes including myosin LC2, ATP synthase A chain, and arginine kinase were found to be down-regulated after WSSV infection. The expression of housekeeping genes such as actin, elongation factor, and tubulin is not stable, and so these genes are not suitable as internal standards for semiquantitative RT-PCR when shrimp are challenged by WSSV. As a substitute, we found that triosephosphate isomerase (TPI) was an ideal candidate of interstandards in this situation.

Characterization and mapping of expressed sequence tags isolated from a subtracted cDNA library of Litopenaeus vannamei injected with white spot syndrome virus

A large number of polymorphic simple sequence repeats (SSRs) or microsatellites are needed to develop a genetic map for shrimp. However, developing an SSR map is very time-consuming, expensive, and most SSRs are not specifically linked to gene loci of immediate interest. We report here on our strategy to develop polymorphic markers using expressed sequence tags (ESTs) by designing primers flanking single or multiple SSRs with three or more repeats. A subtracted cDNA library was prepared using RNA from specific pathogen-free (SPF) Litopenaeus vannamei juveniles (similar to 1 g) collected before (0) and after (48 h) inoculation with the China isolate of white spot syndrome virus (WSSV). A total of 224 clones were sequenced, 194 of which were useful for homology comparisons against annotated genes in NCBI nonredundant (nr) and protein databases, providing 179 sequences encoded by nuclear DNA, 4 mitochondrial DNA, and 11 were similar to portions of WSSV genome. The nuclear sequences clustered in 43 groups, 11 of which were homologous to various ESTs of unknown function, 4 had no homology to any sequence, and 28 showed similarities to known genes of invertebrates and vertebrates, representatives of cellular metabolic processes such as calcium ion balance, cytoskeleton mRNAs, and protein synthesis. A few sequences were homologous to immune system-related (allergens) genes and two were similar to motifs of the sex-lethal gene of Drosophila. A large number of EST sequences were similar to domains of the EF-hand superfamily (Ca2+ binding motif and FRQ protein domain of myosin light chains). Single or multiple SSRs with three or more repeats were found in approximately 61 % of the 179 nuclear sequences. Primer sets were designed from 28 sequences representing 19 known or putative genes and tested for polymorphism (EST-SSR marker) in a small test panel containing 16 individuals. Ten (53%) of the 19 putative or unknown function genes were polymorphic, 4 monomorphic, and 3 either failed to satisfactorily amplify genomic DNA or the allele amplification conditions need to be further optimized. Five polymorphic ESTs were genotyped with the entire reference mapping family, two of them (actin, accession #CX535973 and shrimp allergen arginine kinase, accession #CX535999) did not amplify with all offspring of the IRMF panel suggesting presence of null alleles, and three of them amplified in most of the IRM F offspring and were used for linkage analysis. EF-hand motif of myosin light chain (accession #CX535935) was placed in ShrimpMap's linkage group 7, whereas ribosomal protein S5 (accession #CX535957) and troponin I (accession #CX535976) remained unassigned. Results indicate that (a) a large number of ESTs isolated from this cDNA library are similar to cytoskeleton mRNAs and may reflect a normal pathway of the cellular response after im infection with WSSV, and (b) primers flanking single or multiple SSRs with three or more repeats from shrimp ESTs could be an efficient approach to develop polymorphic markers useful for linkage mapping. Work is underway to map additional SSR-containing ESTs from this and other cDNA libraries as a plausible strategy to increase marker density in ShrimpMap.

Quantitatively distinguishing sediments from the Yangtze River and the Yellow River using delta Eu-N-I REEs pound plot

Sediment samples were collected from the lower channel of the Yangtze River and the Yellow River and the contents of rare earth elements (REEs) were measured. In addition, some historical REEs data were collected from published literatures. Based on the delta Eu-N-I REEs pound plot, a clear boundary was found between the sediments from the two rivers. The boundary can be described as an orthogonal polynomial equation by ordinary linear regression with sediments from the Yangtze River located above the curve and sediments from the Yellow River located below the curve. To validate this method, the REEs contents of sediments collected from the estuaries of the Yangtze River and the Yellow River were measured. In addition, the REEs data of sediment Core 255 from the Yangtze River and Core YA01 from the Yellow River were collected. Results show that the samples from the Yangtze River estuary and Core 255 almost are above the curve and most samples from the Yellow River estuary and Core YA01 are below the curve in the delta Eu-N-I REEs pound plot. The plot and the regression equation can be used to distinguish sediments from the Yangtze River and the Yellow River intuitively and quantitatively, and to trace the sediment provenance of the eastern seas of China. The difference between the sediments from two rivers in the delta Eu-N-I REEs pound plot is caused by different mineral compositions and regional climate patterns of the source areas. The relationship between delta Eu-N and I REEs pound is changed little during the transport from the source area to the river, and from river to the sea. Thus the original information on mineral compositions and climate of the source area was preserved.

Formation and evolution of the modern warm current system in the East China Sea and the Yellow Sea since the last deglaciation

To reconstruct the formation and evolution process of the warm current system within the East China Sea (ECS) and the Yellow Sea (YS) since the last deglaciation, the paleoceangraphic records in core DGKS9603, core CSH1 and core YSDP102, which were retrieved from the mainstream of the Kuroshio Current (KC), the edge of the modern Tsushima Warm Current (TWC) and muddy region under cold waters accreted with the Yellow Sea Warm Current (YSWC) respectively, were synthetically analyzed. The results indicate that the formation and evolution of the modern warm current system in the ECS and the YS has been accompanied by the development of the KC and impulse rising of the sea level since the last deglaciation. The influence of the KC on the Okinawa Trough had enhanced since 16 cal kyr BP, and synchronously the modern TWC began to develop with the rising of sea level and finally formed at about 8.5 cal kyr BP. The KC had experienced two weakening process during the Heinrich event 1 and the Younger Drays event from 16 to 8.5 cal kyr BP. The period of 7-6 cal kyr BP was the strongest stage of the KC and the TWC since the last deglaciation. The YSWC has appeared at about 6.4 cal kyr BP. Thus, the warm current system of the ECS and the YS has ultimately formed. The weakness of the KC, indicated by the occurrence of Pulleniatina minimum event (PME) during the period from 5.3 to 2.8 cal kyr BP, caused the main stream of the TWC to shift eastward to the Pacific Ocean around about 3 cal kyr BP. The process resulted in the intruding of continent shelf cold water mass with rich nutrients. Synchronously, the strength of the YSWC was relatively weak and the related cold water body was active at the early-mid stage of its appearance against the PME background, which resulted in the quick formation of muddy deposit system in the southeastern YS. The strength of the warm current system in the ECS and the YS has enhanced evidently, and approached to the modern condition gradually since 3 cal kyr BP.

Rare earth elements in bottom sediments of major rivers around the Yellow Sea: implications for sediment provenance

Rare earth elements (REEs) of 91 fine-grained bottom sediment samples from five major rivers in Korea (the Han, Keum, and Yeongsan) and China (the Changjiang and Huanghe) were studied to investigate their potential as source indicator for Yellow Sea shelf sediments, this being the first synthetic report on REE trends for bottom sediments of these rivers. The results show distinct differences in REE contents and their upper continental crust (UCC)-normalized patterns: compared to heavy rare earth elements (HREEs), light rare earth elements (LREEs) are highly enriched in Korean river sediments, in contrast to Chinese river sediments that have a characteristic positive Eu anomaly. This phenomenon is observed also in primary source rocks within the river catchments. This suggests that source rock composition is the primary control on the REE signatures of these river sediments, due largely to variations in the levels of chlorite and monazite, which are more abundant in Korean bottom river sediments. Systematic variations in I LREE pound/I HREE pound ratios, and in (La/Yb)-(Gd/Yb)(UCC) but also (La/Lu)-(La/Y)(UCC) and (La/Y)-(Gd/Lu)(UCC) relations have the greatest discriminatory power. These findings are consistent with, but considerably expand on the limited datasets available to date for suspended sediments. Evidently, the REE fingerprints of these river sediments can serve as a useful diagnostic tool for tracing the provenance of sediments in the Yellow Sea, and for reconstructing their dispersal patterns and the circulation system of the modern shelf, as well as the paleoenvironmental record of this and adjoining marginal seas.

Sporopollen analysis of Core B10 in the southern Yellow Sea and the reflected characteristics of climate changes

Eight sporopollen zones have been divided based on the results of high-resolution sporopollen analysis of Core B10 in the southern Yellow Sea. Based on the results along with C-14 datings and the subbottom profiling data, climatic and environmental changes since the last stage of late Pleistocene are discussed. The main conclusions are drawn as follows: (1) the vegetation evolved in the process of coniferous forest-grassland containing broad-leaved treesconiferous and broad-leaved mixed forest --> coniferous and broad-leaved mixed forest-grassland prevailed by coniferous trees --> coniferous and broad-leaved mixed forest-grassland containing evergreen broad-leaved trees- coniferous and broad-leaved mixed forest-grassland prevailed by broad-leaved trees-deciduous broad-leaved forest-meadow containing evergreen broad-leaved trees- coniferous and broadleaved mixed forest-grassland prevailed by broad-leaved trees- coniferous and broad-leaved mixed forest containing evergreen broad-leaved trees; (2) eight stages of climate changes are identified as the cold and dry stage, the temperate and wet stage, the cold and dry stage, the warm and dry stage, the temperate and wet stage, the hot and dry stage, the temperate and dry stage, then the warm and dry stage in turn; (3) the sedimentary environment developed from land, to littoral zone, to land again, then to shore-neritic zone; and (4) the Yellow Sea Warm Current formed during early-Holocene rather than Atlantic stage.

Modern sedimentary environments and dynamic depositional systems in the southern Yellow Sea

Based on analyses of more than 600 surface sediment samples together with large amounts of previous sedimentologic and hydrologic data, the characteristics of modern sedimentary environments and dynamic depositional systems in the southern Yellow Sea (SYS) are expounded, and the controversial formation mechanism of muddy sediments is also discussed. The southern Yellow Sea shelf can be divided into low-energy sedimentary environment and high-energy sedimentary environment; the low-energy sedimentary environment can be further divided into cyclonic and anticyclonic ones, and the high-energy environment is subdivided into high-energy depositional and eroded environments. In the shelf low-energy environments, there developed muddy depositional system. In the central part of the southern Yellow Sea, there deposited the cold eddy sediments under the actions of a meso-scale cyclonic eddy (cold eddy), and in the southeast of the southern Yellow Sea, an anticyclonic eddy muddy depositional system (warm eddy sediment) was formed. These two types of sediments showed evident differences in grain size, sedimentation rate, sediment thickness and mineralogical characteristics. The high-energy environments were covered with sandy sediments on seabed; they appeared mainly in the west, south and northeast of the southern Yellow Sea. In the high-energy eroded environment, large amounts of sandstone gravels were distributed on seabed. In the high-energy depositional environment, the originally deposited fine materials (including clay and fine silt) were gradually re-suspended and then transported to a low-energy area to deposit again. In this paper, the sedimentation model of cyclonic and anticyclonic types of muddy sediments is established, and a systematic interpretation for the formation cause of muddy depositional systems in the southern Yellow Sea is given.

Sediment provenance and province of the southern Yellow Sea: Evidence from light mineral

The distribution for percent content of light mineral is divided in detail to emphasize distributional trends of higher and lower contents by using 222 samples of light mineral in the southern Yellow Sea. 5 mineral provinces are divided, and they are I-north mineral province of the southern Yellow Sea, the sediment dominantly derived from the Yellow River; II-mixed mineral province, the sediment derived from both the Yellow River and Yangtze River; III-middle mineral province, the sediment derived mainly from the Yellow River and a part of sediment derived from Yangtze River; IV-province east of Yangtze River mouth, the sediment derived dominantly from Yangtze River; and V south mineral province, sediment was affected by relict sediment and modern sediment of Yangtze River. In this paper, the assemblage of dominant mineral and diagnostic mineral for the five provinces are discerned.

Clay mineral distributions in the southern Yellow Sea and their significance

To better understand the characteristics of the clay minerals in the southern Yellow Sea, the X-ray quantitative determinations have been carried out for the surface samples obtained from the Yellow Sea. With newly compiled clay mineral synoptic maps, the depositional processes were described for four main clay minerals (illite, chlorite, kaolinite and smectite). The analysis shows that most clay minerals are of terrigenous source with the Huanghe River acting as the major sediment supplier. Besides, the source of muddy sediments in the Yellow Sea was also discussed. As for the central Yellow Sea mud (CYSM), the sediments in its northern part mainly come from the Huanghe River, and those in the rest are of multi-origin. Very similarly, a large amount of sediments in the northern part of the southeastern Yellow Sea Mud (SEYSM) derive from the Keum River and Yeong-san River, while those in the southern part are of multi-origin.

The Shandong mud wedge and post-glacial sediment accumulation in the Yellow Sea

Two well-defined deltaic sequences in the Bohai Sea and in the South Yellow Sea represent post-glacial accumulation of Yellow River-derived sediments. Another prominent depocenter on this epicontinental shelf, a pronounced clinoform in the North Yellow Sea, wraps around the northeastern and southeastern end of the Shandong Peninsula, extending into the South Yellow Sea. This Shandong mud wedge is 20 to 40 m thick and contains an estimated 300 km(3) of sediment. Radiocarbon dating, shallow seismic profiles, and regional sea-level history suggest that the mud wedge formed when the rate of post-glacial sea-level rise slackened and the summer monsoon intensified, at about 11 ka. Geomorphic configuration and mineralogical data indicate that present-day sediment deposited on the Shandong mud wedge comes not only from the Yellow River but also from coastal erosion and local rivers. Basin-wide circulation in the North Yellow Sea may transport and redistribute fine sediments into and out of the mud wedge.

Spatial variation of suspended particulate matter in the Yellow Sea

A joint oceanographic cruise between the Institute of Oceanography, Chinese Academy of Science and the Department of Oceanography, Seoul National University was carried out in the Yellow Sea during the summer of 1996 to investigate the concentration and particle-size distribution of suspended particulate matter (SPM). The general trends in the surface and bottom waters show that SPM concentrations and particle sizes decreased seawards in both the western (Chinese) and eastern (Korean) coastal regions of the Yellow Sea. In the bottom waters, SPM concentrations were higher and particle sizes were larger along the eastern coast than along the western coast. We suggest this is due to the resuspension of bottom sediments by strong onshore summer typhoons in the southwestern coastal waters of Korea.

On the relationships between the radial tidal current field and the radial sand ridges in the southern Yellow Sea: a numerical simulation

The ori-in of the radial sand ridges (RSRs) in the southern Yellow Sea has been a controversial problem since they were discovered in the early 1960s. To resolve the problem, two key questions need to be answered: (1) was the radial tidal current field in the RSR area generated by the submarine topography, or (2) did it exist before the RSRs occurred? In this study, the M-2 tide and tidal currents in the RSR area were simulated with a two-dimensional tidal model using a flat bottom and a shelving slope topography, the results being then compared with the field data. It is demonstrated that the radial tidal current field in the southern Yellow Sea is independent of bottom topography, and may thus be the controlling factor generating the RSRs. The radial tidal current field probably existed before the RSRs were formed.

PYRITE GENESIS DURING EARLY DIAGENESIS IN YELLOW SEA AND EAST-CHINA-SEA

The content and isotopic compositions of different sulphur species in pore-water and solid phases have been examined on five sediment cores taken from muddy sediment region in the Yellow Sea and the East China Sea. Relationships among these data have been investigated with the combination of morphology of mineral pyrite and organic matter so as to role out the diagenetic behaviour of sulphur species at the early stage of diagenesis in modern marine sediment and the origin of pyrite formation.

Response of coastal marine eco-environment to river fluxes into the sea: A case study of the Huanghe (Yellow) River mouth and adjacent waters

The impact of the Huanghe (Yellow) River outflows on its estuary was investigated with river gauging and shipboard hydrographic observations. The river flux has been decreasing dramatically; the discharges of water and sediment in the 1990s dropped to 27.4% and 31.9% of those in the 1950s, respectively, resulting in frequent and lengthy events of downstream channel dry-up since the 1970s. There were accumulatively 897 zero-flow days during the 1990s in the river course below the Lijin Hydrological Station, 100 km upstream from the river mouth, which is 82.4% of that in 1972. As freshwater input decreases, river-borne nutrients to the estuarine increased significantly. Concentration of dissolved inorganic nitrogen (DIN) in the 1990s was four times of that in 1950s. Changes in amount and content of the riverine inputs have greatly affected the estuarine ecosystem. Over the past several decades, sea surface temperature and salinity in the estuary and its adjacent waters increased and their distribution pattern altered in response to the reduction of freshwater inflow. The distribution of and seasonal succession in nutrient concentrations in the surface layer have also changed with a shift of river outlet and the decrease in riverine nutrient loads. Furthermore, deterioration of estuarine ecosystem by less river input has decreased primary productivity in the deltaic region waters, and in turn depressed the fishery. (C) 2008 Published by Elsevier Ltd.